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Repository: RapidsAtHKUST/CommunityDetectionCodes
Branch: master
Commit: 23dbafd2e57a
Files: 2675
Total size: 87.2 MB

Directory structure:
gitextract_5m1t25tj/

├── .gitignore
├── .gitmodules
├── Algorithms/
│   ├── 2008-CliquePercolation/
│   │   ├── ReadMe.md
│   │   ├── algorithm_example.py
│   │   ├── conradlee_clique_percolation.py
│   │   ├── example_edge_list.txt
│   │   ├── src_cpp/
│   │   │   ├── CMakeLists.txt
│   │   │   ├── ReadMe.md
│   │   │   ├── cliqueHash.cpp
│   │   │   ├── cliqueHash.h
│   │   │   ├── communityTracker.cpp
│   │   │   ├── communityTracker.h
│   │   │   ├── dendrogram.cpp
│   │   │   ├── dendrogram.h
│   │   │   ├── doc/
│   │   │   │   ├── License.txt
│   │   │   │   └── makefile
│   │   │   ├── k_clique.cpp
│   │   │   ├── k_clique.h
│   │   │   ├── kruskal.cpp
│   │   │   ├── kruskal.h
│   │   │   ├── nodeCommunities.cpp
│   │   │   ├── nodeCommunities.h
│   │   │   ├── script/
│   │   │   │   └── testScp.py
│   │   │   ├── testData/
│   │   │   │   ├── random_1000_005.edg
│   │   │   │   └── random_1000_005.edg_files/
│   │   │   │       ├── k=3/
│   │   │   │       │   └── communities
│   │   │   │       ├── k=4/
│   │   │   │       │   └── communities
│   │   │   │       └── k=5/
│   │   │   │           └── communities
│   │   │   ├── weighedClique.cpp
│   │   │   └── weighedClique.h
│   │   └── src_python/
│   │       └── seq_clique_percolation.py
│   ├── 2009-Connected-Iterative-Scan/
│   │   ├── .gitignore
│   │   ├── ReadMe.md
│   │   ├── src-orginal/
│   │   │   ├── Libraries/
│   │   │   │   ├── Files/
│   │   │   │   │   ├── IOX.cc
│   │   │   │   │   ├── IOX.h
│   │   │   │   │   ├── StringEx.cc
│   │   │   │   │   ├── StringEx.h
│   │   │   │   │   ├── files.cc
│   │   │   │   │   └── makefile
│   │   │   │   ├── Network/
│   │   │   │   │   ├── Format.cc
│   │   │   │   │   ├── Format.h
│   │   │   │   │   ├── LibNetwork.cc
│   │   │   │   │   ├── Network.cc
│   │   │   │   │   ├── Network.h
│   │   │   │   │   ├── RandomNetwork.h
│   │   │   │   │   ├── TemporalNetwork.cc
│   │   │   │   │   ├── TemporalNetwork.h
│   │   │   │   │   └── makefile
│   │   │   │   └── Params/
│   │   │   │       ├── Parameters.cc
│   │   │   │       ├── Parameters.h
│   │   │   │       └── makefile
│   │   │   ├── ReadMe.md
│   │   │   ├── demo/
│   │   │   │   ├── karate_edges_input_modified.csv
│   │   │   │   ├── karate_output.csv
│   │   │   │   ├── network.cl
│   │   │   │   └── network_seeded.cl
│   │   │   ├── main.cc
│   │   │   └── makefile
│   │   └── src-refactor/
│   │       ├── CMakeLists.txt
│   │       ├── ReadMe.md
│   │       ├── dataset/
│   │       │   ├── karate_edges_input_modified.csv
│   │       │   ├── karate_output.csv
│   │       │   ├── network.cl
│   │       │   └── network_seeded.cl
│   │       ├── graph/
│   │       │   ├── network.cc
│   │       │   ├── network.h
│   │       │   ├── temporal_network.cc
│   │       │   └── temporal_network.h
│   │       ├── main.cc
│   │       ├── useless/
│   │       │   └── RandomNetwork.h
│   │       └── util/
│   │           ├── graph_io_helper.cc
│   │           ├── graph_io_helper.h
│   │           ├── io_helper.cc
│   │           ├── io_helper.h
│   │           ├── parameters_helper.cc
│   │           ├── parameters_helper.h
│   │           ├── string_helper.cc
│   │           └── string_helper.h
│   ├── 2009-EAGLE/
│   │   ├── .gitignore
│   │   ├── ReadMe.md
│   │   ├── graphs/
│   │   │   ├── eagle.edl
│   │   │   ├── eagle.graphml
│   │   │   ├── generate.sh
│   │   │   ├── originals/
│   │   │   │   └── eagle
│   │   │   └── tools/
│   │   │       ├── converter.py
│   │   │       ├── examples.py
│   │   │       ├── progressbar.py
│   │   │       └── utils.pyx
│   │   ├── relazione/
│   │   │   ├── Makefile
│   │   │   └── relazione.lyx
│   │   └── src/
│   │       ├── CMakeLists.txt
│   │       ├── ReadMe.md
│   │       ├── communities.cpp
│   │       ├── communities.h
│   │       ├── eagle.cpp
│   │       ├── eagle.h
│   │       ├── main.cpp
│   │       ├── max_cache.cpp
│   │       └── max_cache.h
│   ├── 2009-LineGraph/
│   │   ├── altix/
│   │   │   ├── axlgc.sh
│   │   │   └── axmakelgc.sh
│   │   ├── deprecated/
│   │   │   ├── LineGraphCreator.html
│   │   │   ├── lgc.bat
│   │   │   ├── makefileClever
│   │   │   ├── makefileTSE
│   │   │   └── makelgc.bat
│   │   ├── readme.txt
│   │   └── src/
│   │       ├── TseGraph.cpp
│   │       ├── TseGraph.h
│   │       └── main.cpp
│   ├── 2010-CONGA/
│   │   ├── ReadMe.md
│   │   └── conga_src/
│   │       ├── ReadMe.md
│   │       ├── dataset/
│   │       │   ├── dolphins_edges.txt
│   │       │   └── karate.txt
│   │       ├── pom.xml
│   │       └── src/
│   │           └── main/
│   │               ├── java/
│   │               │   ├── clique_modularity/
│   │               │   │   ├── CM.java
│   │               │   │   ├── algorithm/
│   │               │   │   │   ├── BK/
│   │               │   │   │   │   ├── BK.java
│   │               │   │   │   │   └── BronKerboschCFFast.java
│   │               │   │   │   ├── KJ/
│   │               │   │   │   │   └── KJ.java
│   │               │   │   │   └── MaxClique.java
│   │               │   │   ├── input_output/
│   │               │   │   │   ├── ReadEdges.java
│   │               │   │   │   └── WriteCliques.java
│   │               │   │   └── util/
│   │               │   │       ├── ARRAY2.java
│   │               │   │       ├── ARRAY_FIX.java
│   │               │   │       ├── Pair.java
│   │               │   │       ├── Tree.java
│   │               │   │       ├── benchmark/
│   │               │   │       │   ├── GG.java
│   │               │   │       │   └── GGResult.java
│   │               │   │       ├── community/
│   │               │   │       │   ├── CPP.java
│   │               │   │       │   ├── CommPair.java
│   │               │   │       │   ├── CommPairSet.java
│   │               │   │       │   ├── CompleteCliques.java
│   │               │   │       │   ├── CompleteCliques1.java
│   │               │   │       │   ├── RebuildCommunities.java
│   │               │   │       │   └── RemoveCliques.java
│   │               │   │       ├── graph/
│   │               │   │       │   └── ELEMENT.java
│   │               │   │       └── metric/
│   │               │   │           ├── Modularity.java
│   │               │   │           └── Omega.java
│   │               │   ├── conga/
│   │               │   │   ├── CONGA.java
│   │               │   │   ├── algorithm/
│   │               │   │   │   ├── Between.java
│   │               │   │   │   ├── CPP.java
│   │               │   │   │   └── PB.java
│   │               │   │   └── util/
│   │               │   │       ├── Pair.java
│   │               │   │       ├── StrPair.java
│   │               │   │       ├── Tree.java
│   │               │   │       ├── benchmark/
│   │               │   │       │   └── GResult.java
│   │               │   │       ├── community/
│   │               │   │       │   ├── BP.java
│   │               │   │       │   ├── ClusterInfo.java
│   │               │   │       │   └── Stats.java
│   │               │   │       ├── graph/
│   │               │   │       │   ├── Edge.java
│   │               │   │       │   ├── LabelledEdge.java
│   │               │   │       │   ├── Split.java
│   │               │   │       │   └── Vertex.java
│   │               │   │       └── metric/
│   │               │   │           └── ModOverlap.java
│   │               │   └── copra/
│   │               │       ├── Project.java
│   │               │       ├── algorithm/
│   │               │       │   └── COPRA.java
│   │               │       └── util/
│   │               │           ├── LabelPair.java
│   │               │           ├── SetPair.java
│   │               │           ├── VecPair.java
│   │               │           ├── Vert.java
│   │               │           ├── community/
│   │               │           │   └── ClusterLabel.java
│   │               │           └── metric/
│   │               │               └── ModOverlap.java
│   │               └── resources/
│   │                   ├── CM.jar
│   │                   ├── conga.jar
│   │                   └── copra.jar
│   ├── 2010-LinkCommunity/
│   │   ├── README.markdown
│   │   ├── cpp/
│   │   │   ├── COPYING
│   │   │   ├── README
│   │   │   ├── calcAndWrite_Jaccards.cpp
│   │   │   ├── clusterJaccsFile.cpp
│   │   │   ├── edgelist2pairs.py
│   │   │   ├── karate.pairs
│   │   │   ├── lesmis.pairs
│   │   │   ├── link_clustering.sh
│   │   │   ├── loop_thresholds.sh
│   │   │   └── partition_density.py
│   │   ├── python/
│   │   │   ├── karate.pairs
│   │   │   └── link_clustering.py
│   │   └── python_yche_refactor/
│   │       ├── ReadMe.md
│   │       ├── example_edge_list.txt
│   │       ├── graph_io_helper.py
│   │       ├── link_clustering.py
│   │       ├── link_clustering_algo.py
│   │       ├── play_ground.py
│   │       └── results_sample/
│   │           ├── example_edge_list_maxS0.166667_maxD0.703704.comm2edges.txt
│   │           ├── example_edge_list_maxS0.166667_maxD0.703704.comm2nodes.txt
│   │           ├── example_edge_list_maxS0.166667_maxD0.703704.edge2comm.txt
│   │           └── example_edge_list_thr_D.txt
│   ├── 2010-TopGC/
│   │   ├── ReadMe.md
│   │   ├── src_original/
│   │   │   ├── Graphs/
│   │   │   │   ├── graph.sample
│   │   │   │   ├── graph.sample.clusters_directed
│   │   │   │   └── original/
│   │   │   │       ├── graph.raw
│   │   │   │       ├── graph1.idx
│   │   │   │       ├── graph1.raw
│   │   │   │       ├── graph_temp.idx
│   │   │   │       ├── graph_temp.raw
│   │   │   │       ├── graph_temp2.raw
│   │   │   │       ├── mkidx
│   │   │   │       └── mkidx.c
│   │   │   ├── README
│   │   │   ├── TopGC.jar
│   │   │   ├── edgew.txt
│   │   │   ├── idxdFile
│   │   │   └── mkidx.c
│   │   └── src_refactor/
│   │       ├── pom.xml
│   │       └── src/
│   │           └── main/
│   │               ├── java/
│   │               │   ├── FindMostProm.java
│   │               │   ├── HoldBucket.java
│   │               │   ├── HoldInt.java
│   │               │   ├── IntAndDouble.java
│   │               │   ├── LSH.java
│   │               │   ├── LSHThread.java
│   │               │   ├── LSH_Cluster.java
│   │               │   ├── Look3.java
│   │               │   ├── MaxHeap.java
│   │               │   ├── MinHeap.java
│   │               │   ├── Prime.java
│   │               │   ├── TempDouble2.java
│   │               │   └── TopGC.java
│   │               └── resources/
│   │                   └── TopGC.jar
│   ├── 2010-iLCD/
│   │   ├── .gitignore
│   │   ├── ReadMe.md
│   │   ├── dataset/
│   │   │   └── exempleGraph.lnd
│   │   ├── doc/
│   │   │   └── ReadMe.rtf
│   │   ├── jars/
│   │   │   ├── iLCD-2013.jar
│   │   │   └── temporalGraphVisu.jar
│   │   └── src/
│   │       ├── pom.xml
│   │       └── src/
│   │           └── main/
│   │               └── java/
│   │                   ├── CorePackage/
│   │                   │   └── Main.java
│   │                   ├── Inputs/
│   │                   │   ├── InputCTNFhandler.java
│   │                   │   ├── InputHandlerInterface.java
│   │                   │   ├── InputNCOLhandler.java
│   │                   │   └── InputOLDLNDhandler.java
│   │                   ├── Outputs/
│   │                   │   ├── OutputCTNF.java
│   │                   │   ├── OutputHandlerInterface.java
│   │                   │   ├── OutputMultipleHandler.java
│   │                   │   ├── OutputStatic.java
│   │                   │   └── OutputSummary.java
│   │                   ├── TemporalNetworkManipulation/
│   │                   │   ├── Community.java
│   │                   │   ├── CoreProcessor.java
│   │                   │   ├── Interface.java
│   │                   │   ├── MyDate.java
│   │                   │   ├── MyDateManager.java
│   │                   │   ├── Network.java
│   │                   │   ├── Node.java
│   │                   │   ├── Operations/
│   │                   │   │   ├── AddEdgeOperation.java
│   │                   │   │   ├── BirthCommunityOperation.java
│   │                   │   │   ├── ContractCommunityOperation.java
│   │                   │   │   ├── DeathCommunityOperation.java
│   │                   │   │   ├── FusionCommunityOperation.java
│   │                   │   │   ├── GrowthCommunityOperation.java
│   │                   │   │   ├── Operation.java
│   │                   │   │   └── RemoveEdgeOperation.java
│   │                   │   └── OperationsHandler.java
│   │                   ├── communityDetectionPackage/
│   │                   │   └── ILCDMetaAlgorithm.java
│   │                   ├── implementable/
│   │                   │   ├── Implementation.java
│   │                   │   └── ImplementationRNHM.java
│   │                   └── tools/
│   │                       ├── DebugMode.java
│   │                       ├── SortEdges.java
│   │                       ├── Sorter.java
│   │                       ├── TextFileHandler.java
│   │                       └── ToolDate.java
│   ├── 2011-GCE/
│   │   ├── ReadMe.md
│   │   ├── src-original/
│   │   │   ├── Community_Finder.cpp
│   │   │   ├── Community_Finder.h
│   │   │   ├── Range.hpp
│   │   │   ├── Seed.cpp
│   │   │   ├── Seed.h
│   │   │   ├── aaron_utils.cpp
│   │   │   ├── aaron_utils.hpp
│   │   │   ├── build/
│   │   │   │   ├── .gitignore
│   │   │   │   ├── karate_edges_input.csv
│   │   │   │   ├── karate_gce_output.csv
│   │   │   │   └── makefile
│   │   │   ├── clique_percolation.hpp
│   │   │   ├── cliques.cpp
│   │   │   ├── cliques.hpp
│   │   │   ├── find_communities.cpp
│   │   │   ├── graph_analysis.hpp
│   │   │   ├── graph_loading.cpp
│   │   │   ├── graph_loading.hpp
│   │   │   ├── graph_representation.cpp
│   │   │   ├── graph_representation.hpp
│   │   │   ├── iterative.hpp
│   │   │   ├── modularity.hpp
│   │   │   └── options.hpp
│   │   └── src-refactor/
│   │       ├── CMakeLists.txt
│   │       ├── ReadMe.md
│   │       ├── algorithm/
│   │       │   ├── cliques.cpp
│   │       │   ├── cliques.hpp
│   │       │   ├── community_finder.cpp
│   │       │   ├── community_finder.h
│   │       │   ├── find_communities.cpp
│   │       │   ├── seed.cpp
│   │       │   └── seed.h
│   │       ├── useless/
│   │       │   ├── clique_percolation.hpp
│   │       │   ├── graph_analysis.hpp
│   │       │   ├── iterative.hpp
│   │       │   ├── modularity.hpp
│   │       │   └── options.hpp
│   │       └── util/
│   │           ├── aaron_utils.cpp
│   │           ├── aaron_utils.hpp
│   │           ├── graph/
│   │           │   ├── graph_loading.cpp
│   │           │   ├── graph_loading.hpp
│   │           │   ├── graph_representation.cpp
│   │           │   └── graph_representation.hpp
│   │           └── range.hpp
│   ├── 2011-MOSES/
│   │   ├── LICENSE-2.0.txt
│   │   ├── NOTICE
│   │   ├── ReadMe.md
│   │   ├── comment.txt
│   │   ├── src-original/
│   │   │   ├── Makefile
│   │   │   ├── Range.cpp
│   │   │   ├── Range.hpp
│   │   │   ├── aaron_utils.cpp
│   │   │   ├── aaron_utils.hpp
│   │   │   ├── gitstatus.cpp
│   │   │   ├── gitstatus.hpp
│   │   │   ├── graph_loading.cpp
│   │   │   ├── graph_loading.hpp
│   │   │   ├── graph_representation.cpp
│   │   │   ├── graph_representation.hpp
│   │   │   ├── groupStats.cpp
│   │   │   ├── grouping.cpp
│   │   │   ├── grouping.hpp
│   │   │   ├── iterative.hpp
│   │   │   ├── moses.cpp
│   │   │   ├── options.hpp
│   │   │   ├── overlapping.cpp
│   │   │   └── overlapping.hpp
│   │   └── src-refactor/
│   │       ├── CMakeLists.txt
│   │       ├── algorithm/
│   │       │   ├── ReadMe.md
│   │       │   ├── group_status_exec.cpp
│   │       │   ├── grouping.cpp
│   │       │   ├── grouping.hpp
│   │       │   ├── moses.cpp
│   │       │   ├── overlapping.cpp
│   │       │   └── overlapping.hpp
│   │       ├── doc/
│   │       │   ├── Makefile
│   │       │   └── comment.txt
│   │       └── util/
│   │           ├── aaron_utils.cpp
│   │           ├── aaron_utils.hpp
│   │           ├── graph/
│   │           │   ├── graph_loading.cpp
│   │           │   ├── graph_loading.hpp
│   │           │   ├── graph_representation.cpp
│   │           │   ├── graph_representation.hpp
│   │           │   └── iterative.hpp
│   │           ├── program_options/
│   │           │   └── options.hpp
│   │           ├── range.cpp
│   │           └── range.hpp
│   ├── 2011-OSLOM-v2/
│   │   ├── Sources_2_5/
│   │   │   ├── OSLOM_files/
│   │   │   │   ├── dir_weighted_tabdeg.h
│   │   │   │   ├── directed_network.h
│   │   │   │   ├── directed_oslomnet_evaluate.h
│   │   │   │   ├── egocentric_undir.h
│   │   │   │   ├── hierarchies.h
│   │   │   │   ├── log_table.h
│   │   │   │   ├── louvain_oslomnet.h
│   │   │   │   ├── louvain_oslomnet_dir.h
│   │   │   │   ├── main_body.cpp
│   │   │   │   ├── main_directed.cpp
│   │   │   │   ├── main_undirected.cpp
│   │   │   │   ├── module_collection.h
│   │   │   │   ├── oslom_net_check_overlap.cpp
│   │   │   │   ├── oslom_net_global.h
│   │   │   │   ├── oslom_net_unions.cpp
│   │   │   │   ├── set_parameters.h
│   │   │   │   ├── standard_package/
│   │   │   │   │   ├── cast.cpp
│   │   │   │   │   ├── combinatorics.cpp
│   │   │   │   │   ├── deque_numeric.cpp
│   │   │   │   │   ├── histograms.cpp
│   │   │   │   │   ├── mutual.cpp
│   │   │   │   │   ├── pajek.cpp
│   │   │   │   │   ├── partition.cpp
│   │   │   │   │   ├── print.cpp
│   │   │   │   │   ├── random.cpp
│   │   │   │   │   ├── standard_include.cpp
│   │   │   │   │   └── tabdeg.cpp
│   │   │   │   ├── try_homeless_dir.cpp
│   │   │   │   ├── try_homeless_undir.cpp
│   │   │   │   ├── undir_weighted_tabdeg.h
│   │   │   │   ├── undirected_network.h
│   │   │   │   ├── undirected_oslomnet_evaluate.h
│   │   │   │   └── wsarray.h
│   │   │   ├── ReadMe.tex
│   │   │   ├── infomap_dir/
│   │   │   │   ├── Greedy.cc
│   │   │   │   ├── Greedy.h
│   │   │   │   ├── GreedyBase.cc
│   │   │   │   ├── GreedyBase.h
│   │   │   │   ├── Makefile
│   │   │   │   ├── MersenneTwister.h
│   │   │   │   ├── Node.cc
│   │   │   │   ├── Node.h
│   │   │   │   ├── flow.net
│   │   │   │   ├── infomap.cc
│   │   │   │   ├── infomap.h
│   │   │   │   ├── infomap_scr.cpp
│   │   │   │   ├── source-sink.net
│   │   │   │   └── standard_package/
│   │   │   │       ├── cast.cpp
│   │   │   │       ├── combinatorics.cpp
│   │   │   │       ├── deque_numeric.cpp
│   │   │   │       ├── histograms.cpp
│   │   │   │       ├── mutual.cpp
│   │   │   │       ├── pajek.cpp
│   │   │   │       ├── partition.cpp
│   │   │   │       ├── print.cpp
│   │   │   │       ├── random.cpp
│   │   │   │       ├── standard_include.cpp
│   │   │   │       └── tabdeg.cpp
│   │   │   ├── infomap_undir/
│   │   │   │   ├── Greedy.cc
│   │   │   │   ├── Greedy.h
│   │   │   │   ├── GreedyBase.cc
│   │   │   │   ├── GreedyBase.h
│   │   │   │   ├── Makefile
│   │   │   │   ├── MersenneTwister.h
│   │   │   │   ├── Node.cc
│   │   │   │   ├── Node.h
│   │   │   │   ├── infomap.cc
│   │   │   │   ├── infomap.h
│   │   │   │   ├── infomap_scr.cpp
│   │   │   │   ├── karate.net
│   │   │   │   └── standard_package/
│   │   │   │       ├── cast.cpp
│   │   │   │       ├── combinatorics.cpp
│   │   │   │       ├── deque_numeric.cpp
│   │   │   │       ├── histograms.cpp
│   │   │   │       ├── mutual.cpp
│   │   │   │       ├── pajek.cpp
│   │   │   │       ├── partition.cpp
│   │   │   │       ├── print.cpp
│   │   │   │       ├── random.cpp
│   │   │   │       ├── standard_include.cpp
│   │   │   │       └── tabdeg.cpp
│   │   │   ├── louvain/
│   │   │   │   ├── Makefile
│   │   │   │   ├── a.out
│   │   │   │   ├── community.cpp
│   │   │   │   ├── community.h
│   │   │   │   ├── graph.cpp
│   │   │   │   ├── graph.h
│   │   │   │   ├── graph_binary.cpp
│   │   │   │   ├── graph_binary.h
│   │   │   │   ├── graph_binary_linux.h
│   │   │   │   ├── graph_binary_mac.h
│   │   │   │   ├── list_out
│   │   │   │   ├── main_community.cpp
│   │   │   │   ├── main_convert.cpp
│   │   │   │   ├── main_hierarchy.cpp
│   │   │   │   ├── order.cpp
│   │   │   │   ├── script_to_compile.cpp
│   │   │   │   ├── standard_package/
│   │   │   │   │   ├── cast.cpp
│   │   │   │   │   ├── combinatorics.cpp
│   │   │   │   │   ├── deque_numeric.cpp
│   │   │   │   │   ├── histograms.cpp
│   │   │   │   │   ├── mutual.cpp
│   │   │   │   │   ├── pajek.cpp
│   │   │   │   │   ├── partition.cpp
│   │   │   │   │   ├── print.cpp
│   │   │   │   │   ├── random.cpp
│   │   │   │   │   ├── standard_include.cpp
│   │   │   │   │   └── tabdeg.cpp
│   │   │   │   ├── static_network.h
│   │   │   │   └── wsarray.h
│   │   │   └── visualSources/
│   │   │       ├── hier.h
│   │   │       ├── main.cpp
│   │   │       ├── main_pajek.cpp
│   │   │       ├── main_pajek_directed.cpp
│   │   │       ├── netvi.h
│   │   │       ├── position.h
│   │   │       ├── standard_package/
│   │   │       │   ├── cast.cpp
│   │   │       │   ├── combinatorics.cpp
│   │   │       │   ├── deque_numeric.cpp
│   │   │       │   ├── histograms.cpp
│   │   │       │   ├── mutual.cpp
│   │   │       │   ├── pajek.cpp
│   │   │       │   ├── partition.cpp
│   │   │       │   ├── print.cpp
│   │   │       │   ├── random.cpp
│   │   │       │   ├── standard_include.cpp
│   │   │       │   └── tabdeg.cpp
│   │   │       ├── static_network.h
│   │   │       ├── visual_net.h
│   │   │       └── wsarray.h
│   │   ├── compile_all.sh
│   │   ├── copra.jar
│   │   └── src-refactor/
│   │       ├── CMakeLists.txt
│   │       ├── algorithm/
│   │       │   ├── infomap/
│   │       │   │   ├── dir/
│   │       │   │   │   ├── Greedy.cc
│   │       │   │   │   ├── Greedy.h
│   │       │   │   │   ├── GreedyBase.cc
│   │       │   │   │   ├── GreedyBase.h
│   │       │   │   │   ├── MersenneTwister.h
│   │       │   │   │   ├── Node.cc
│   │       │   │   │   ├── Node.h
│   │       │   │   │   ├── doc/
│   │       │   │   │   │   ├── Makefile
│   │       │   │   │   │   ├── ReadMe.md
│   │       │   │   │   │   ├── flow.net
│   │       │   │   │   │   ├── infomap_scr.cpp
│   │       │   │   │   │   └── source-sink.net
│   │       │   │   │   ├── infomap.cc
│   │       │   │   │   └── infomap.h
│   │       │   │   └── undir/
│   │       │   │       ├── Greedy.cc
│   │       │   │       ├── Greedy.h
│   │       │   │       ├── GreedyBase.cc
│   │       │   │       ├── GreedyBase.h
│   │       │   │       ├── MersenneTwister.h
│   │       │   │       ├── Node.cc
│   │       │   │       ├── Node.h
│   │       │   │       ├── doc/
│   │       │   │       │   ├── Makefile
│   │       │   │       │   ├── ReadMe.md
│   │       │   │       │   ├── infomap_scr.cpp
│   │       │   │       │   └── karate.net
│   │       │   │       ├── infomap.cc
│   │       │   │       └── infomap.h
│   │       │   ├── louvain/
│   │       │   │   ├── community.cpp
│   │       │   │   ├── community.h
│   │       │   │   ├── doc/
│   │       │   │   │   ├── Makefile
│   │       │   │   │   ├── ReadMe.md
│   │       │   │   │   ├── list_out
│   │       │   │   │   ├── order.cpp
│   │       │   │   │   ├── script_to_compile.cpp
│   │       │   │   │   └── static_network.h
│   │       │   │   ├── graph.cpp
│   │       │   │   ├── graph.h
│   │       │   │   ├── graph_binary.cpp
│   │       │   │   ├── graph_binary.h
│   │       │   │   ├── graph_binary_linux.h
│   │       │   │   ├── graph_binary_mac.h
│   │       │   │   ├── main_community.cpp
│   │       │   │   ├── main_convert.cpp
│   │       │   │   └── main_hierarchy.cpp
│   │       │   └── oslom/
│   │       │       ├── hierarchies.cpp
│   │       │       ├── hierarchies.h
│   │       │       ├── main_directed.cpp
│   │       │       └── main_undirected.cpp
│   │       ├── graph/
│   │       │   ├── directed/
│   │       │   │   ├── dir_weighted_tabdeg.cpp
│   │       │   │   ├── dir_weighted_tabdeg.h
│   │       │   │   ├── directed_network.cpp
│   │       │   │   ├── directed_network.h
│   │       │   │   ├── directed_oslomnet_evaluate.cpp
│   │       │   │   ├── directed_oslomnet_evaluate.h
│   │       │   │   ├── louvain_oslomnet_dir.cpp
│   │       │   │   ├── louvain_oslomnet_dir.h
│   │       │   │   └── try_homeless_dir.cpp
│   │       │   ├── louvain_oslomnet.cpp
│   │       │   ├── louvain_oslomnet.h
│   │       │   ├── oslom_net_global.cpp
│   │       │   ├── oslom_net_global.h
│   │       │   └── undirected/
│   │       │       ├── egocentric_undir.cpp
│   │       │       ├── egocentric_undir.h
│   │       │       ├── try_homeless_undir.cpp
│   │       │       ├── undir_weighted_tabdeg.cpp
│   │       │       ├── undir_weighted_tabdeg.h
│   │       │       ├── undirected_network.cpp
│   │       │       ├── undirected_network.h
│   │       │       ├── undirected_oslomnet_evaluate.cpp
│   │       │       └── undirected_oslomnet_evaluate.h
│   │       ├── util/
│   │       │   ├── collection/
│   │       │   │   ├── module_collection.cpp
│   │       │   │   ├── module_collection.h
│   │       │   │   ├── wsarray.cpp
│   │       │   │   └── wsarray.h
│   │       │   ├── common/
│   │       │   │   ├── cast.cpp
│   │       │   │   ├── cast.h
│   │       │   │   ├── cc.cpp
│   │       │   │   ├── cc.h
│   │       │   │   ├── combinatorics.cpp
│   │       │   │   ├── combinatorics.h
│   │       │   │   ├── deque_numeric.cpp
│   │       │   │   ├── deque_numeric.h
│   │       │   │   ├── histograms.cpp
│   │       │   │   ├── histograms.h
│   │       │   │   ├── log_table.cpp
│   │       │   │   ├── log_table.h
│   │       │   │   ├── random.cpp
│   │       │   │   └── random.h
│   │       │   ├── input_output/
│   │       │   │   ├── pajek.cpp
│   │       │   │   ├── pajek.h
│   │       │   │   ├── partition.cpp
│   │       │   │   ├── partition.h
│   │       │   │   ├── pretty_print.h
│   │       │   │   ├── tab_degree.cpp
│   │       │   │   └── tab_degree.h
│   │       │   ├── metric/
│   │       │   │   ├── mutual.cpp
│   │       │   │   └── mutual.h
│   │       │   └── program_options/
│   │       │       ├── set_parameters.cpp
│   │       │       └── set_parameters.h
│   │       └── visualization/
│   │           ├── main.cpp
│   │           ├── main_pajek.cpp
│   │           ├── main_pajek_directed.cpp
│   │           ├── unused/
│   │           │   ├── netvi.cpp
│   │           │   └── netvi.h
│   │           └── util/
│   │               ├── hier.cpp
│   │               ├── hier.h
│   │               ├── position.cpp
│   │               ├── position.h
│   │               ├── static_network.cpp
│   │               ├── static_network.h
│   │               ├── visual_net.cpp
│   │               ├── visual_net.h
│   │               ├── wsarray.cpp
│   │               └── wsarray.h
│   ├── 2011-SLPA/
│   │   ├── ReadMe.md
│   │   ├── src_original/
│   │   │   ├── GANXiS-S_v1.0/
│   │   │   │   ├── CommonFuns.cpp
│   │   │   │   ├── CommonFuns.h
│   │   │   │   ├── CommonFuns_Measure.cpp
│   │   │   │   ├── CommonFuns_Measure.h
│   │   │   │   ├── CommonFuns_TMP.h
│   │   │   │   ├── CommonFuns_TMP_Measure.h
│   │   │   │   ├── ComputeSnapshotChange.cpp
│   │   │   │   ├── ComputeSnapshotChange.h
│   │   │   │   ├── DisjointM.cpp
│   │   │   │   ├── DisjointM.h
│   │   │   │   ├── LPA.cpp
│   │   │   │   ├── LPA.h
│   │   │   │   ├── LRTPrama.cpp
│   │   │   │   ├── LRTPrama.h
│   │   │   │   ├── LabelRank.cpp
│   │   │   │   ├── LabelRank.h
│   │   │   │   ├── MersenneTwister.h
│   │   │   │   ├── NODE.cpp
│   │   │   │   ├── NODE.h
│   │   │   │   ├── Net.cpp
│   │   │   │   ├── Net.h
│   │   │   │   ├── TieLabel.cpp
│   │   │   │   ├── TieLabel.h
│   │   │   │   ├── fileOpts.cpp
│   │   │   │   ├── fileOpts.h
│   │   │   │   ├── main_LabelRank_release.cpp
│   │   │   │   ├── rndNumbers.cpp
│   │   │   │   ├── rndNumbers.h
│   │   │   │   └── test.ipairs
│   │   │   └── GANXiS_v3.0.2/
│   │   │       ├── GANXiSw.jar
│   │   │       ├── commons-collections-3.2.1.jar
│   │   │       ├── output/
│   │   │       │   ├── SLPAw_test_run1_r0.01_v3_T100.icpm
│   │   │       │   ├── SLPAw_test_run1_r0.05_v3_T100.icpm
│   │   │       │   ├── SLPAw_test_run1_r0.15_v3_T100.icpm
│   │   │       │   ├── SLPAw_test_run1_r0.1_v3_T100.icpm
│   │   │       │   ├── SLPAw_test_run1_r0.25_v3_T100.icpm
│   │   │       │   ├── SLPAw_test_run1_r0.2_v3_T100.icpm
│   │   │       │   ├── SLPAw_test_run1_r0.35_v3_T100.icpm
│   │   │       │   ├── SLPAw_test_run1_r0.3_v3_T100.icpm
│   │   │       │   ├── SLPAw_test_run1_r0.45_v3_T100.icpm
│   │   │       │   ├── SLPAw_test_run1_r0.4_v3_T100.icpm
│   │   │       │   └── SLPAw_test_run1_r0.5_v3_T100.icpm
│   │   │       ├── test.ipairs
│   │   │       ├── testLong.ipairs
│   │   │       ├── test_str.ipairs
│   │   │       └── test_w01.ipairs
│   │   ├── src_python/
│   │   │   ├── romain-fontugne/
│   │   │   │   └── slpa.py
│   │   │   └── ying_nus/
│   │   │       ├── README.md
│   │   │       ├── karate.txt
│   │   │       ├── nmi.py
│   │   │       ├── slpa.py
│   │   │       └── test_slpa.py
│   │   └── src_refactor/
│   │       ├── pom.xml
│   │       └── src/
│   │           └── main/
│   │               ├── java/
│   │               │   ├── CollectionFuns.java
│   │               │   ├── NODE.java
│   │               │   ├── Net.java
│   │               │   ├── SLPAw.java
│   │               │   └── fileOpts.java
│   │               └── resources/
│   │                   └── GANXiSw.jar
│   ├── 2012-CPMOnSteroids/
│   │   ├── ReadMe.md
│   │   ├── src_original/
│   │   │   ├── COPYING
│   │   │   ├── Makefile.in
│   │   │   ├── README
│   │   │   ├── cliques.c
│   │   │   ├── configure
│   │   │   ├── configure.in
│   │   │   ├── cos.c
│   │   │   ├── cospoc.c
│   │   │   ├── dsforest.c
│   │   │   ├── extras/
│   │   │   │   ├── Makefile.in
│   │   │   │   └── maximal_cliques.c
│   │   │   ├── include/
│   │   │   │   ├── cliques.h
│   │   │   │   ├── common.h
│   │   │   │   ├── cos.h
│   │   │   │   ├── cospoc.h
│   │   │   │   ├── debug.h
│   │   │   │   ├── dsforest.h
│   │   │   │   ├── matrix.h
│   │   │   │   └── output_communities.h
│   │   │   ├── main.c
│   │   │   ├── matrix.c
│   │   │   └── output_communities.c
│   │   └── src_refactor/
│   │       ├── doc/
│   │       │   ├── COPYING
│   │       │   └── README
│   │       └── src/
│   │           ├── CMakeLists.txt
│   │           ├── cliques.c
│   │           ├── cliques.h
│   │           ├── common.h
│   │           ├── cos.c
│   │           ├── cos.h
│   │           ├── cospoc.c
│   │           ├── cospoc.h
│   │           ├── debug.h
│   │           ├── dsforest.c
│   │           ├── dsforest.h
│   │           ├── extras/
│   │           │   └── maximal_cliques.c
│   │           ├── main.c
│   │           ├── matrix.c
│   │           ├── matrix.h
│   │           ├── output_communities.c
│   │           └── output_communities.h
│   ├── 2012-DEMON/
│   │   ├── .gitignore
│   │   ├── Demon.py
│   │   ├── HDemon.py
│   │   ├── change_input_format.py
│   │   └── test_networkx.py
│   ├── 2012-Fast-Clique-Percolation/
│   │   ├── ReadMe.md
│   │   ├── src_original/
│   │   │   ├── Makefile
│   │   │   ├── README
│   │   │   ├── cliques.cpp
│   │   │   ├── cliques.hpp
│   │   │   ├── cmdline.c
│   │   │   ├── cmdline.ggo
│   │   │   ├── cmdline.h
│   │   │   ├── gpl.txt
│   │   │   ├── graph/
│   │   │   │   ├── bloom.cpp
│   │   │   │   ├── bloom.hpp
│   │   │   │   ├── graph.cpp
│   │   │   │   ├── graph.hpp
│   │   │   │   ├── loading.cpp
│   │   │   │   ├── loading.hpp
│   │   │   │   ├── network.cpp
│   │   │   │   ├── network.hpp
│   │   │   │   ├── saving.cpp
│   │   │   │   ├── saving.hpp
│   │   │   │   ├── strings.cpp
│   │   │   │   ├── strings.hpp
│   │   │   │   ├── weights.cpp
│   │   │   │   └── weights.hpp
│   │   │   ├── percolateCliques.cpp
│   │   │   └── pp.hpp
│   │   ├── src_python/
│   │   │   ├── clique_percoaltion_naive.py
│   │   │   └── clique_percolation_fast.py
│   │   └── src_refactor/
│   │       ├── CMakeLists.txt
│   │       ├── ReadMe.md
│   │       ├── cliques.cpp
│   │       ├── cliques.hpp
│   │       ├── cmdline.c
│   │       ├── cmdline.ggo
│   │       ├── cmdline.h
│   │       ├── graph/
│   │       │   ├── bloom.cpp
│   │       │   ├── bloom.hpp
│   │       │   ├── graph.cpp
│   │       │   ├── graph.hpp
│   │       │   ├── loading.cpp
│   │       │   ├── loading.hpp
│   │       │   ├── network.cpp
│   │       │   ├── network.hpp
│   │       │   ├── saving.cpp
│   │       │   ├── saving.hpp
│   │       │   ├── strings.cpp
│   │       │   ├── strings.hpp
│   │       │   ├── weights.cpp
│   │       │   └── weights.hpp
│   │       ├── original_doc/
│   │       │   ├── Makefile
│   │       │   ├── README
│   │       │   └── gpl.txt
│   │       ├── percolateCliques.cpp
│   │       └── pp.hpp
│   ├── 2013-MSCD/
│   │   ├── MSCD.xcodeproj/
│   │   │   ├── elemarte.mode1v3
│   │   │   ├── elemarte.pbxuser
│   │   │   ├── project.pbxproj
│   │   │   ├── project.xcworkspace/
│   │   │   │   ├── contents.xcworkspacedata
│   │   │   │   └── xcuserdata/
│   │   │   │       └── elemarte.xcuserdatad/
│   │   │   │           ├── UserInterfaceState.xcuserstate
│   │   │   │           └── WorkspaceSettings.xcsettings
│   │   │   └── xcuserdata/
│   │   │       └── elemarte.xcuserdatad/
│   │   │           ├── xcdebugger/
│   │   │           │   └── Breakpoints.xcbkptlist
│   │   │           └── xcschemes/
│   │   │               ├── MSCD.xcscheme
│   │   │               └── xcschememanagement.plist
│   │   ├── Makefile
│   │   ├── ReadMe.md
│   │   ├── Readme.txt
│   │   ├── analyse.xcodeproj/
│   │   │   ├── elemarte.mode1v3
│   │   │   ├── elemarte.pbxuser
│   │   │   ├── project.pbxproj
│   │   │   ├── project.xcworkspace/
│   │   │   │   ├── contents.xcworkspacedata
│   │   │   │   └── xcuserdata/
│   │   │   │       └── elemarte.xcuserdatad/
│   │   │   │           └── UserInterfaceState.xcuserstate
│   │   │   └── xcuserdata/
│   │   │       └── elemarte.xcuserdatad/
│   │   │           └── xcschemes/
│   │   │               ├── analyse.xcscheme
│   │   │               └── xcschememanagement.plist
│   │   ├── conv.xcodeproj/
│   │   │   ├── elemarte.mode1v3
│   │   │   ├── elemarte.pbxuser
│   │   │   ├── project.pbxproj
│   │   │   ├── project.xcworkspace/
│   │   │   │   ├── contents.xcworkspacedata
│   │   │   │   └── xcuserdata/
│   │   │   │       └── elemarte.xcuserdatad/
│   │   │   │           └── UserInterfaceState.xcuserstate
│   │   │   └── xcuserdata/
│   │   │       └── elemarte.xcuserdatad/
│   │   │           └── xcschemes/
│   │   │               ├── conv.xcscheme
│   │   │               └── xcschememanagement.plist
│   │   ├── examples/
│   │   │   ├── dolphins.edges
│   │   │   ├── dolphins.qs
│   │   │   ├── dolphins_0.1.coms
│   │   │   ├── dolphins_0.2.coms
│   │   │   ├── dolphins_0.3.coms
│   │   │   ├── dolphins_0.4.coms
│   │   │   ├── dolphins_0.5.coms
│   │   │   ├── dolphins_0.6.coms
│   │   │   ├── dolphins_0.7.coms
│   │   │   ├── dolphins_0.8.coms
│   │   │   ├── dolphins_0.9.coms
│   │   │   ├── dolphins_0.coms
│   │   │   ├── dolphins_1.1.coms
│   │   │   ├── dolphins_1.2.coms
│   │   │   ├── dolphins_1.3.coms
│   │   │   ├── dolphins_1.4.coms
│   │   │   ├── dolphins_1.5.coms
│   │   │   ├── dolphins_1.6.coms
│   │   │   ├── dolphins_1.7.coms
│   │   │   ├── dolphins_1.8.coms
│   │   │   ├── dolphins_1.87905e-14.coms
│   │   │   ├── dolphins_1.9.coms
│   │   │   ├── dolphins_1.coms
│   │   │   ├── dolphins_10.coms
│   │   │   ├── dolphins_2.1.coms
│   │   │   ├── dolphins_2.2.coms
│   │   │   ├── dolphins_2.3.coms
│   │   │   ├── dolphins_2.4.coms
│   │   │   ├── dolphins_2.5.coms
│   │   │   ├── dolphins_2.6.coms
│   │   │   ├── dolphins_2.7.coms
│   │   │   ├── dolphins_2.8.coms
│   │   │   ├── dolphins_2.9.coms
│   │   │   ├── dolphins_2.coms
│   │   │   ├── dolphins_3.1.coms
│   │   │   ├── dolphins_3.2.coms
│   │   │   ├── dolphins_3.3.coms
│   │   │   ├── dolphins_3.4.coms
│   │   │   ├── dolphins_3.5.coms
│   │   │   ├── dolphins_3.6.coms
│   │   │   ├── dolphins_3.7.coms
│   │   │   ├── dolphins_3.8.coms
│   │   │   ├── dolphins_3.9.coms
│   │   │   ├── dolphins_3.coms
│   │   │   ├── dolphins_4.1.coms
│   │   │   ├── dolphins_4.2.coms
│   │   │   ├── dolphins_4.3.coms
│   │   │   ├── dolphins_4.4.coms
│   │   │   ├── dolphins_4.5.coms
│   │   │   ├── dolphins_4.6.coms
│   │   │   ├── dolphins_4.7.coms
│   │   │   ├── dolphins_4.8.coms
│   │   │   ├── dolphins_4.9.coms
│   │   │   ├── dolphins_4.coms
│   │   │   ├── dolphins_5.1.coms
│   │   │   ├── dolphins_5.2.coms
│   │   │   ├── dolphins_5.3.coms
│   │   │   ├── dolphins_5.4.coms
│   │   │   ├── dolphins_5.5.coms
│   │   │   ├── dolphins_5.6.coms
│   │   │   ├── dolphins_5.7.coms
│   │   │   ├── dolphins_5.8.coms
│   │   │   ├── dolphins_5.9.coms
│   │   │   ├── dolphins_5.coms
│   │   │   ├── dolphins_6.1.coms
│   │   │   ├── dolphins_6.2.coms
│   │   │   ├── dolphins_6.3.coms
│   │   │   ├── dolphins_6.4.coms
│   │   │   ├── dolphins_6.5.coms
│   │   │   ├── dolphins_6.6.coms
│   │   │   ├── dolphins_6.7.coms
│   │   │   ├── dolphins_6.8.coms
│   │   │   ├── dolphins_6.9.coms
│   │   │   ├── dolphins_6.coms
│   │   │   ├── dolphins_7.1.coms
│   │   │   ├── dolphins_7.2.coms
│   │   │   ├── dolphins_7.3.coms
│   │   │   ├── dolphins_7.4.coms
│   │   │   ├── dolphins_7.5.coms
│   │   │   ├── dolphins_7.6.coms
│   │   │   ├── dolphins_7.7.coms
│   │   │   ├── dolphins_7.8.coms
│   │   │   ├── dolphins_7.9.coms
│   │   │   ├── dolphins_7.coms
│   │   │   ├── dolphins_8.1.coms
│   │   │   ├── dolphins_8.2.coms
│   │   │   ├── dolphins_8.3.coms
│   │   │   ├── dolphins_8.4.coms
│   │   │   ├── dolphins_8.5.coms
│   │   │   ├── dolphins_8.6.coms
│   │   │   ├── dolphins_8.7.coms
│   │   │   ├── dolphins_8.8.coms
│   │   │   ├── dolphins_8.9.coms
│   │   │   ├── dolphins_8.coms
│   │   │   ├── dolphins_9.1.coms
│   │   │   ├── dolphins_9.2.coms
│   │   │   ├── dolphins_9.3.coms
│   │   │   ├── dolphins_9.4.coms
│   │   │   ├── dolphins_9.5.coms
│   │   │   ├── dolphins_9.6.coms
│   │   │   ├── dolphins_9.7.coms
│   │   │   ├── dolphins_9.8.coms
│   │   │   ├── dolphins_9.9.coms
│   │   │   ├── dolphins_9.coms
│   │   │   ├── football.edges
│   │   │   ├── karate.edges
│   │   │   └── miserables.edges
│   │   ├── speedtest.xcodeproj/
│   │   │   ├── project.pbxproj
│   │   │   ├── project.xcworkspace/
│   │   │   │   ├── contents.xcworkspacedata
│   │   │   │   └── xcuserdata/
│   │   │   │       └── elemarte.xcuserdatad/
│   │   │   │           └── UserInterfaceState.xcuserstate
│   │   │   └── xcuserdata/
│   │   │       └── elemarte.xcuserdatad/
│   │   │           ├── xcdebugger/
│   │   │           │   └── Breakpoints.xcbkptlist
│   │   │           └── xcschemes/
│   │   │               ├── speedtest.xcscheme
│   │   │               └── xcschememanagement.plist
│   │   └── src/
│   │       ├── analyse_main.cpp
│   │       ├── config.h
│   │       ├── conv_main.cpp
│   │       ├── mscd/
│   │       │   ├── alg/
│   │       │   │   ├── mscd_afg.cpp
│   │       │   │   ├── mscd_afg.h
│   │       │   │   ├── mscd_algorithm.h
│   │       │   │   ├── mscd_hslsw.cpp
│   │       │   │   ├── mscd_hslsw.h
│   │       │   │   ├── mscd_lfk.cpp
│   │       │   │   ├── mscd_lfk.h
│   │       │   │   ├── mscd_lfk2.cpp
│   │       │   │   ├── mscd_lfk2.h
│   │       │   │   ├── mscd_rb.cpp
│   │       │   │   ├── mscd_rb.h
│   │       │   │   ├── mscd_rn.cpp
│   │       │   │   ├── mscd_rn.h
│   │       │   │   ├── mscd_so.cpp
│   │       │   │   ├── mscd_so.h
│   │       │   │   ├── mscd_som.cpp
│   │       │   │   └── mscd_som.h
│   │       │   ├── ds/
│   │       │   │   ├── communities.h
│   │       │   │   └── graph.h
│   │       │   └── io/
│   │       │       ├── in/
│   │       │       │   ├── community_list_reader.cpp
│   │       │       │   ├── community_list_reader.h
│   │       │       │   ├── community_reader.h
│   │       │       │   ├── edge_list_graph_reader.cpp
│   │       │       │   ├── edge_list_graph_reader.h
│   │       │       │   ├── graph_reader copy.h
│   │       │       │   ├── graph_reader.h
│   │       │       │   ├── lf_community_reader.cpp
│   │       │       │   ├── lf_community_reader.h
│   │       │       │   ├── pajek_community_reader.cpp
│   │       │       │   ├── pajek_community_reader.h
│   │       │       │   ├── pajek_graph_reader.cpp
│   │       │       │   └── pajek_graph_reader.h
│   │       │       └── out/
│   │       │           ├── community_list_writer.cpp
│   │       │           ├── community_list_writer.h
│   │       │           ├── community_writer.h
│   │       │           ├── edge_list_graph_writer.cpp
│   │       │           ├── edge_list_graph_writer.h
│   │       │           ├── graph_writer.h
│   │       │           ├── lf_community_writer.cpp
│   │       │           ├── lf_community_writer.h
│   │       │           ├── pajek_community_writer.cpp
│   │       │           ├── pajek_community_writer.h
│   │       │           ├── pajek_graph_writer.cpp
│   │       │           └── pajek_graph_writer.h
│   │       ├── mscd_main.cpp
│   │       ├── speedtest_main.cpp
│   │       └── toolkit/
│   │           ├── atomic_set.h
│   │           ├── nmi.h
│   │           ├── registry.h
│   │           ├── tokeniser.cpp
│   │           ├── tokeniser.h
│   │           └── tools.h
│   ├── 2013-SVINET/
│   │   ├── ReadMe.md
│   │   ├── src-cmake/
│   │   │   ├── authors_doc/
│   │   │   │   ├── AUTHORS
│   │   │   │   ├── COPYING
│   │   │   │   ├── ChangeLog
│   │   │   │   ├── NEWS
│   │   │   │   ├── README
│   │   │   │   ├── README.md
│   │   │   │   ├── aclocal.m4
│   │   │   │   ├── detailed_readme.txt
│   │   │   │   └── validation-test-file-options-patch.txt
│   │   │   ├── example/
│   │   │   │   ├── LFR-ground-truth-n1000-k28.txt
│   │   │   │   ├── LFR-network-n1000-k28.txt
│   │   │   │   ├── assort-75-4.txt
│   │   │   │   ├── ca-AstroPh.csv
│   │   │   │   ├── n1000-k28-LFR-linksampling.tgz
│   │   │   │   ├── n17903-k20-mmsb-linksampling.tgz
│   │   │   │   └── n75-k4-mmsb-batch.tgz
│   │   │   ├── patches/
│   │   │   │   └── ammsb1.patch
│   │   │   └── src/
│   │   │       ├── CMakeLists.txt
│   │   │       ├── collection/
│   │   │       │   ├── fastqueue.hh
│   │   │       │   ├── matrix.hh
│   │   │       │   └── tsqueue.hh
│   │   │       ├── community.hh
│   │   │       ├── env.hh
│   │   │       ├── fastamm.cc
│   │   │       ├── fastamm.hh
│   │   │       ├── fastamm2.cc
│   │   │       ├── fastamm2.hh
│   │   │       ├── fastinit.cc
│   │   │       ├── fastinit.hh
│   │   │       ├── linksampling.cc
│   │   │       ├── linksampling.hh
│   │   │       ├── log.cc
│   │   │       ├── log.hh
│   │   │       ├── main.cc
│   │   │       ├── mmsbgen.cc
│   │   │       ├── mmsbgen.hh
│   │   │       ├── mmsbinfer.cc
│   │   │       ├── mmsbinfer.hh
│   │   │       ├── mmsbinferorig.cc
│   │   │       ├── mmsbinferorig.hh
│   │   │       ├── mmsborig.cc
│   │   │       ├── mmsborig.hh
│   │   │       ├── network.cc
│   │   │       ├── network.hh
│   │   │       ├── sbm.cc
│   │   │       ├── sbm.hh
│   │   │       ├── thread.cc
│   │   │       └── thread.hh
│   │   └── svinet-master/
│   │       ├── AUTHORS
│   │       ├── COPYING
│   │       ├── ChangeLog
│   │       ├── INSTALL
│   │       ├── Makefile.am
│   │       ├── Makefile.in
│   │       ├── NEWS
│   │       ├── README
│   │       ├── README.md
│   │       ├── aclocal.m4
│   │       ├── config.guess
│   │       ├── config.h.in
│   │       ├── config.sub
│   │       ├── configure
│   │       ├── configure.ac
│   │       ├── depcomp
│   │       ├── detailed_readme.txt
│   │       ├── example/
│   │       │   ├── LFR-ground-truth-n1000-k28.txt
│   │       │   ├── LFR-network-n1000-k28.txt
│   │       │   ├── assort-75-4.txt
│   │       │   ├── ca-AstroPh.csv
│   │       │   ├── n1000-k28-LFR-linksampling.tgz
│   │       │   ├── n17903-k20-mmsb-linksampling.tgz
│   │       │   └── n75-k4-mmsb-batch.tgz
│   │       ├── install-sh
│   │       ├── missing
│   │       ├── mkinstalldirs
│   │       ├── patches/
│   │       │   └── ammsb1.patch
│   │       ├── src/
│   │       │   ├── Makefile.am
│   │       │   ├── Makefile.in
│   │       │   ├── community.hh
│   │       │   ├── env.hh
│   │       │   ├── fastamm.cc
│   │       │   ├── fastamm.hh
│   │       │   ├── fastamm2.cc
│   │       │   ├── fastamm2.hh
│   │       │   ├── fastinit.cc
│   │       │   ├── fastinit.hh
│   │       │   ├── fastqueue.hh
│   │       │   ├── linksampling.cc
│   │       │   ├── linksampling.hh
│   │       │   ├── log.cc
│   │       │   ├── log.hh
│   │       │   ├── main.cc
│   │       │   ├── matrix.hh
│   │       │   ├── mmsbgen.cc
│   │       │   ├── mmsbgen.hh
│   │       │   ├── mmsbinfer.cc
│   │       │   ├── mmsbinfer.hh
│   │       │   ├── mmsbinferorig.cc
│   │       │   ├── mmsbinferorig.hh
│   │       │   ├── mmsborig.cc
│   │       │   ├── mmsborig.hh
│   │       │   ├── network.cc
│   │       │   ├── network.hh
│   │       │   ├── sbm.cc
│   │       │   ├── sbm.hh
│   │       │   ├── thread.cc
│   │       │   ├── thread.hh
│   │       │   └── tsqueue.hh
│   │       └── validation-test-file-options-patch.txt
│   ├── 2013-Seed-Set-Expansion/
│   │   ├── ReadMe.md
│   │   ├── dependencies/
│   │   │   ├── GraclusSeeds/
│   │   │   │   └── graclus1.2/
│   │   │   │       ├── Makefile
│   │   │   │       ├── Makefile.in
│   │   │   │       ├── README_Graclus
│   │   │   │       ├── graclus
│   │   │   │       ├── libmetis.a
│   │   │   │       ├── libmultilevel.a
│   │   │   │       ├── matlab/
│   │   │   │       │   ├── ComputeCenterNodes.m
│   │   │   │       │   ├── ComputeDistances.m
│   │   │   │       │   ├── GraclusImageSegmentation.m
│   │   │   │       │   ├── discretisation.m
│   │   │   │       │   ├── discretisationEigenVectorData.asv
│   │   │   │       │   ├── discretisationEigenVectorData.m
│   │   │   │       │   ├── displayLatex.m
│   │   │   │       │   ├── eigs2.m
│   │   │   │       │   ├── get_hrc_graclus_seeds.m
│   │   │   │       │   ├── graclus.m
│   │   │   │       │   ├── graclus_compile_script.m
│   │   │   │       │   ├── graclus_mex.cpp
│   │   │   │       │   ├── graclus_mex.o
│   │   │   │       │   ├── hrcGraclus.m
│   │   │   │       │   ├── io.cpp
│   │   │   │       │   ├── io.o
│   │   │   │       │   ├── mlkkm.cpp
│   │   │   │       │   ├── mlkkm.o
│   │   │   │       │   ├── ncut.asv
│   │   │   │       │   ├── ncut.m
│   │   │   │       │   ├── ncutW.asv
│   │   │   │       │   ├── ncutW.m
│   │   │   │       │   ├── readMetis.m
│   │   │   │       │   ├── wkkm.cpp
│   │   │   │       │   └── wkkm.o
│   │   │   │       ├── metisLib/
│   │   │   │       │   ├── Makefile
│   │   │   │       │   ├── balance.c
│   │   │   │       │   ├── balance.o
│   │   │   │       │   ├── bucketsort.c
│   │   │   │       │   ├── bucketsort.o
│   │   │   │       │   ├── ccgraph.c
│   │   │   │       │   ├── ccgraph.o
│   │   │   │       │   ├── coarsen.c
│   │   │   │       │   ├── coarsen.o
│   │   │   │       │   ├── compress.c
│   │   │   │       │   ├── compress.o
│   │   │   │       │   ├── debug.c
│   │   │   │       │   ├── debug.o
│   │   │   │       │   ├── defs.h
│   │   │   │       │   ├── estmem.c
│   │   │   │       │   ├── estmem.o
│   │   │   │       │   ├── fm.c
│   │   │   │       │   ├── fm.o
│   │   │   │       │   ├── fortran.c
│   │   │   │       │   ├── fortran.o
│   │   │   │       │   ├── frename.c
│   │   │   │       │   ├── frename.o
│   │   │   │       │   ├── graph.c
│   │   │   │       │   ├── graph.o
│   │   │   │       │   ├── initpart.c
│   │   │   │       │   ├── initpart.o
│   │   │   │       │   ├── kmetis.c
│   │   │   │       │   ├── kmetis.o
│   │   │   │       │   ├── kvmetis.c
│   │   │   │       │   ├── kvmetis.o
│   │   │   │       │   ├── kwayfm.c
│   │   │   │       │   ├── kwayfm.o
│   │   │   │       │   ├── kwayrefine.c
│   │   │   │       │   ├── kwayrefine.o
│   │   │   │       │   ├── kwayvolfm.c
│   │   │   │       │   ├── kwayvolfm.o
│   │   │   │       │   ├── kwayvolrefine.c
│   │   │   │       │   ├── kwayvolrefine.o
│   │   │   │       │   ├── macros.h
│   │   │   │       │   ├── match.c
│   │   │   │       │   ├── match.o
│   │   │   │       │   ├── mbalance.c
│   │   │   │       │   ├── mbalance.o
│   │   │   │       │   ├── mbalance2.c
│   │   │   │       │   ├── mbalance2.o
│   │   │   │       │   ├── mcoarsen.c
│   │   │   │       │   ├── mcoarsen.o
│   │   │   │       │   ├── memory.c
│   │   │   │       │   ├── memory.o
│   │   │   │       │   ├── mesh.c
│   │   │   │       │   ├── mesh.o
│   │   │   │       │   ├── meshpart.c
│   │   │   │       │   ├── meshpart.o
│   │   │   │       │   ├── metis.h
│   │   │   │       │   ├── mfm.c
│   │   │   │       │   ├── mfm.o
│   │   │   │       │   ├── mfm2.c
│   │   │   │       │   ├── mfm2.o
│   │   │   │       │   ├── mincover.c
│   │   │   │       │   ├── mincover.o
│   │   │   │       │   ├── minitpart.c
│   │   │   │       │   ├── minitpart.o
│   │   │   │       │   ├── minitpart2.c
│   │   │   │       │   ├── minitpart2.o
│   │   │   │       │   ├── mkmetis.c
│   │   │   │       │   ├── mkmetis.o
│   │   │   │       │   ├── mkwayfmh.c
│   │   │   │       │   ├── mkwayfmh.o
│   │   │   │       │   ├── mkwayrefine.c
│   │   │   │       │   ├── mkwayrefine.o
│   │   │   │       │   ├── mmatch.c
│   │   │   │       │   ├── mmatch.o
│   │   │   │       │   ├── mmd.c
│   │   │   │       │   ├── mmd.o
│   │   │   │       │   ├── mpmetis.c
│   │   │   │       │   ├── mpmetis.o
│   │   │   │       │   ├── mrefine.c
│   │   │   │       │   ├── mrefine.o
│   │   │   │       │   ├── mrefine2.c
│   │   │   │       │   ├── mrefine2.o
│   │   │   │       │   ├── mutil.c
│   │   │   │       │   ├── mutil.o
│   │   │   │       │   ├── myqsort.c
│   │   │   │       │   ├── myqsort.o
│   │   │   │       │   ├── ometis.c
│   │   │   │       │   ├── ometis.o
│   │   │   │       │   ├── parmetis.c
│   │   │   │       │   ├── parmetis.o
│   │   │   │       │   ├── pmetis.c
│   │   │   │       │   ├── pmetis.o
│   │   │   │       │   ├── pqueue.c
│   │   │   │       │   ├── pqueue.o
│   │   │   │       │   ├── proto.h
│   │   │   │       │   ├── refine.c
│   │   │   │       │   ├── refine.o
│   │   │   │       │   ├── rename.h
│   │   │   │       │   ├── separator.c
│   │   │   │       │   ├── separator.o
│   │   │   │       │   ├── sfm.c
│   │   │   │       │   ├── sfm.o
│   │   │   │       │   ├── srefine.c
│   │   │   │       │   ├── srefine.o
│   │   │   │       │   ├── stat.c
│   │   │   │       │   ├── stat.o
│   │   │   │       │   ├── struct.h
│   │   │   │       │   ├── subdomains.c
│   │   │   │       │   ├── subdomains.o
│   │   │   │       │   ├── timing.c
│   │   │   │       │   ├── timing.o
│   │   │   │       │   ├── util.c
│   │   │   │       │   └── util.o
│   │   │   │       ├── multilevelLib/
│   │   │   │       │   ├── Makefile
│   │   │   │       │   ├── mlkkm.c
│   │   │   │       │   ├── mlkkm.o
│   │   │   │       │   ├── wkkm.c
│   │   │   │       │   ├── wkkm.o
│   │   │   │       │   ├── wkkm_boundary_only.c
│   │   │   │       │   ├── wkkm_experiment.c
│   │   │   │       │   └── wkkm_old.c
│   │   │   │       └── programs/
│   │   │   │           ├── Makefile
│   │   │   │           ├── graclus.c
│   │   │   │           ├── graclus.o
│   │   │   │           ├── io.c
│   │   │   │           ├── io.h
│   │   │   │           └── io.o
│   │   │   └── matlab_bgl/
│   │   │       ├── .project
│   │   │       ├── @inplace/
│   │   │       │   ├── assign.m
│   │   │       │   ├── display.m
│   │   │       │   ├── double.m
│   │   │       │   ├── end.m
│   │   │       │   ├── inplace.m
│   │   │       │   ├── size.m
│   │   │       │   ├── subsasgn.m
│   │   │       │   └── subsref.m
│   │   │       ├── @ipdouble/
│   │   │       │   └── ipdouble.m
│   │   │       ├── @ipint32/
│   │   │       │   └── ipint32.m
│   │   │       ├── Contents.m
│   │   │       ├── all_shortest_paths.m
│   │   │       ├── astar_search.m
│   │   │       ├── bellman_ford_sp.m
│   │   │       ├── betweenness_centrality.m
│   │   │       ├── bfs.m
│   │   │       ├── biconnected_components.m
│   │   │       ├── boyer_myrvold_planarity_test.m
│   │   │       ├── breadth_first_search.m
│   │   │       ├── chrobak_payne_straight_line_drawing.m
│   │   │       ├── circle_graph_layout.m
│   │   │       ├── clique_graph.m
│   │   │       ├── clustering_coefficients.m
│   │   │       ├── combine_visitors.m
│   │   │       ├── components.m
│   │   │       ├── core_numbers.m
│   │   │       ├── custom/
│   │   │       │   ├── dijkstra_all_sp.m
│   │   │       │   └── path_histogram.m
│   │   │       ├── cycle_graph.m
│   │   │       ├── dag_sp.m
│   │   │       ├── depth_first_search.m
│   │   │       ├── dfs.m
│   │   │       ├── dijkstra_sp.m
│   │   │       ├── doc/
│   │   │       │   ├── changed.txt
│   │   │       │   ├── html/
│   │   │       │   │   ├── changes.html
│   │   │       │   │   ├── core_numbers_example/
│   │   │       │   │   │   └── core_numbers_example.html
│   │   │       │   │   ├── faq.html
│   │   │       │   │   ├── index.html
│   │   │       │   │   ├── new_in_3/
│   │   │       │   │   │   └── new_in_3_0.html
│   │   │       │   │   ├── new_in_4/
│   │   │       │   │   │   └── new_in_4_0.html
│   │   │       │   │   ├── old.html
│   │   │       │   │   ├── planar_graphs/
│   │   │       │   │   │   └── planar_graphs.html
│   │   │       │   │   ├── record_alg/
│   │   │       │   │   │   └── record_alg.html
│   │   │       │   │   ├── red_black/
│   │   │       │   │   │   └── red_black.html
│   │   │       │   │   ├── reweighted_graphs/
│   │   │       │   │   │   └── reweighted_graphs.html
│   │   │       │   │   ├── site.css
│   │   │       │   │   └── style.css
│   │   │       │   ├── mxdom2mbgl-html.xsl
│   │   │       │   └── write_examples_html.m
│   │   │       ├── edge_weight_index.m
│   │   │       ├── edge_weight_vector.m
│   │   │       ├── edmonds_maximum_cardinality_matching.m
│   │   │       ├── edmunds_karp_max_flow.m
│   │   │       ├── erdos_reyni.m
│   │   │       ├── examples/
│   │   │       │   ├── approx_multiway_cut.m
│   │   │       │   ├── bacon_numbers.m
│   │   │       │   ├── bfs_example.m
│   │   │       │   ├── bfs_in_mbgl.m
│   │   │       │   ├── bfs_in_mbgl_efficient.m
│   │   │       │   ├── core_numbers_example.m
│   │   │       │   ├── dfs_example.m
│   │   │       │   ├── edge_index_example.m
│   │   │       │   ├── max_flow_example.m
│   │   │       │   ├── multiway_example.m
│   │   │       │   ├── new_in_3_0.m
│   │   │       │   ├── new_in_4_0.m
│   │   │       │   ├── planar_graphs.m
│   │   │       │   ├── record_alg.m
│   │   │       │   ├── red_black.m
│   │   │       │   └── reweighted_graphs.m
│   │   │       ├── floyd_warshall_all_sp.m
│   │   │       ├── fruchterman_reingold_force_directed_layout.m
│   │   │       ├── graphs/
│   │   │       │   ├── all_shortest_paths_example.mat
│   │   │       │   ├── bfs_example.mat
│   │   │       │   ├── bgl_cities.mat
│   │   │       │   ├── clique-10.mat
│   │   │       │   ├── clr-24-1.mat
│   │   │       │   ├── clr-25-2.mat
│   │   │       │   ├── clr-26-1.mat
│   │   │       │   ├── clr-27-1.mat
│   │   │       │   ├── cores_example.mat
│   │   │       │   ├── cs-stanford.mat
│   │   │       │   ├── dfs_example.mat
│   │   │       │   ├── dominator_tree_example.mat
│   │   │       │   ├── kt-3-2.mat
│   │   │       │   ├── kt-3-7.mat
│   │   │       │   ├── kt-6-23.mat
│   │   │       │   ├── kt-7-2.mat
│   │   │       │   ├── line-7.mat
│   │   │       │   ├── matching_example.mat
│   │   │       │   ├── max_flow_example.mat
│   │   │       │   ├── minnesota.mat
│   │   │       │   ├── padgett-florentine.mat
│   │   │       │   ├── tapir.mat
│   │   │       │   └── tarjan-biconn.mat
│   │   │       ├── grid_graph.m
│   │   │       ├── gursoy_atun_layout.m
│   │   │       ├── indexed_sparse.m
│   │   │       ├── is_kuratowski_graph.m
│   │   │       ├── is_straight_line_drawing.m
│   │   │       ├── johnson_all_sp.m
│   │   │       ├── kamada_kawai_spring_layout.m
│   │   │       ├── kolmogorov_max_flow.m
│   │   │       ├── kruskal_mst.m
│   │   │       ├── kuratowski_subgraph.m
│   │   │       ├── lengauer_tarjan_dominator_tree.m
│   │   │       ├── libmbgl/
│   │   │       │   ├── ccfiles.sh
│   │   │       │   ├── compile-linux-32.sh
│   │   │       │   ├── compile-linux-64-large.sh
│   │   │       │   ├── compile-linux-64.sh
│   │   │       │   ├── compile-macosx-intel-32.sh
│   │   │       │   ├── compile-macosx-ppc-32.sh
│   │   │       │   ├── compile-win32.bat
│   │   │       │   ├── compile-win64.bat
│   │   │       │   ├── components.cc
│   │   │       │   ├── crm_graph.hpp
│   │   │       │   ├── include/
│   │   │       │   │   ├── matlab_bgl.h
│   │   │       │   │   └── matlab_bgl_types.h
│   │   │       │   ├── layouts.cc
│   │   │       │   ├── libmbgl.sln
│   │   │       │   ├── libmbgl.vcproj
│   │   │       │   ├── libmbgl_test/
│   │   │       │   │   ├── Makefile
│   │   │       │   │   ├── fr_layout_test.cc
│   │   │       │   │   ├── layout_funcs_test.cc
│   │   │       │   │   ├── libmbgl_funcs_test.cc
│   │   │       │   │   ├── libmbgl_funcs_test.h
│   │   │       │   │   ├── libmbgl_test.cc
│   │   │       │   │   ├── libmbgl_test.vcproj
│   │   │       │   │   ├── planar_funcs_test.cc
│   │   │       │   │   ├── planar_is_straight_line_test.cc
│   │   │       │   │   ├── planar_ksubgraph_test.cc
│   │   │       │   │   ├── property_map_test.cc
│   │   │       │   │   ├── simple_prop_map_test.cc
│   │   │       │   │   ├── simple_prop_map_test_2.cc
│   │   │       │   │   ├── simple_prop_map_test_3.cc
│   │   │       │   │   └── simple_prop_map_test_4.cc
│   │   │       │   ├── libmbgl_util.hpp
│   │   │       │   ├── max_flow.cc
│   │   │       │   ├── orderings.cc
│   │   │       │   ├── planar.cc
│   │   │       │   ├── searches.cc
│   │   │       │   ├── shortest_path.cc
│   │   │       │   ├── spanning_trees.cc
│   │   │       │   ├── statistics.cc
│   │   │       │   ├── stop_visitors.hpp
│   │   │       │   ├── visitor_macros.hpp
│   │   │       │   └── yasmic/
│   │   │       │       ├── .sconsign
│   │   │       │       ├── bgl_kcore.hpp
│   │   │       │       ├── binary_ifstream_graph.hpp
│   │   │       │       ├── binary_ifstream_matrix.hpp
│   │   │       │       ├── bind_utility.hpp
│   │   │       │       ├── boost_mod/
│   │   │       │       │   ├── .sconsign
│   │   │       │       │   ├── bellman_ford_shortest_paths.hpp
│   │   │       │       │   ├── betweenness_centrality.hpp
│   │   │       │       │   ├── chrobak_payne_drawing.hpp
│   │   │       │       │   ├── core_numbers.hpp
│   │   │       │       │   ├── floyd_warshall_shortest.hpp
│   │   │       │       │   ├── fruchterman_reingold.hpp
│   │   │       │       │   ├── gzip.hpp
│   │   │       │       │   ├── integer_extra.hpp
│   │   │       │       │   ├── is_straight_line_drawing.hpp
│   │   │       │       │   ├── johnson_all_pairs_shortest.hpp
│   │   │       │       │   ├── kolmogorov_max_flow.hpp
│   │   │       │       │   ├── kruskal_min_spanning_tree.hpp
│   │   │       │       │   └── zlib.cpp
│   │   │       │       ├── bvgraph_matrix.hpp
│   │   │       │       ├── cluto_ifstream_matrix.hpp
│   │   │       │       ├── compressed_row_matrix.hpp
│   │   │       │       ├── compressed_row_matrix_graph.hpp
│   │   │       │       ├── generic_matrix_operations.hpp
│   │   │       │       ├── graph_ifstream_matrix.hpp
│   │   │       │       ├── ifstream_as_matrix.hpp
│   │   │       │       ├── ifstream_matrix.hpp
│   │   │       │       ├── indexed_list.hpp
│   │   │       │       ├── indexed_list.old.hpp
│   │   │       │       ├── indexed_list_as_graph.hpp
│   │   │       │       ├── istream_as_matrix.hpp
│   │   │       │       ├── iterator_utility.hpp
│   │   │       │       ├── matrix_row_col_graph.hpp
│   │   │       │       ├── nonzero_union.hpp
│   │   │       │       ├── simple_csr_matrix.hpp
│   │   │       │       ├── simple_csr_matrix_as_graph.hpp
│   │   │       │       ├── simple_row_and_column_matrix.hpp
│   │   │       │       ├── simple_row_and_column_matrix_as_graph.hpp
│   │   │       │       ├── smatrix_traits.hpp
│   │   │       │       ├── transpose_matrix.hpp
│   │   │       │       ├── tuple_utility.hpp
│   │   │       │       ├── undir_simple_csr_matrix.hpp
│   │   │       │       ├── undir_simple_csr_matrix_as_graph.hpp
│   │   │       │       ├── util/
│   │   │       │       │   ├── .sconsign
│   │   │       │       │   ├── crm_matrix.hpp
│   │   │       │       │   ├── filtered_matrix.hpp
│   │   │       │       │   ├── load_crm_graph.hpp
│   │   │       │       │   ├── load_crm_matrix.hpp
│   │   │       │       │   ├── write_matrix.hpp
│   │   │       │       │   └── write_petsc_matrix.hpp
│   │   │       │       ├── verbose_util.hpp
│   │   │       │       ├── yasmic.cbp
│   │   │       │       ├── yasmic.layout
│   │   │       │       └── yasmic.vcproj
│   │   │       ├── make_biconnected_planar.m
│   │   │       ├── make_connected.m
│   │   │       ├── make_maximal_planar.m
│   │   │       ├── matching.m
│   │   │       ├── max_flow.m
│   │   │       ├── maximal_matching.m
│   │   │       ├── mst.m
│   │   │       ├── num_edges.m
│   │   │       ├── num_vertices.m
│   │   │       ├── path_from_pred.m
│   │   │       ├── planar_canonical_ordering.m
│   │   │       ├── prim_mst.m
│   │   │       ├── private/
│   │   │       │   ├── astar_search_mex.c
│   │   │       │   ├── betweenness_centrality_mex.c
│   │   │       │   ├── bfs_dfs_vis_mex.c
│   │   │       │   ├── bfs_mex.c
│   │   │       │   ├── biconnected_components_mex.c
│   │   │       │   ├── check_matlab_bgl.m
│   │   │       │   ├── clustering_coefficients_mex.c
│   │   │       │   ├── common_functions.h
│   │   │       │   ├── common_macros.h
│   │   │       │   ├── compile.m
│   │   │       │   ├── components_mex.c
│   │   │       │   ├── core_numbers_mex.c
│   │   │       │   ├── dfs_mex.c
│   │   │       │   ├── dominator_tree_mex.c
│   │   │       │   ├── expand_macros.h
│   │   │       │   ├── fruchterman_reingold_mex.c
│   │   │       │   ├── get_matlab_bgl_options.m
│   │   │       │   ├── gursoy_atun_mex.c
│   │   │       │   ├── kamada_kawai_spring_layout_mex.c
│   │   │       │   ├── matching_mex.c
│   │   │       │   ├── matlab_bgl_all_sp_mex.c
│   │   │       │   ├── matlab_bgl_sp_mex.c
│   │   │       │   ├── max_flow_mex.c
│   │   │       │   ├── merge_options.m
│   │   │       │   ├── merge_structs.m
│   │   │       │   ├── mst_mex.c
│   │   │       │   ├── path_from_pred_mex.c
│   │   │       │   ├── planar_drawing_mex.c
│   │   │       │   ├── planar_edges_mex.c
│   │   │       │   ├── planar_test_mex.c
│   │   │       │   ├── test_matching_mex.c
│   │   │       │   ├── todo.m
│   │   │       │   ├── todo_3_0_release.m
│   │   │       │   ├── topological_order_mex.c
│   │   │       │   └── visitor_macros.h
│   │   │       ├── push_relabel_max_flow.m
│   │   │       ├── random_graph_layout.m
│   │   │       ├── set_matlab_bgl_default.m
│   │   │       ├── shortest_paths.m
│   │   │       ├── star_graph.m
│   │   │       ├── test/
│   │   │       │   ├── assert.m
│   │   │       │   ├── rtest_1.m
│   │   │       │   ├── rtest_2.m
│   │   │       │   ├── rtest_3_cojocaru.m
│   │   │       │   ├── rtest_5_henderson.m
│   │   │       │   ├── rtest_6.m
│   │   │       │   ├── rtest_7_karsi.m
│   │   │       │   ├── rtest_all.m
│   │   │       │   ├── test_all.m
│   │   │       │   ├── test_benchmark.m
│   │   │       │   ├── test_breadth_first_search.m
│   │   │       │   ├── test_components.m
│   │   │       │   ├── test_depth_first_search.m
│   │   │       │   ├── test_examples.m
│   │   │       │   ├── test_layouts.m
│   │   │       │   ├── test_main.m
│   │   │       │   ├── test_planar.m
│   │   │       │   ├── test_searches.m
│   │   │       │   ├── test_shortest_paths.m
│   │   │       │   ├── test_spanning_trees.m
│   │   │       │   ├── test_statistics.m
│   │   │       │   └── test_trivial.m
│   │   │       ├── test_dag.m
│   │   │       ├── test_matching.m
│   │   │       ├── test_planar_graph.m
│   │   │       ├── topological_order.m
│   │   │       ├── tree_from_pred.m
│   │   │       └── wheel_graph.m
│   │   └── src/
│   │       ├── Assign_bi.m
│   │       ├── add_extra_community_data.m
│   │       ├── biconncore.m
│   │       ├── compile.m
│   │       ├── cutcond_mex.cc
│   │       ├── evaluate_clusters.m
│   │       ├── filter_community_conductance.m
│   │       ├── flip_C.m
│   │       ├── graphprep.m
│   │       ├── growclusters.m
│   │       ├── largest_component.m
│   │       ├── localEgoSeeds.m
│   │       ├── merge_community_data.m
│   │       ├── neighborhoodmin.m
│   │       ├── nise.m
│   │       ├── pprgrow.m
│   │       ├── pprgrow_mex.cc
│   │       ├── seed_report_expand.m
│   │       ├── spHubSeeds.m
│   │       ├── triangleclusters.m
│   │       ├── triangleclusters_mex.cc
│   │       ├── vpprgrow.m
│   │       └── vpprgrow_mex.cc
│   ├── 2014-Heat-Kernel/
│   │   ├── ReadMe.md
│   │   ├── authors_original_files/
│   │   │   ├── data/
│   │   │   │   ├── amazon.mat
│   │   │   │   ├── four_clusters.smat
│   │   │   │   └── netscience-cc.smat
│   │   │   ├── experiments/
│   │   │   │   ├── chirikov/
│   │   │   │   │   ├── chirikov_example.m
│   │   │   │   │   ├── chirikov_operator.m
│   │   │   │   │   ├── compile.m
│   │   │   │   │   ├── imwrite_scaled.m
│   │   │   │   │   └── pprgrow_mex.cc
│   │   │   │   ├── experimenthkgrow.m
│   │   │   │   ├── experimentpprgrow.m
│   │   │   │   ├── ground_truth/
│   │   │   │   │   ├── amazoncommunity.m
│   │   │   │   │   ├── dblpcommunity.m
│   │   │   │   │   ├── friendstercommunity.m
│   │   │   │   │   ├── ljournalcommunity.m
│   │   │   │   │   ├── orkutcommunity.m
│   │   │   │   │   └── youtubecommunity.m
│   │   │   │   ├── heavyhood.m
│   │   │   │   ├── heavyseed.m
│   │   │   │   ├── heavytwitter.m
│   │   │   │   ├── pathweights_figure.m
│   │   │   │   ├── pprfriendster.m
│   │   │   │   ├── pprheavytwitter.m
│   │   │   │   ├── pprljournal.m
│   │   │   │   ├── pprtwitter.m
│   │   │   │   ├── randhood.m
│   │   │   │   ├── randseed.m
│   │   │   │   ├── set_figure_size.m
│   │   │   │   ├── subplot3.m
│   │   │   │   ├── trials_friendster.m
│   │   │   │   ├── trials_hkgrow.m
│   │   │   │   ├── trials_ljournal.m
│   │   │   │   ├── trials_pprgrow.m
│   │   │   │   └── trials_twitter.m
│   │   │   ├── plotting/
│   │   │   │   ├── conductances.m
│   │   │   │   ├── plotconductances.m
│   │   │   │   ├── plotruntimes.m
│   │   │   │   ├── runtimes.m
│   │   │   │   └── twitcondvsclust.m
│   │   │   ├── ppr_src/
│   │   │   │   ├── compile.m
│   │   │   │   ├── pprgrow.m
│   │   │   │   └── pprgrow_mex.cc
│   │   │   └── src/
│   │   │       ├── README.md
│   │   │       ├── compile.m
│   │   │       ├── hkgrow.m
│   │   │       ├── hkgrow1.m
│   │   │       ├── hkgrow_mex.cpp
│   │   │       ├── hkgrow_mex_kdd.cpp
│   │   │       ├── load_graph.m
│   │   │       ├── normout.m
│   │   │       ├── readSMAT.m
│   │   │       ├── symmatfriend.m
│   │   │       ├── symmattwit.m
│   │   │       ├── test_hkgrow.m
│   │   │       └── test_hkgrow_mex.m
│   │   ├── src_cpp_matlab/
│   │   │   ├── hkgrow.m
│   │   │   ├── hkgrow1.m
│   │   │   ├── hkgrow_mex.cpp
│   │   │   ├── hkgrow_mex_kdd.cpp
│   │   │   ├── test_hkgrow.m
│   │   │   └── test_hkgrow_mex.m
│   │   ├── src_python/
│   │   │   ├── .gitignore
│   │   │   ├── ReadMe.md
│   │   │   ├── __init__.py
│   │   │   ├── dataset/
│   │   │   │   ├── __init__.py
│   │   │   │   ├── get_data.sh
│   │   │   │   └── graph_eval_script.txt
│   │   │   ├── demo_files/
│   │   │   │   ├── __init__.py
│   │   │   │   ├── gexpmq.py
│   │   │   │   ├── hr_relax.py
│   │   │   │   ├── yche_exp.py
│   │   │   │   └── yche_numerical_linear_algebra_exp.py
│   │   │   └── main_files/
│   │   │       ├── __init__.py
│   │   │       ├── algo_hr_grow.py
│   │   │       ├── algo_ppr.py
│   │   │       └── util_helper.py
│   │   └── yche_refactor/
│   │       ├── CMakeLists.txt
│   │       ├── ReadMe.md
│   │       ├── hkgrow_mex_kdd.cpp
│   │       └── main.cpp
│   └── 2015-LEMON/
│       ├── .gitignore
│       ├── LEMON/
│       │   └── __init__.py
│       ├── LICENSE
│       ├── README.md
│       ├── example/
│       │   └── amazon/
│       │       ├── README
│       │       ├── community
│       │       ├── graph
│       │       └── seed
│       └── python_yche_refactor/
│           ├── eval_ground_truth.txt
│           ├── io_helper.py
│           └── lemon.py
├── Benchmark/
│   └── 2009-LFR-Benchmark/
│       ├── ReadMe.md
│       ├── src_original_cpp/
│       │   ├── ReadMe.md
│       │   ├── binary_networks/
│       │   │   ├── ReadMe.txt
│       │   │   ├── Sources/
│       │   │   │   ├── benchm.cpp
│       │   │   │   ├── cast.cpp
│       │   │   │   ├── cc.cpp
│       │   │   │   ├── combinatorics.cpp
│       │   │   │   ├── histograms.cpp
│       │   │   │   ├── print.cpp
│       │   │   │   ├── random.cpp
│       │   │   │   ├── set_parameters.cpp
│       │   │   │   └── standard_include.cpp
│       │   │   ├── Thanks.txt
│       │   │   └── makefile
│       │   ├── directed_networks/
│       │   │   ├── ReadMe.txt
│       │   │   ├── Sources/
│       │   │   │   ├── benchm.cpp
│       │   │   │   ├── cast.cpp
│       │   │   │   ├── combinatorics.cpp
│       │   │   │   ├── histograms.cpp
│       │   │   │   ├── print.cpp
│       │   │   │   ├── random.cpp
│       │   │   │   ├── set_parameters.cpp
│       │   │   │   └── standard_include.cpp
│       │   │   ├── Thanks.txt
│       │   │   ├── gpl.txt
│       │   │   └── makefile
│       │   ├── hierarchical_bench2_2/
│       │   │   ├── ReadMe.txt
│       │   │   ├── Thanks.txt
│       │   │   ├── gpl.txt
│       │   │   ├── hier_ben_Sources/
│       │   │   │   ├── a.out
│       │   │   │   ├── benchm.cpp
│       │   │   │   ├── binary_benchm.cpp
│       │   │   │   ├── cc.cpp
│       │   │   │   ├── set_parameters.cpp
│       │   │   │   └── standard_package/
│       │   │   │       ├── cast.cpp
│       │   │   │       ├── combinatorics.cpp
│       │   │   │       ├── deque_numeric.cpp
│       │   │   │       ├── histograms.cpp
│       │   │   │       ├── mutual.cpp
│       │   │   │       ├── pajek.cpp
│       │   │   │       ├── partition.cpp
│       │   │   │       ├── print.cpp
│       │   │   │       ├── random.cpp
│       │   │   │       ├── standard_include.cpp
│       │   │   │       └── tabdeg.cpp
│       │   │   └── makefile
│       │   ├── weighted_directed_nets/
│       │   │   ├── ReadMe.txt
│       │   │   ├── Sources/
│       │   │   │   ├── benchm.cpp
│       │   │   │   ├── cast.cpp
│       │   │   │   ├── combinatorics.cpp
│       │   │   │   ├── dir_benchm.cpp
│       │   │   │   ├── histograms.cpp
│       │   │   │   ├── print.cpp
│       │   │   │   ├── random.cpp
│       │   │   │   ├── set_parameters.cpp
│       │   │   │   └── standard_include.cpp
│       │   │   ├── Thanks.txt
│       │   │   ├── benchmark
│       │   │   ├── gpl.txt
│       │   │   └── makefile
│       │   └── weighted_networks/
│       │       ├── ReadMe.txt
│       │       ├── Sources/
│       │       │   ├── Icon_
│       │       │   ├── benchm.cpp
│       │       │   ├── binary_benchm.cpp
│       │       │   ├── cast.cpp
│       │       │   ├── cc.cpp
│       │       │   ├── combinatorics.cpp
│       │       │   ├── histograms.cpp
│       │       │   ├── print.cpp
│       │       │   ├── random.cpp
│       │       │   ├── set_parameters.cpp
│       │       │   └── standard_include.cpp
│       │       ├── Thanks.txt
│       │       ├── gpl.txt
│       │       └── makefile
│       └── src_refactor_cpp/
│           ├── .gitignore
│           ├── CMakeLists.txt
│           ├── ReadMe.md
│           ├── benchmark_gen.py
│           ├── directed_graph/
│           │   ├── CMakeLists.txt
│           │   ├── ReadMe.md
│           │   ├── benchm.cpp
│           │   ├── doc/
│           │   │   ├── ReadMe.txt
│           │   │   ├── Thanks.txt
│           │   │   └── gpl.txt
│           │   ├── set_parameters.cpp
│           │   └── set_parameters.h
│           ├── documents/
│           │   └── ReadMe.md
│           ├── hierarchical_comm_graph/
│           │   ├── CMakeLists.txt
│           │   ├── ReadMe.md
│           │   ├── benchm.cpp
│           │   ├── binary_benchm.cpp
│           │   ├── binary_benchm.h
│           │   ├── doc/
│           │   │   ├── ReadMe.txt
│           │   │   ├── Thanks.txt
│           │   │   ├── gpl.txt
│           │   │   └── makefile
│           │   ├── set_parameters.cpp
│           │   └── set_parameters.h
│           ├── playground/
│           │   ├── CMakeLists.txt
│           │   ├── nmi_usage_demo.cpp
│           │   └── tabdeg_demo.cpp
│           ├── run_undir_gperf.sh
│           ├── run_undir_perf.sh
│           ├── undirected_graph/
│           │   ├── CMakeLists.txt
│           │   ├── ReadMe.md
│           │   ├── benchm.cpp
│           │   ├── doc/
│           │   │   ├── ReadMe.txt
│           │   │   └── Thanks.txt
│           │   ├── set_parameters.cpp
│           │   └── set_parameters.h
│           ├── util/
│           │   ├── cast.cpp
│           │   ├── cast.h
│           │   ├── cc.cpp
│           │   ├── cc.h
│           │   ├── combinatorics.cpp
│           │   ├── combinatorics.h
│           │   ├── histograms.cpp
│           │   ├── histograms.h
│           │   ├── input_output/
│           │   │   ├── tab_degree.cpp
│           │   │   └── tab_degree.h
│           │   ├── metric/
│           │   │   ├── mutual.cpp
│           │   │   └── mutual.h
│           │   ├── pretty_print.h
│           │   ├── random.cpp
│           │   ├── random.h
│           │   └── unused/
│           │       ├── deque_numeric.cpp
│           │       ├── deque_numeric.h
│           │       └── input_output/
│           │           ├── pajek.cpp
│           │           └── partition.cpp
│           ├── weighted_directed_graph/
│           │   ├── CMakeLists.txt
│           │   ├── ReadMe.md
│           │   ├── benchm.cpp
│           │   ├── dir_benchm.cpp
│           │   ├── dir_benchm.h
│           │   ├── doc/
│           │   │   ├── ReadMe.txt
│           │   │   ├── Thanks.txt
│           │   │   ├── gpl.txt
│           │   │   └── makefile
│           │   ├── set_parameters.cpp
│           │   └── set_parameters.h
│           └── weighted_graph/
│               ├── CMakeLists.txt
│               ├── ReadMe.md
│               ├── benchm.cpp
│               ├── binary_benchm.cpp
│               ├── binary_benchm.h
│               ├── doc/
│               │   ├── ReadMe.txt
│               │   ├── Thanks.txt
│               │   └── gpl.txt
│               ├── set_parameters.cpp
│               └── set_parameters.h
├── CONTRIBUTING.md
├── Datasets/
│   ├── ReadMe.md
│   ├── collaboration_edge_list.txt
│   ├── epinions_edge_list.txt
│   ├── facebook_edge_list.txt
│   ├── football_edge_list.txt
│   ├── karate_edge_list.txt
│   ├── slashdot0811_edge_list.txt
│   ├── slashdot0902_edge_list.txt
│   └── wiki_vote_edge_list.txt
├── License.md
├── Metrics/
│   ├── MultiplexNMI-Benchmark/
│   │   ├── MultiplexBenchmark/
│   │   │   ├── ReadMe.txt
│   │   │   ├── Sources/
│   │   │   │   ├── benchm.cpp
│   │   │   │   ├── cast.cpp
│   │   │   │   ├── cc.cpp
│   │   │   │   ├── combinatorics.cpp
│   │   │   │   ├── histograms.cpp
│   │   │   │   ├── print.cpp
│   │   │   │   ├── random.cpp
│   │   │   │   ├── set_parameters.cpp
│   │   │   │   ├── standard_bench.cpp
│   │   │   │   └── standard_include.cpp
│   │   │   ├── Thanks.txt
│   │   │   ├── gpl.txt
│   │   │   └── makefile
│   │   └── MultiplexNMI/
│   │       ├── ReadMe.txt
│   │       ├── clu1
│   │       ├── clu2
│   │       ├── nmi_multiplex.cpp
│   │       └── standard_package/
│   │           ├── assert.cpp
│   │           ├── cast.cpp
│   │           ├── combinatorics.cpp
│   │           ├── deque_numeric.cpp
│   │           ├── histograms.cpp
│   │           ├── map_utilities.cpp
│   │           ├── mutual.cpp
│   │           ├── pajek.cpp
│   │           ├── partition.cpp
│   │           ├── print.cpp
│   │           ├── random.cpp
│   │           ├── standard_include.cpp
│   │           └── tabdeg.cpp
│   ├── ReadMe.md
│   ├── __init__.py
│   ├── analyze_algo_quality.py
│   ├── cis_fb.out
│   ├── facebook_combined.txt
│   ├── metrics/
│   │   ├── __init__.py
│   │   ├── demo_graph.csv
│   │   ├── link_belong_modularity.py
│   │   ├── omega_idx.py
│   │   ├── overlap_nmi.py
│   │   └── util.py
│   ├── mutual3/
│   │   ├── ReadMe.txt
│   │   ├── makefile
│   │   ├── mutual
│   │   ├── mutual3.cpp
│   │   └── standard_package/
│   │       ├── Icon
│   │       ├── cast.cpp
│   │       ├── combinatorics.cpp
│   │       ├── deque_numeric.cpp
│   │       ├── histograms.cpp
│   │       ├── mutual.cpp
│   │       ├── partition.cpp
│   │       ├── print.cpp
│   │       ├── random.cpp
│   │       └── standard_include.cpp
│   └── play_ground/
│       ├── __init__.py
│       └── play_ground.py
├── NonOverlappingCodes/
│   ├── 2005-Markov-Clustering/
│   │   ├── ReadMe.md
│   │   └── mcl-14-137/
│   │       ├── AUTHORS
│   │       ├── COPYING
│   │       ├── ChangeLog
│   │       ├── INSTALL
│   │       ├── LICENSE
│   │       ├── Makefile.am
│   │       ├── Makefile.in
│   │       ├── NEWS
│   │       ├── README
│   │       ├── THANKS
│   │       ├── TODO
│   │       ├── VERSION
│   │       ├── acinclude.m4
│   │       ├── aclocal.m4
│   │       ├── autofoo/
│   │       │   ├── config.guess
│   │       │   ├── config.sub
│   │       │   ├── depcomp
│   │       │   ├── install-sh
│   │       │   └── missing
│   │       ├── bootstrap
│   │       ├── config.h.in
│   │       ├── configure
│   │       ├── configure.ac
│   │       ├── configure.ac.in
│   │       ├── doc/
│   │       │   ├── Makefile.am
│   │       │   ├── Makefile.in
│   │       │   ├── clm.1
│   │       │   ├── clm.azm
│   │       │   ├── clm.html
│   │       │   ├── clm.ps
│   │       │   ├── clmclose.1
│   │       │   ├── clmclose.azm
│   │       │   ├── clmclose.html
│   │       │   ├── clmclose.ps
│   │       │   ├── clmdist.1
│   │       │   ├── clmdist.azm
│   │       │   ├── clmdist.html
│   │       │   ├── clmdist.ps
│   │       │   ├── clmformat.1
│   │       │   ├── clmformat.azm
│   │       │   ├── clmformat.html
│   │       │   ├── clmformat.ps
│   │       │   ├── clmimac.1
│   │       │   ├── clmimac.azm
│   │       │   ├── clmimac.html
│   │       │   ├── clmimac.ps
│   │       │   ├── clminfo.1
│   │       │   ├── clminfo.azm
│   │       │   ├── clminfo.html
│   │       │   ├── clminfo.ps
│   │       │   ├── clminfo2.1
│   │       │   ├── clminfo2.azm
│   │       │   ├── clminfo2.html
│   │       │   ├── clminfo2.ps
│   │       │   ├── clmmate.1
│   │       │   ├── clmmate.azm
│   │       │   ├── clmmate.html
│   │       │   ├── clmmate.ps
│   │       │   ├── clmmeet.1
│   │       │   ├── clmmeet.azm
│   │       │   ├── clmmeet.html
│   │       │   ├── clmmeet.ps
│   │       │   ├── clmoptics.1
│   │       │   ├── clmoptics.azm
│   │       │   ├── clmoptics.html
│   │       │   ├── clmoptics.ps
│   │       │   ├── clmorder.1
│   │       │   ├── clmorder.azm
│   │       │   ├── clmorder.html
│   │       │   ├── clmorder.ps
│   │       │   ├── clmprotocols.5
│   │       │   ├── clmprotocols.azm
│   │       │   ├── clmprotocols.html
│   │       │   ├── clmprotocols.ps
│   │       │   ├── clmprotocols2.5
│   │       │   ├── clmprotocols2.azm
│   │       │   ├── clmprotocols2.html
│   │       │   ├── clmprotocols2.ps
│   │       │   ├── clmresidue.1
│   │       │   ├── clmresidue.azm
│   │       │   ├── clmresidue.html
│   │       │   ├── clmresidue.ps
│   │       │   ├── clmvol.1
│   │       │   ├── clmvol.azm
│   │       │   ├── clmvol.html
│   │       │   ├── clmvol.ps
│   │       │   ├── distindex.html
│   │       │   ├── index.html
│   │       │   ├── index.in.azm
│   │       │   ├── mcl.1
│   │       │   ├── mcl.azm
│   │       │   ├── mcl.html
│   │       │   ├── mcl.ps
│   │       │   ├── mcl.txt
│   │       │   ├── mclblastline.html
│   │       │   ├── mclblastline.ps
│   │       │   ├── mclcm.1
│   │       │   ├── mclcm.azm
│   │       │   ├── mclcm.html
│   │       │   ├── mclcm.ps
│   │       │   ├── mclcm.txt
│   │       │   ├── mclfamily.7
│   │       │   ├── mclfamily.azm
│   │       │   ├── mclfamily.html
│   │       │   ├── mclfamily.ps
│   │       │   ├── mclfaq.7
│   │       │   ├── mclfaq.azm
│   │       │   ├── mclfaq.html
│   │       │   ├── mclfaq.ps
│   │       │   ├── mclfaq.txt
│   │       │   ├── mclindex.7
│   │       │   ├── mclindex.ps
│   │       │   ├── mclmcl.txt
│   │       │   ├── mclpipeline.1
│   │       │   ├── mclpipeline.azm
│   │       │   ├── mclpipeline.html
│   │       │   ├── mclpipeline.ps
│   │       │   ├── mcx.1
│   │       │   ├── mcx.azm
│   │       │   ├── mcx.html
│   │       │   ├── mcx.ps
│   │       │   ├── mcx.zmm
│   │       │   ├── mcxalter.1
│   │       │   ├── mcxalter.azm
│   │       │   ├── mcxalter.html
│   │       │   ├── mcxalter.ps
│   │       │   ├── mcxarray.1
│   │       │   ├── mcxarray.azm
│   │       │   ├── mcxarray.html
│   │       │   ├── mcxarray.ps
│   │       │   ├── mcxassemble.1
│   │       │   ├── mcxassemble.azm
│   │       │   ├── mcxassemble.html
│   │       │   ├── mcxassemble.ps
│   │       │   ├── mcxclcf.1
│   │       │   ├── mcxclcf.azm
│   │       │   ├── mcxclcf.html
│   │       │   ├── mcxclcf.ps
│   │       │   ├── mcxconvert.1
│   │       │   ├── mcxconvert.azm
│   │       │   ├── mcxconvert.html
│   │       │   ├── mcxconvert.ps
│   │       │   ├── mcxctty.1
│   │       │   ├── mcxctty.azm
│   │       │   ├── mcxctty.html
│   │       │   ├── mcxctty.ps
│   │       │   ├── mcxdeblast.html
│   │       │   ├── mcxdeblast.ps
│   │       │   ├── mcxdiameter.1
│   │       │   ├── mcxdiameter.azm
│   │       │   ├── mcxdiameter.html
│   │       │   ├── mcxdiameter.ps
│   │       │   ├── mcxdump.1
│   │       │   ├── mcxdump.azm
│   │       │   ├── mcxdump.html
│   │       │   ├── mcxdump.ps
│   │       │   ├── mcxerdos.1
│   │       │   ├── mcxerdos.azm
│   │       │   ├── mcxerdos.html
│   │       │   ├── mcxerdos.ps
│   │       │   ├── mcxi.1
│   │       │   ├── mcxi.azm
│   │       │   ├── mcxi.html
│   │       │   ├── mcxi.ps
│   │       │   ├── mcxio.5
│   │       │   ├── mcxio.azm
│   │       │   ├── mcxio.html
│   │       │   ├── mcxio.ps
│   │       │   ├── mcxload.1
│   │       │   ├── mcxload.azm
│   │       │   ├── mcxload.html
│   │       │   ├── mcxload.ps
│   │       │   ├── mcxmap.1
│   │       │   ├── mcxmap.azm
│   │       │   ├── mcxmap.html
│   │       │   ├── mcxmap.ps
│   │       │   ├── mcxquery.1
│   │       │   ├── mcxquery.azm
│   │       │   ├── mcxquery.html
│   │       │   ├── mcxquery.ps
│   │       │   ├── mcxrand.1
│   │       │   ├── mcxrand.azm
│   │       │   ├── mcxrand.html
│   │       │   ├── mcxrand.ps
│   │       │   ├── mcxsubs.1
│   │       │   ├── mcxsubs.azm
│   │       │   ├── mcxsubs.html
│   │       │   ├── mcxsubs.ps
│   │       │   ├── minimcl
│   │       │   ├── stamp.day
│   │       │   ├── stamp.month
│   │       │   ├── stamp.stamp
│   │       │   ├── stamp.year
│   │       │   ├── tingea.log.7
│   │       │   ├── tingea.log.azm
│   │       │   ├── tingea.log.html
│   │       │   └── tingea.log.ps
│   │       ├── graphs/
│   │       │   ├── Makefile.am
│   │       │   ├── Makefile.in
│   │       │   ├── T
│   │       │   ├── Tx
│   │       │   ├── Txy
│   │       │   ├── Ty
│   │       │   ├── data.abc.hdr
│   │       │   ├── data.abc.raw
│   │       │   ├── data.hdr
│   │       │   ├── data.raw
│   │       │   ├── data.tab
│   │       │   ├── falkner.coords
│   │       │   ├── falkner.mci
│   │       │   ├── falkner2.mci
│   │       │   ├── friends
│   │       │   ├── fznyy.mci
│   │       │   ├── fznyy.tab
│   │       │   ├── honey.mci
│   │       │   ├── infinity.mci
│   │       │   ├── lattice.mci
│   │       │   ├── make-falkner.pl
│   │       │   ├── matula.mci
│   │       │   ├── petersen.mci
│   │       │   ├── proteins.mci
│   │       │   ├── seven.mci
│   │       │   ├── small.mci
│   │       │   ├── small.tab
│   │       │   ├── small64.mci
│   │       │   ├── tiny-min.mci
│   │       │   ├── tiny-nil.mci
│   │       │   ├── tiny-nilnine.mci
│   │       │   ├── tiny-ninenil.mci
│   │       │   ├── tiny-one.mci
│   │       │   └── tiny-zero.mci
│   │       ├── img/
│   │       │   ├── Makefile.am
│   │       │   ├── Makefile.in
│   │       │   ├── fa.ps
│   │       │   ├── falkner-bidi.ps
│   │       │   ├── falkner.ps
│   │       │   └── small.ps
│   │       ├── include/
│   │       │   ├── Makefile.am
│   │       │   ├── Makefile.in
│   │       │   └── include.am
│   │       ├── mkinstalldirs
│   │       ├── scripts/
│   │       │   ├── Makefile.am
│   │       │   ├── Makefile.in
│   │       │   ├── TODO
│   │       │   ├── clmsnare
│   │       │   ├── clxcoarse
│   │       │   ├── clxdo
│   │       │   ├── docme
│   │       │   ├── gengraph
│   │       │   ├── mcxplotlines.R
│   │       │   ├── minimcl
│   │       │   ├── mlm-analyze
│   │       │   ├── mlm-fifofum
│   │       │   ├── mlm-quilt
│   │       │   ├── mlm-summary
│   │       │   ├── movgraph
│   │       │   ├── packed-example.sh
│   │       │   ├── packed-example2.sh
│   │       │   ├── pichi
│   │       │   ├── piclo
│   │       │   └── tree3.pl
│   │       ├── setversion
│   │       ├── src/
│   │       │   ├── Makefile.am
│   │       │   ├── Makefile.in
│   │       │   ├── README
│   │       │   ├── alien/
│   │       │   │   ├── Makefile.am
│   │       │   │   ├── Makefile.in
│   │       │   │   └── oxygen/
│   │       │   │       ├── Makefile.am
│   │       │   │       ├── Makefile.in
│   │       │   │       ├── doc/
│   │       │   │       │   ├── Makefile.am
│   │       │   │       │   ├── Makefile.in
│   │       │   │       │   ├── mclblastline.1
│   │       │   │       │   ├── mclblastline.azm
│   │       │   │       │   ├── mclblastline.html
│   │       │   │       │   ├── mclblastline.ps
│   │       │   │       │   ├── mcxdeblast.1
│   │       │   │       │   ├── mcxdeblast.azm
│   │       │   │       │   ├── mcxdeblast.html
│   │       │   │       │   └── mcxdeblast.ps
│   │       │   │       └── src/
│   │       │   │           ├── Makefile.am
│   │       │   │           ├── Makefile.in
│   │       │   │           ├── mclblastline
│   │       │   │           └── mcxdeblast
│   │       │   ├── clew/
│   │       │   │   ├── Makefile.am
│   │       │   │   ├── Makefile.in
│   │       │   │   ├── cat.c
│   │       │   │   ├── cat.h
│   │       │   │   ├── claw.c
│   │       │   │   ├── claw.h
│   │       │   │   ├── clm.c
│   │       │   │   ├── clm.h
│   │       │   │   ├── scan.c
│   │       │   │   └── scan.h
│   │       │   ├── gryphon/
│   │       │   │   ├── Makefile.am
│   │       │   │   ├── Makefile.in
│   │       │   │   ├── path.c
│   │       │   │   └── path.h
│   │       │   ├── impala/
│   │       │   │   ├── Makefile.am
│   │       │   │   ├── Makefile.in
│   │       │   │   ├── app.c
│   │       │   │   ├── app.h
│   │       │   │   ├── compose.c
│   │       │   │   ├── compose.h
│   │       │   │   ├── edge.c
│   │       │   │   ├── edge.h
│   │       │   │   ├── iface.c
│   │       │   │   ├── iface.h
│   │       │   │   ├── io.c
│   │       │   │   ├── io.h
│   │       │   │   ├── ivp.c
│   │       │   │   ├── ivp.h
│   │       │   │   ├── ivptypes.h
│   │       │   │   ├── matrix.c
│   │       │   │   ├── matrix.h
│   │       │   │   ├── pval.c
│   │       │   │   ├── pval.h
│   │       │   │   ├── stream.c
│   │       │   │   ├── stream.h
│   │       │   │   ├── tab.c
│   │       │   │   ├── tab.h
│   │       │   │   ├── vector.c
│   │       │   │   ├── vector.h
│   │       │   │   ├── version.c
│   │       │   │   └── version.h
│   │       │   ├── mcl/
│   │       │   │   ├── Makefile.am
│   │       │   │   ├── Makefile.in
│   │       │   │   ├── alg.c
│   │       │   │   ├── alg.h
│   │       │   │   ├── dpsd.c
│   │       │   │   ├── dpsd.h
│   │       │   │   ├── expand.c
│   │       │   │   ├── expand.h
│   │       │   │   ├── inflate.c
│   │       │   │   ├── inflate.h
│   │       │   │   ├── interpret.c
│   │       │   │   ├── interpret.h
│   │       │   │   ├── proc.c
│   │       │   │   ├── proc.h
│   │       │   │   ├── procinit.c
│   │       │   │   ├── procinit.h
│   │       │   │   ├── shadow.c
│   │       │   │   ├── shadow.h
│   │       │   │   ├── transform.c
│   │       │   │   └── transform.h
│   │       │   ├── shcl/
│   │       │   │   ├── Makefile.am
│   │       │   │   ├── Makefile.in
│   │       │   │   ├── clm.c
│   │       │   │   ├── clm.h
│   │       │   │   ├── clmadjust.c
│   │       │   │   ├── clmadjust.h
│   │       │   │   ├── clmclose.c
│   │       │   │   ├── clmclose.h
│   │       │   │   ├── clmdag.c
│   │       │   │   ├── clmdist.c
│   │       │   │   ├── clmdist.h
│   │       │   │   ├── clmformat.c
│   │       │   │   ├── clmformat.zmm
│   │       │   │   ├── clmformat.zmm.h
│   │       │   │   ├── clmframe.c
│   │       │   │   ├── clmimac.c
│   │       │   │   ├── clmimac.h
│   │       │   │   ├── clminfo.c
│   │       │   │   ├── clminfo.h
│   │       │   │   ├── clminfo2.c
│   │       │   │   ├── clminfo2.h
│   │       │   │   ├── clmmate.c
│   │       │   │   ├── clmmate.h
│   │       │   │   ├── clmmeet.c
│   │       │   │   ├── clmmeet.h
│   │       │   │   ├── clmoptics.c
│   │       │   │   ├── clmoptics.h
│   │       │   │   ├── clmorder.c
│   │       │   │   ├── clmorder.h
│   │       │   │   ├── clmps.c
│   │       │   │   ├── clmps.defs
│   │       │   │   ├── clmps.defs.h
│   │       │   │   ├── clmps.h
│   │       │   │   ├── clmresidue.c
│   │       │   │   ├── clmresidue.h
│   │       │   │   ├── mclgraga
│   │       │   │   ├── mclgrep
│   │       │   │   ├── mclpipeline
│   │       │   │   ├── report.c
│   │       │   │   └── report.h
│   │       │   ├── shmcl/
│   │       │   │   ├── Makefile.am
│   │       │   │   ├── Makefile.in
│   │       │   │   ├── mcl.c
│   │       │   │   └── mclcm.c
│   │       │   ├── shmcx/
│   │       │   │   ├── Makefile.am
│   │       │   │   ├── Makefile.in
│   │       │   │   ├── TODO
│   │       │   │   ├── glob.c
│   │       │   │   ├── glob.h
│   │       │   │   ├── mcxi.c
│   │       │   │   ├── ops.c
│   │       │   │   ├── ops.h
│   │       │   │   ├── stack.c
│   │       │   │   ├── stack.h
│   │       │   │   ├── util.c
│   │       │   │   └── util.h
│   │       │   ├── shmcxquery/
│   │       │   │   ├── Makefile.am
│   │       │   │   ├── Makefile.in
│   │       │   │   ├── TODO
│   │       │   │   └── mcxquery.c
│   │       │   └── shmx/
│   │       │       ├── Makefile.am
│   │       │       ├── Makefile.in
│   │       │       ├── README
│   │       │       ├── TODO
│   │       │       ├── fake
│   │       │       ├── mcx.c
│   │       │       ├── mcx.h
│   │       │       ├── mcxalter.c
│   │       │       ├── mcxalter.h
│   │       │       ├── mcxarray.c
│   │       │       ├── mcxassemble.c
│   │       │       ├── mcxclcf.c
│   │       │       ├── mcxclcf.h
│   │       │       ├── mcxcollect.c
│   │       │       ├── mcxcollect.h
│   │       │       ├── mcxconvert.c
│   │       │       ├── mcxconvert.h
│   │       │       ├── mcxdiameter.c
│   │       │       ├── mcxdiameter.h
│   │       │       ├── mcxdump.c
│   │       │       ├── mcxerdos.c
│   │       │       ├── mcxerdos.h
│   │       │       ├── mcxfp.c
│   │       │       ├── mcxfp.h
│   │       │       ├── mcxload.c
│   │       │       ├── mcxmap.c
│   │       │       ├── mcxmetric.c
│   │       │       ├── mcxminusmeet.c
│   │       │       ├── mcxmm.c
│   │       │       ├── mcxquery.c
│   │       │       ├── mcxquery.h
│   │       │       ├── mcxrand.c
│   │       │       ├── mcxsubs.c
│   │       │       ├── mcxtab.c
│   │       │       ├── mcxtab.h
│   │       │       ├── mcxtest.c
│   │       │       └── mcxtest2.c
│   │       ├── testing/
│   │       │   ├── Makefile.am
│   │       │   ├── Makefile.in
│   │       │   ├── blast/
│   │       │   │   ├── Makefile.am
│   │       │   │   ├── Makefile.in
│   │       │   │   ├── blastfile
│   │       │   │   └── blastfile9
│   │       │   ├── setops/
│   │       │   │   ├── Makefile.am
│   │       │   │   ├── Makefile.in
│   │       │   │   └── set-test.sh
│   │       │   └── stream/
│   │       │       ├── Makefile.am
│   │       │       ├── Makefile.in
│   │       │       ├── abc-pairs.pl
│   │       │       ├── abc-test.sh
│   │       │       ├── abc.pl
│   │       │       └── az.tab
│   │       └── util/
│   │           ├── Makefile.am
│   │           ├── Makefile.in
│   │           ├── alloc.c
│   │           ├── alloc.h
│   │           ├── array.c
│   │           ├── array.h
│   │           ├── compile.h
│   │           ├── ding.c
│   │           ├── ding.h
│   │           ├── equate.c
│   │           ├── equate.h
│   │           ├── err.c
│   │           ├── err.h
│   │           ├── getpagesize.h
│   │           ├── gralloc.c
│   │           ├── gralloc.h
│   │           ├── hash.c
│   │           ├── hash.h
│   │           ├── heap.c
│   │           ├── heap.h
│   │           ├── inttypes.h
│   │           ├── io.c
│   │           ├── io.h
│   │           ├── let.c
│   │           ├── let.h
│   │           ├── list.c
│   │           ├── list.h
│   │           ├── minmax.h
│   │           ├── opt.c
│   │           ├── opt.h
│   │           ├── rand.c
│   │           ├── rand.h
│   │           ├── ting.c
│   │           ├── ting.h
│   │           ├── tok.c
│   │           ├── tok.h
│   │           ├── tr.c
│   │           ├── tr.h
│   │           ├── types.c
│   │           └── types.h
│   ├── 2008-Louvain-MultiLevel-Aggregation-Opt-Modularity/
│   │   ├── Makefile
│   │   ├── ReadMe.md
│   │   ├── community.cpp
│   │   ├── community.h
│   │   ├── graph.cpp
│   │   ├── graph.h
│   │   ├── graph_binary.cpp
│   │   ├── graph_binary.h
│   │   ├── main_community.cpp
│   │   ├── main_convert.cpp
│   │   ├── main_hierarchy.cpp
│   │   ├── main_random.cpp
│   │   └── readme.txt
│   ├── 2008-Sequential-Clique-Percolation/
│   │   ├── License.txt
│   │   ├── ReadMe.md
│   │   ├── cliqueHash.cpp
│   │   ├── cliqueHash.h
│   │   ├── communityTracker.cpp
│   │   ├── communityTracker.h
│   │   ├── dendrogram.cpp
│   │   ├── dendrogram.h
│   │   ├── k_clique.cpp
│   │   ├── k_clique.h
│   │   ├── kruskal.cpp
│   │   ├── kruskal.h
│   │   ├── lcelib/
│   │   │   ├── Containers.H
│   │   │   ├── License.txt
│   │   │   ├── Nets.H
│   │   │   ├── Neural/
│   │   │   │   └── NNet.H
│   │   │   ├── PrefetchPolicy.H
│   │   │   ├── Randgens.H
│   │   │   ├── bits/
│   │   │   │   ├── EmbBoolSelector.H
│   │   │   │   ├── FiboHeapCore.H
│   │   │   │   └── hashcore.H
│   │   │   ├── containers/
│   │   │   │   ├── ArrayBase.H
│   │   │   │   ├── ContainerPolicies.H
│   │   │   │   ├── DefaultIndexParams.H
│   │   │   │   ├── KeyPolicy.H
│   │   │   │   ├── Pair.H
│   │   │   │   ├── WeightPolicy.H
│   │   │   │   ├── indices/
│   │   │   │   │   ├── Array.H
│   │   │   │   │   ├── AutoVec.H
│   │   │   │   │   ├── HashControllers.H
│   │   │   │   │   ├── LinearHash.H
│   │   │   │   │   ├── OrderedArray.H
│   │   │   │   │   ├── TableWithStatus.H
│   │   │   │   │   └── Vector.H
│   │   │   │   └── tables/
│   │   │   │       ├── ExplSumTreeTable.H
│   │   │   │       ├── ImplSumTreeTable.H
│   │   │   │       ├── ImplTreeHelper.H
│   │   │   │       ├── StubBase.H
│   │   │   │       ├── ValueTable.H
│   │   │   │       └── WeightSumTable.H
│   │   │   ├── hashes.H
│   │   │   ├── k_clique/
│   │   │   │   ├── cliqueHash.H
│   │   │   │   ├── multiIter.H
│   │   │   │   ├── numSet.H
│   │   │   │   ├── numSet2.H
│   │   │   │   └── weighedClique.H
│   │   │   ├── misc/
│   │   │   │   ├── Bindata.H
│   │   │   │   ├── BinomialSampler.H
│   │   │   │   ├── CalQueue.H
│   │   │   │   ├── EventQueue.H
│   │   │   │   ├── FiboHeap.H
│   │   │   │   ├── KruskalTree.H
│   │   │   │   └── KruskalTree2.H
│   │   │   ├── nets/
│   │   │   │   ├── Dijkstrator.H
│   │   │   │   ├── DirNetExtras.H
│   │   │   │   ├── Distributions.H
│   │   │   │   ├── Models.H
│   │   │   │   ├── NetExtras.H
│   │   │   │   ├── NetExtras2.H
│   │   │   │   ├── OldModels.H
│   │   │   │   ├── Randomizer.H
│   │   │   │   ├── UnweightedDijk.H
│   │   │   │   └── models/
│   │   │   │       ├── BA.H
│   │   │   │       ├── BBV.H
│   │   │   │       ├── Boguna.H
│   │   │   │       ├── CommunityNet.H
│   │   │   │       ├── Davidsen.H
│   │   │   │       ├── ErdosRenyi.H
│   │   │   │       ├── HolmeKim.H
│   │   │   │       ├── Marsili.H
│   │   │   │       ├── SeedNet.H
│   │   │   │       ├── SimpleNets.H
│   │   │   │       ├── VDEB.H
│   │   │   │       └── Wong.H
│   │   │   └── packedqueue.H
│   │   ├── makefile
│   │   ├── nodeCommunities.cpp
│   │   ├── nodeCommunities.h
│   │   ├── testData/
│   │   │   ├── random_1000_005.edg
│   │   │   └── random_1000_005.edg_files/
│   │   │       ├── k=3/
│   │   │       │   └── communities
│   │   │       ├── k=4/
│   │   │       │   └── communities
│   │   │       └── k=5/
│   │   │           └── communities
│   │   ├── testScp.py
│   │   ├── weighedClique.cpp
│   │   └── weighedClique.h
│   ├── 2009-Community-Infomap-MapEquation/
│   │   ├── .gitignore
│   │   ├── .hgignore
│   │   ├── CHANGES.txt
│   │   ├── LICENSE_AGPLv3.txt
│   │   ├── Makefile
│   │   ├── README.txt
│   │   ├── ReadMe.md
│   │   ├── examples/
│   │   │   ├── R/
│   │   │   │   ├── Makefile
│   │   │   │   ├── example-igraph.R
│   │   │   │   ├── example-minimal.R
│   │   │   │   └── load-infomap.R
│   │   │   ├── cpp/
│   │   │   │   ├── Infomap-igraph-interface-library/
│   │   │   │   │   ├── Makefile
│   │   │   │   │   └── src/
│   │   │   │   │       ├── Infomap-igraph-interface.cpp
│   │   │   │   │       └── Infomap-igraph-interface.h
│   │   │   │   ├── igraph/
│   │   │   │   │   ├── Makefile
│   │   │   │   │   └── example-igraph.cpp
│   │   │   │   └── minimal/
│   │   │   │       ├── Makefile
│   │   │   │       ├── example.cpp
│   │   │   │       ├── mem-example.cpp
│   │   │   │       └── multi-example.cpp
│   │   │   ├── js/
│   │   │   │   ├── Infomap-worker.html
│   │   │   │   └── Makefile
│   │   │   └── python/
│   │   │       ├── Infomap.py
│   │   │       ├── Makefile
│   │   │       ├── example-file-io.py
│   │   │       └── example-networkx.py
│   │   ├── interfaces/
│   │   │   ├── js/
│   │   │   │   └── pre-worker-module.js
│   │   │   ├── python/
│   │   │   │   └── setup.py
│   │   │   └── swig/
│   │   │       ├── Config.i
│   │   │       ├── Date.i
│   │   │       ├── HierarchicalNetwork.i
│   │   │       ├── Infomap.i
│   │   │       └── Network.i
│   │   ├── ninetriangles.net
│   │   └── src/
│   │       ├── Infomap.cpp
│   │       ├── Infomap.h
│   │       ├── Informatter.cpp
│   │       ├── infomap/
│   │       │   ├── Edge.h
│   │       │   ├── FlowNetwork.cpp
│   │       │   ├── FlowNetwork.h
│   │       │   ├── InfomapBase.cpp
│   │       │   ├── InfomapBase.h
│   │       │   ├── InfomapContext.cpp
│   │       │   ├── InfomapContext.h
│   │       │   ├── InfomapGreedy.h
│   │       │   ├── InfomapGreedyCommon.h
│   │       │   ├── InfomapGreedySpecialized.h
│   │       │   ├── InfomapGreedyTypeSpecialized.h
│   │       │   ├── MemFlowNetwork.cpp
│   │       │   ├── MemFlowNetwork.h
│   │       │   ├── MemNetwork.cpp
│   │       │   ├── MemNetwork.h
│   │       │   ├── MemoryNetworkAdapter.cpp
│   │       │   ├── MemoryNetworkAdapter.h
│   │       │   ├── MultiplexNetwork.cpp
│   │       │   ├── MultiplexNetwork.h
│   │       │   ├── Network.cpp
│   │       │   ├── Network.h
│   │       │   ├── NetworkAdapter.cpp
│   │       │   ├── NetworkAdapter.h
│   │       │   ├── Node.cpp
│   │       │   ├── Node.h
│   │       │   ├── NodeFactory.h
│   │       │   ├── TreeData.cpp
│   │       │   ├── TreeData.h
│   │       │   ├── flowData.h
│   │       │   ├── flowData_traits.h
│   │       │   └── treeIterators.h
│   │       ├── io/
│   │       │   ├── BipartiteClusterReader.cpp
│   │       │   ├── BipartiteClusterReader.h
│   │       │   ├── ClusterReader.cpp
│   │       │   ├── ClusterReader.h
│   │       │   ├── Config.h
│   │       │   ├── HierarchicalNetwork.cpp
│   │       │   ├── HierarchicalNetwork.h
│   │       │   ├── ProgramInterface.cpp
│   │       │   ├── ProgramInterface.h
│   │       │   ├── SafeFile.h
│   │       │   ├── TreeDataWriter.cpp
│   │       │   ├── TreeDataWriter.h
│   │       │   ├── convert.h
│   │       │   ├── version.cpp
│   │       │   └── version.h
│   │       └── utils/
│   │           ├── Date.h
│   │           ├── FileURI.cpp
│   │           ├── FileURI.h
│   │           ├── Logger.cpp
│   │           ├── Logger.h
│   │           ├── MersenneTwister.h
│   │           ├── Stopwatch.h
│   │           ├── gap_iterator.h
│   │           ├── infomath.h
│   │           └── types.h
│   ├── 2014-Grappolo/
│   │   ├── Makefile
│   │   ├── README.txt
│   │   ├── RngStream.cpp
│   │   ├── RngStream.h
│   │   ├── binary/
│   │   │   └── convertFileToBinary
│   │   ├── buildNextPhase.cpp
│   │   ├── coloringDistanceOne.cpp
│   │   ├── convertFileToBinary.cpp
│   │   ├── convertFileToEdgeList.cpp
│   │   ├── convertSnapFileToBinary.cpp
│   │   ├── defs.h
│   │   ├── driverForColoringExperiments.cpp
│   │   ├── driverForGraphClustering.cpp
│   │   ├── driverForGraphClusteringBigMem.cpp
│   │   ├── driverForPartitioningWithMetis.cpp
│   │   ├── driverProcessPowerGridNetworks.cpp
│   │   ├── generateRGG.cpp
│   │   ├── generateRMAT.cpp
│   │   ├── input/
│   │   │   ├── karate.graph
│   │   │   └── west1505.gr
│   │   ├── louvainMultiPhaseRun.cpp
│   │   ├── parallelLouvainMethod.cpp
│   │   ├── parallelLouvainMethodEager.cpp
│   │   ├── parallelLouvainWithColoring.cpp
│   │   ├── parseInputFiles.cpp
│   │   ├── parseInputParameters.cpp
│   │   ├── scripts/
│   │   │   └── RunWithValgrind.sh
│   │   ├── utilityClusteringFunctions.cpp
│   │   ├── utilityClusteringFunctions.h
│   │   ├── utilityFunctions.cpp
│   │   ├── utilityGraphPartitioner.cpp
│   │   ├── utilityGraphPartitioner.h
│   │   ├── utilityParseInputParameters.hpp
│   │   ├── utilityStringTokenizer.hpp
│   │   ├── vertexFollowing.cpp
│   │   └── writeGraphDimacsFormat.cpp
│   └── ReadMe.md
├── Prensentation/
│   ├── ReadMe.md
│   ├── __init__.py
│   ├── algorithms/
│   │   ├── clique_percolation/
│   │   │   ├── community_result_visualization.py
│   │   │   ├── conradlee_clique_percolation.py
│   │   │   ├── example_edge_list.txt
│   │   │   └── problem_vis.py
│   │   ├── dynamics/
│   │   │   ├── async_lp_res0.txt
│   │   │   ├── example_edge_list.txt
│   │   │   ├── label_propagation.py
│   │   │   ├── label_propagation_yche.py
│   │   │   ├── others/
│   │   │   │   ├── aync_vs_sync.py
│   │   │   │   ├── copra_lpa.py
│   │   │   │   └── lpa.py
│   │   │   ├── prev/
│   │   │   │   ├── disjoint_community.txt
│   │   │   │   └── disjoint_visualization.py
│   │   │   ├── problem_vis.py
│   │   │   └── sync_lp_res0.txt
│   │   ├── link_partition/
│   │   │   ├── example_edge_list.txt
│   │   │   ├── graph_io_helper.py
│   │   │   ├── input/
│   │   │   │   └── get_karate_edge_list.py
│   │   │   ├── link_clustering.py
│   │   │   ├── link_clustering_algo.py
│   │   │   ├── result/
│   │   │   │   ├── example_edge_list_dendro.cid2edge.txt
│   │   │   │   ├── example_edge_list_dendro.linkage.txt
│   │   │   │   ├── example_edge_list_maxS0.250000_maxD0.777778.comm2edges.txt
│   │   │   │   ├── example_edge_list_maxS0.250000_maxD0.777778.comm2nodes.txt
│   │   │   │   ├── example_edge_list_maxS0.250000_maxD0.777778.edge2comm.txt
│   │   │   │   ├── example_edge_list_thr_D.txt
│   │   │   │   ├── karate_edge_list_maxS0.333333_maxD0.284758.comm2edges.txt
│   │   │   │   ├── karate_edge_list_maxS0.333333_maxD0.284758.comm2nodes.txt
│   │   │   │   ├── karate_edge_list_maxS0.333333_maxD0.284758.edge2comm.txt
│   │   │   │   └── karate_edge_list_thr_D.txt
│   │   │   └── visualization/
│   │   │       ├── dendrogram/
│   │   │       │   ├── dendrogram_vis.py
│   │   │       │   ├── radial_demo.py
│   │   │       │   ├── radial_grouper.py
│   │   │       │   ├── radial_support.py
│   │   │       │   └── radial_visualizer.py
│   │   │       └── link_clustering_visualization.py
│   │   ├── local_expansion/
│   │   │   ├── cis_algo.py
│   │   │   ├── cis_algo_output.txt
│   │   │   ├── cis_algo_res.txt
│   │   │   ├── cis_algo_visualization.py
│   │   │   ├── example_edge_list.txt
│   │   │   ├── karate_edge_list.txt
│   │   │   ├── problem_vis.py
│   │   │   ├── result_for_vis.txt
│   │   │   └── src/
│   │   │       ├── CMakeLists.txt
│   │   │       ├── cis_algo_output.txt
│   │   │       ├── cis_sequential_algorithm.cpp
│   │   │       ├── cis_sequential_algorithm.h
│   │   │       ├── demo_cis.cpp
│   │   │       └── util/
│   │   │           ├── ReadMe.md
│   │   │           ├── basic_io_helper.h
│   │   │           ├── graph_io_helper.cpp
│   │   │           ├── graph_io_helper.h
│   │   │           └── pretty_print.h
│   │   └── statistical_inference/
│   │       └── block_model_demo.py
│   ├── graph_serialization/
│   │   ├── __init__.py
│   │   ├── graph_formats.py
│   │   ├── input/
│   │   │   ├── __init__.py
│   │   │   └── example_graph.edgelist
│   │   ├── output_json/
│   │   │   ├── adjacency.json
│   │   │   └── node_link.json
│   │   ├── output_other/
│   │   │   ├── example_graph.gml
│   │   │   └── example_graph.pajek
│   │   ├── output_raw/
│   │   │   ├── __init__.py
│   │   │   ├── example_graph.adjlist
│   │   │   ├── example_graph.edgelist
│   │   │   └── example_graph.multiline_adjlist
│   │   ├── output_serialization/
│   │   │   ├── __init__.py
│   │   │   ├── example_graph.graph6
│   │   │   ├── example_graph.pickle
│   │   │   └── example_graph.yaml
│   │   └── output_xml/
│   │       ├── __init__.py
│   │       ├── example_graph.gexf
│   │       └── example_graph.graphml
│   ├── graph_tool_usage/
│   │   ├── intro_graph_tool/
│   │   │   ├── .gitignore
│   │   │   ├── begining.py
│   │   │   ├── draw_pie_graph.py
│   │   │   ├── graph_creation_basics.py
│   │   │   ├── graph_notations.md
│   │   │   └── nx2gt.py
│   │   └── play.py
│   ├── jupter_playground/
│   │   ├── .gitignore
│   │   ├── .ipynb_checkpoints/
│   │   │   ├── graph_draw_study0-checkpoint.ipynb
│   │   │   └── pie_graph-checkpoint.ipynb
│   │   ├── graph_draw_study0.ipynb
│   │   └── pie_graph.ipynb
│   ├── metrics/
│   │   ├── ReadMe.md
│   │   ├── __init__.py
│   │   ├── demo_graph.csv
│   │   ├── link_belong_modularity.py
│   │   ├── omega_idx.py
│   │   ├── overlap_nmi.py
│   │   ├── rand_idx_example.py
│   │   └── util.py
│   ├── problem_definition/
│   │   ├── demo_cis_output_result.txt
│   │   ├── demo_input_graph.txt
│   │   └── problem_vis.py
│   ├── social_network/
│   │   ├── disjoint_community_detection.py
│   │   ├── others/
│   │   │   └── visualization_different_colors.py
│   │   ├── visualization_karate.py
│   │   └── zachary_karate_club/
│   │       ├── __init__.py
│   │       ├── gml_formatter.py
│   │       ├── gml_parser.py
│   │       ├── karate.gml
│   │       ├── karate.txt
│   │       └── karate_new.gml
│   └── test.gml
├── README.md
├── Scripts/
│   └── dataset_aggragation.py
├── SubModules/
│   └── ReadMe.md
└── Survey/
    ├── Community-Detection-New-Findings.md
    ├── Community-Detection-Reading-List.md
    ├── Community-Detection-Survey.md
    ├── Community-Search-Survey.md
    ├── Conference-Papers-About-Graph/
    │   └── VLDB.md
    ├── Overlapping-Community-Detection-Codes.md
    ├── ReadMe.md
    └── Social-Media-Recommendation.md

================================================
FILE CONTENTS
================================================

================================================
FILE: .gitignore
================================================
# jetbrains config
.idea
cmake-build-debug
*.iml

*.log
*.aux
*.gz

#maven build
target

# src_cpp_matlab-python files
*.pyc

# output data
output*.txt

# matlab
*.mex*

# datasets
facebook100.zip


================================================
FILE: .gitmodules
================================================
[submodule "SubModules/igraph"]
	path = SubModules/igraph
	url = git@github.com:igraph/igraph.git
[submodule "SubModules/Graclus"]
	path = SubModules/Graclus
	url = git@github.com:GraphProcessor/Graclus.git
[submodule "SubModules/lcelib"]
	path = SubModules/lcelib
	url = git@github.com:CxAalto/lcelib.git
[submodule "SubModules/matlab-bgl"]
	path = SubModules/matlab-bgl
	url = git@github.com:dgleich/matlab-bgl.git


================================================
FILE: Algorithms/2008-CliquePercolation/ReadMe.md
================================================
# Clique Percolation
## Description

The sequential clique percolation algorithm is method for detecting clique percolation communities. 
It is an alternative to CFinder: instead of finding maximal cliques in a graph and producing 
communities of all the possible clique sizes, 
the SCP algorithm finds all the cliques of single size and 
produces the community structure for all the possible thresholds. 
The SCP algorithm should work well even for large sparse networks, 
but might have trouble for dense networks and cliques of large size.

## Links
- [python implementation elaboration](http://www.lce.hut.fi/~mtkivela/kclique.html)
- [c++ implementation elaboration](http://www.lce.hut.fi/research/mm/complex/software/scp_0.1.tar.gz)
- [authors' paper, A sequential algorithm for fast clique percolation](https://arxiv.org/abs/0805.1449)

================================================
FILE: Algorithms/2008-CliquePercolation/algorithm_example.py
================================================
import networkx as nx

from conradlee_clique_percolation import *

if __name__ == '__main__':
    with open('example_edge_list.txt', 'r') as ifs:
        edge_list = map(lambda ele: ele.strip().split(), ifs.readlines())
    data_graph = nx.Graph(edge_list)
    comm_list = list(get_percolated_cliques(data_graph, 3))
    print comm_list


================================================
FILE: Algorithms/2008-CliquePercolation/conradlee_clique_percolation.py
================================================
import networkx as nx
from collections import defaultdict


def get_percolated_cliques(G, k):
    percolation_graph = nx.Graph()
    cliques = [frozenset(c) for c in nx.find_cliques(G) if len(c) >= k]
    percolation_graph.add_nodes_from(cliques)

    # First index which nodes are in which cliques
    membership_dict = defaultdict(list)
    for clique in cliques:
        for node in clique:
            membership_dict[node].append(clique)

    def get_adjacent_cliques(clique, membership_dict):
        adjacent_cliques = set()
        for n in clique:
            for adj_clique in membership_dict[n]:
                if clique != adj_clique:
                    adjacent_cliques.add(adj_clique)
        return adjacent_cliques

    # For each clique, see which adjacent cliques percolate
    for clique in cliques:
        for adj_clique in get_adjacent_cliques(clique, membership_dict):
            if len(clique.intersection(adj_clique)) >= (k - 1):
                percolation_graph.add_edge(clique, adj_clique)

    print 'percolation graph nodes:', percolation_graph.nodes()
    print 'percolation graph edges:', percolation_graph.edges()

    # Connected components of clique graph with perc edges
    # are the percolated cliques
    for component in nx.connected_components(percolation_graph):
        yield (frozenset.union(*component))


================================================
FILE: Algorithms/2008-CliquePercolation/example_edge_list.txt
================================================
1 2
1 3
2 3
3 4
4 5
4 7
5 7
5 6
6 7

================================================
FILE: Algorithms/2008-CliquePercolation/src_cpp/CMakeLists.txt
================================================
cmake_minimum_required(VERSION 2.8)
project(2008-clique-percolation)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++14 -O3 -g")

find_package(Boost REQUIRED COMPONENTS)
include_directories(${Boost_INCLUDE_DIRS})
include_directories("../../../SubModules/")

FIND_PACKAGE(OpenMP REQUIRED)
if (OPENMP_FOUND)
    message("OPENMP FOUND")
    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
    set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
endif ()

set(SourceFiles k_clique.cpp dendrogram.cpp nodeCommunities.cpp weighedClique.cpp cliqueHash.cpp communityTracker.cpp kruskal.cpp)
add_executable(k_clique ${SourceFiles})

================================================
FILE: Algorithms/2008-CliquePercolation/src_cpp/ReadMe.md
================================================
## Issues

all fixed

================================================
FILE: Algorithms/2008-CliquePercolation/src_cpp/cliqueHash.cpp
================================================
/*
scp, The sequential clique percolation algorithm.
Copyright (C) 2011  Aalto University

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*/

#include "cliqueHash.h"


size_t cliqueHash::hash_function(const clique key)
{
    const size_t keySize = key.size();


    // std::cerr << "clique size for hash_function is " << key.size() << "\n";
    size_t hash_key;
    size_t newInd[keySize];
    for (size_t i = 0; i < keySize; i++)
        newInd[i] = key.at(keySize-1-i) & b;


    //     for (size_t i = 1; i < keySize; i++) new_ind[i] = A*key.at(i);
    hash_key = newInd[0] << hash_bits - offSet; // move to the left
    size_t move;
    for (size_t i = 1; i < keySize; i++)
    {
        move = hash_bits - (i+1)*offSet;
        newInd[i] = newInd[i] << move;
        hash_key = hash_key | newInd[i] ;      // take
    }


    hash_key = hash_key | ( key.at(keySize-2) & c );

    // now take only the last hash_bits bits

    //     hash_key = hash_key & a;
    //     std::cerr << "hash key is: " << hash_key << "\n";

    /*
    hash_key = key.at(0)+1;
    for (size_t i = 1; i < key.size(); i++) hash_key *= key.at(i);
    hash_key = hash_key%size;
    //     hash_key = (key.at(0)+1)*key.at(1)*key.at(2)*key.at(3)%size;
    // hash_key = ( key.at(0) * key.at(3) + key.at(1) * key.at(2) )%size;
    */
    if (hash_key >= size || hash_key < 0 )
    {
        std::cerr << "hash function did not work!\n";
        // std::cerr << "nodes were: " << key.at(0) << " " << key.at(1) << " " << key.at(2) << " " << key.at(3) << "\n";
        std::cerr << "hash key was: " << hash_key << "\n";
        std::cerr << "hash key size was: " << keySize << "\n";	
    }


    return hash_key;
}


cliqueHash::cliqueHash(const size_t hashSize, const size_t t, const size_t keySize)
{
  hashTable.resize(hashSize); // reserve memory
    keyCount = 0;
    size = hashSize;
    hash_bits = t;
    offSet = hash_bits/keySize; // this is how much we can move bits for each index
    a = 1;
    a = a << hash_bits;
    a = a - 1;    // beginning is zeros, only hash_bits lasts bits are one
    b = 1;
    b = b << offSet;
    b = b-1;
    c = 1;
    c = c << ( hash_bits - keySize*offSet );
    c = c - 1;
}


cliqueHash::cliqueHash()
{
    cliqueHash(0, 1, 1);
}


bool cliqueHash::contains(const clique & key)
{
    // std::cerr << "entering contains-function\n";
    size_t hash_key = hash_function(key);
    //     std::cerr << "hash-key is:" << hash_key << "\n";

    bool key_found = false;
    for (cliqueIndexSet::iterator i = hashTable.at(hash_key).begin(); !key_found && i != hashTable.at(hash_key).end(); i++)
    {
        if ( (*i).first == key ) key_found = true;
    }
    //    std::cerr << "leaving contains-function\n";
    return key_found;
}


int cliqueHash::getValue(const clique & key)
{
    size_t hash_key = hash_function(key);

    int value = -1;
    bool key_found = false;
    for (cliqueIndexSet::iterator i = hashTable.at(hash_key).begin(); !key_found && i != hashTable.at(hash_key).end(); i++)
    {
        if ( (*i).first == key )
        {
            value = (*i).second;
            key_found = true;
        }
    }
    return value;
}


void cliqueHash::put(const clique & key, const size_t value)
{
    size_t hash_key = hash_function(key);

    if ( contains(key) )
    {
        bool key_found = false;
        for (cliqueIndexSet::iterator i = hashTable.at(hash_key).begin(); !key_found && i != hashTable.at(hash_key).end(); i++)
        {
            if ( (*i).first == key )
            {
                (*i).second = value;
                key_found = true;
            }
        }
    }
    else
    {
        std::pair<clique,size_t> cliqueValPair(key,value);
        hashTable.at(hash_key).push_back( cliqueValPair );
        keyCount++;
    }
}


std::pair<clique,size_t> cliqueHash::begin()
{
    curr_hash_key = 0;
    while ( curr_hash_key < size && hashTable.at(curr_hash_key).size() == 0  )
    {
        curr_hash_key++;
    }
    if ( curr_hash_key < size )         // now we have found the first slot that is not empty
    {
        iter = hashTable.at(curr_hash_key).begin();
        return *iter;
    }
    else
    {
        clique tmpClique;
        currPair = std::make_pair( tmpClique, 0);
        return currPair;
    }
}

std::pair<clique,size_t> cliqueHash::next()
{
    iter++;
    if ( iter == hashTable.at(curr_hash_key).end() )    // move to the next non-empty slot
    {
        do
        {
            curr_hash_key++;
        }
        while ( curr_hash_key < size && hashTable.at(curr_hash_key).size() == 0  );
        if ( curr_hash_key < size )         // now we have found the first slot that is not empty
        {
            iter = hashTable.at(curr_hash_key).begin();
            return *iter;
        }
        else
        {
            clique tmpClique;
            currPair = std::make_pair(tmpClique, 0);
            return currPair;
        }
    }
    else
    {
        return *iter;
    }
}


bool cliqueHash::finished()
{

    if ( curr_hash_key == size ) return true;
    else if ( getKeyCount() == 0 ) return true;
    else return false;

}


================================================
FILE: Algorithms/2008-CliquePercolation/src_cpp/cliqueHash.h
================================================
/*
scp, The sequential clique percolation algorithm.
Copyright (C) 2011  Aalto University

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*/

#ifndef CLIQUE_HASH
#define CLIQUE_HASH

#include <list>
#include "weighedClique.h"


class cliqueHash
{

    // typedef std::list<std::pair<clique,size_t> > cliqueIndexSet;
    typedef std::list<std::pair<clique,size_t> > cliqueIndexSet;

private:

    size_t size;
    std::vector<cliqueIndexSet> hashTable;
    size_t hash_bits;
    size_t a, b, c, offSet;

    size_t hash_function(const clique key);

    cliqueIndexSet::iterator iter;
    std::pair<clique,size_t> currPair;
    size_t curr_hash_key;
    size_t keyCount;

public:

    cliqueHash(const size_t hashSize, const size_t t, const size_t keySize);


    cliqueHash();


    bool contains(const clique & key);


    int getValue(const clique & key);


    void put(const clique & key, const size_t value);


    std::pair<clique,size_t> begin();


    std::pair<clique,size_t> next();


    bool finished();


    size_t getKeyCount()
    {
        return keyCount;
    }

};

#endif


================================================
FILE: Algorithms/2008-CliquePercolation/src_cpp/communityTracker.cpp
================================================
/*
scp, The sequential clique percolation algorithm.
Copyright (C) 2011  Aalto University

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*/

#include "communityTracker.h"

CommunityTracker::CommunityTracker(cliqueHash & hash, KruskalTree & tree, nodeCommunities & nodeComs, Dendrogram & dendrogram, NetType & net) : hash(hash), tree(tree), nodeComs(nodeComs), dendrogram(dendrogram), net(net) {}

void CommunityTracker::addClique(weighedClique & kclique)
{
    // the index of the first (k-1)-clique found, others (k-1)-cliques will be connected to that one
    // may change during merging of (k-1)-communities, but always tells the community where to add other (k-1)-cliques
    int firstCliqueIndex;

    // true if this k-clique forms a new community, false otherwise, e.g. when community size changes
    bool formsNewCommunity = true;

    // the starting size of the community, used to track if the size of the community changes
    size_t initialSize;

    // tells if the initialSize has been initialized
    // this prevents us from changing the initialSize after initialization
    bool sizeInitialized = false;

    for (size_t i = 0; i < kclique.size(); i++)
    {
        // clear the tempVector and push all nodes to it except the i-th node
        tempVector.clear();
        for (size_t j = 0; j < kclique.size(); j++)
            if (i != j)
                tempVector.push_back(kclique.at(j));

        // replace the nodes in the k1clique to thos of the tempVector
        k1clique.replaceNodes(tempVector, net);

        // find the k1clique from the cliqueHash and store it's index
        // this is smaller than 0 if the clique is not in the hash, otherwise this is the cliques index
        int currentCliqueIndex = hash.getValue(k1clique);

        if (!i) // first (k-1)-clique from this k-clique
        {
            if (currentCliqueIndex >= 0) // found before
            {
                // we store the index of the first (k-1)-clique so others can be connected to it
                firstCliqueIndex = tree.findRoot(currentCliqueIndex);

                // belongs to an existing community, so no new community can form
                formsNewCommunity = false;

                // get the initial size of the excisting community from nodeComs
                initialSize = nodeComs.getSize(firstCliqueIndex);

                // mark that the initialSize has been initialized
                sizeInitialized = true;
            }
            else // not found before
            {
                // add this (k-1)-clique to the kruskal tree and store its index
                firstCliqueIndex = tree.add();

                // use the index to put the clique into cliqueHash and nodeComs
                hash.put(k1clique, firstCliqueIndex);
                nodeComs.addClique(firstCliqueIndex, k1clique);
            }
        }
        else // not the first (k-1)-clique from this k-clique
        {
            if (currentCliqueIndex >= 0) // found before
            {
                // check if the (k-1)-cliques are already in the same community
                // if they're not, merge the communities
                if (!tree.inSameSet(currentCliqueIndex, firstCliqueIndex))
                {
                    // if the size is not initialized, initialize it
                    if (!sizeInitialized)
                    {
                        // we use currentCliqueIndex here because if the sizeInitialized is not true, the firstCliqueIndex
                        // does not point to any existing community and so the community pointed by currentCliqueIndex
                        // becomes the initial community
                        initialSize = nodeComs.getSize(tree.findRoot(currentCliqueIndex));
                        sizeInitialized = true;
                    }

                    // connect the communities in nodeComs
                    nodeComs.connect(tree.findRoot(firstCliqueIndex), tree.findRoot(currentCliqueIndex));

                    // if a new community does not form, add the indexes to comsToMerge
                    if (!formsNewCommunity)
                    {
                        comsToMerge.insert(tree.findRoot(currentCliqueIndex));
                        comsToMerge.insert(tree.findRoot(firstCliqueIndex));
                    }

                    // connect the communities in the kruskal tree
                    tree.connect(firstCliqueIndex, currentCliqueIndex);

                    // update the firstCliqueIndex so that it points to the root of the kruskal tree
                    firstCliqueIndex = tree.findRoot(currentCliqueIndex);

                    // this k-clique belongs to an existing community, so no new community can form
                    formsNewCommunity = false;
                }
            }
            else // not found before
            {
                // add the new (k-1)-clique to the kruskal tree and store the index
                size_t newCliqueIndex = tree.add();

                // store it to the cliqueHash
                hash.put(k1clique, newCliqueIndex);

                // connect it to the first (k-1)-clique in the kruskal tree and in nodeComs
                tree.connect(newCliqueIndex, firstCliqueIndex);
                nodeComs.addClique(tree.findRoot(firstCliqueIndex), k1clique);
            }
        }
    }

    // new community has formed, so we add a new bottom to the dendrogram
    if (formsNewCommunity)
        dendrogram.addNewBottom(kclique.getWeight(), kclique.size(), tree.findRoot(firstCliqueIndex));

    // there are communities merging, so merge these to make a new dendrogram node
    if (comsToMerge.size())
        dendrogram.addConnection(kclique.getWeight(), nodeComs.getSize(tree.findRoot(firstCliqueIndex)), comsToMerge, tree.findRoot(firstCliqueIndex));

    // if no communities are merging, but the initialSize has been initialized and has changed after initialization
    // then add a new size change into the dendrogram
    else if (!comsToMerge.size() && nodeComs.getSize(tree.findRoot(firstCliqueIndex)) != initialSize && sizeInitialized)
        dendrogram.changeSize(kclique.getWeight(), nodeComs.getSize(tree.findRoot(firstCliqueIndex)), tree.findRoot(firstCliqueIndex));

    comsToMerge.clear();
}

void CommunityTracker::print(std::ostream & file) const
{
    file << "tree:" << std::endl;
    tree.printTree(file);
    file << std::endl;
    file << "nodeComs:" << std::endl;
    nodeComs.printCommunities(file);
    file << "-------------------" << std::endl;
}


================================================
FILE: Algorithms/2008-CliquePercolation/src_cpp/communityTracker.h
================================================
/*
scp, The sequential clique percolation algorithm.
Copyright (C) 2011  Aalto University

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*/

#ifndef COMMUNITYTRACKER_H
#define COMMUNITYTRACKER_H

#include <iostream>
#include <vector>
#include <utility>

#include "lcelib/Nets.H"
#include "cliqueHash.h"
#include "nodeCommunities.h"
#include "kruskal.h"
#include "dendrogram.h"

class CommunityTracker
{
public:

    CommunityTracker(cliqueHash & hash, KruskalTree & tree, nodeCommunities & nodeComs, Dendrogram & dendrogram, NetType & net);

    void addClique(weighedClique & kclique);

    void print(std::ostream & file) const;

private:

    cliqueHash & hash;
    KruskalTree & tree;
    nodeCommunities & nodeComs;
    Dendrogram & dendrogram;
    NetType & net;

    std::vector<size_t> tempVector; // used when creating (k-1)-cliques, this way we avoid creating a new vector object for every k-clique
    weighedClique k1clique;

    //std::vector<std::pair<size_t, size_t> > mergingCommunities; // tells which communities merge as a result from adding a clique
    std::set<size_t> comsToMerge;

};

#endif


================================================
FILE: Algorithms/2008-CliquePercolation/src_cpp/dendrogram.cpp
================================================
/*
scp, The sequential clique percolation algorithm.
Copyright (C) 2011  Aalto University

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*/

#include "dendrogram.h"

void Dendrogram::addNewBottom(const float weight, const size_t size, const size_t comIndex)
{
    DendrogramNode *newNode = new DendrogramNode(weight, size, comIndex);
    comIndexMap[comIndex] = newNode;
    bottom.push_back(newNode);
    nodes.push_back(newNode);
}

void Dendrogram::changeSize(const float weight, const size_t size, const size_t comIndex)
{
    DendrogramNode *newNode = new DendrogramNode(weight, size, comIndex);
    nodes.push_back(newNode);
    newNode->addChild(comIndexMap[comIndex]); // TESTI
    comIndexMap[comIndex]->parent = newNode;
    comIndexMap[comIndex] = newNode;
}

void Dendrogram::addConnection(const float weight, const size_t size, const std::set<size_t> & comsToMerge, const size_t newComIndex)
{
    DendrogramNode *newNode = new DendrogramNode(weight, size, newComIndex);
    nodes.push_back(newNode);
    for (std::set<size_t>::iterator i = comsToMerge.begin(); i != comsToMerge.end(); i++)
    {
        comIndexMap[*i]->parent = newNode;
        newNode->addChild(comIndexMap[*i]); // TESTI
    }
}

void Dendrogram::printFromNode(const size_t comIndex, std::ostream & file)
{
    DendrogramNode *node = comIndexMap[comIndex];
    while (node)
    {
        file << node->weight << " " << node->size << " " << node->comIndex << std::endl;
        node = node->parent;
    }
}

void Dendrogram::printTree(std::ostream & file)
{
    std::sort(nodes.begin(), nodes.end(), compareNodes);
    for (std::vector<DendrogramNode*>::iterator i = nodes.begin(); i != nodes.end(); i++)
    {
        file << (*i)->weight << "\t" << (*i)->comIndex << "\t" << (*i)->size;
        for (std::set<DendrogramNode*>::iterator j = (*i)->children.begin(); j != (*i)->children.end(); j++) // TESTI
            file << "\t|\t" << (*j)->comIndex << "\t" << (*j)->size; // TESTI
        file << std::endl;
    }
}

Dendrogram::~Dendrogram()
{
    for (std::vector<DendrogramNode*>::iterator i = nodes.begin(); i != nodes.end(); i++)
        delete *i;
}


================================================
FILE: Algorithms/2008-CliquePercolation/src_cpp/dendrogram.h
================================================
/*
scp, The sequential clique percolation algorithm.
Copyright (C) 2011  Aalto University

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*/

#ifndef DENDRO_TREE_H
#define DENDRO_TREE_H

#include <cstddef>
#include <vector>
#include <map>
#include <iostream>
#include <set>
#include <algorithm>

class Dendrogram
{
public:
    Dendrogram() {}

    void addNewBottom(const float weight, const size_t size, const size_t comIndex);

    void changeSize(const float weight, const size_t size, const size_t comIndex);

    void addConnection(const float weight, const size_t size, const std::set<size_t> & comsToMerge, const size_t newComIndex);

    void printFromNode(const size_t comIndex, std::ostream & file);

    void printTree(std::ostream & file);

    ~Dendrogram();

private:

    class DendrogramNode
    {
        friend class Dendrogram;

        public:
            DendrogramNode(float weight, size_t size, size_t comIndex) : weight(weight), size(size), comIndex(comIndex), parent(NULL) {}

            void addChild(DendrogramNode * child) { children.insert(child); } // TESTI

        private:
            float weight;
            size_t size;
            size_t comIndex;
            DendrogramNode * parent;

            std::set<DendrogramNode*> children; // TESTI
    };

    static bool compareNodes(DendrogramNode * first, DendrogramNode * second) { return first->weight > second->weight; }

    // the nodes which no other node points to
    std::vector<DendrogramNode*> bottom;

    // all nodes in the dendrogram, used for freeing the memory
    std::vector<DendrogramNode*> nodes;

    // map that holds the mapping from community indexes
    std::map<size_t, DendrogramNode*> comIndexMap;
};

#endif


================================================
FILE: Algorithms/2008-CliquePercolation/src_cpp/doc/License.txt
================================================
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================================================
FILE: Algorithms/2008-CliquePercolation/src_cpp/doc/makefile
================================================
all:
	g++ k_clique.cpp dendrogram.cpp nodeCommunities.cpp weighedClique.cpp cliqueHash.cpp communityTracker.cpp kruskal.cpp -o k_clique -O3

================================================
FILE: Algorithms/2008-CliquePercolation/src_cpp/k_clique.cpp
================================================
/*
scp, The sequential clique percolation algorithm.
Copyright (C) 2011  Aalto University

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*/

/*
A C++ implementation of the sequential clique percolation (SCP) algorithm. This version is seriously cripled and only unweighted clique percolation without 
thresholding is allowed. However, all the code to include further functionality is already included in the source code.

If you use this code to produce results for a publication, please cite:
A sequential algorithm for fast clique percolation, J.M. Kumpula, M. Kivelä, K. Kaski,and J. Saramäki, Phys. Rev. E 79, 026109 (2008)

The article contains detailed introduction to the SCP.

Authors: Eetu Latja, Mikko Kivelä and Jussi Kumpula.
*/


#include "k_clique.h"
#include "dendrogram.h"

#define HELPSTR "Usage: ./k_clique [inputfile] [options]\n\
The input file must be in the edge list format, where at each \
line there three columns: node1Index, node2Index and edge weight separated \
by a white space. Node indices must be integers from 0 to n-1, where n is the \
number of nodes in the network. Edges are undirected and there can only be \
at most one edge between two nodes in the edge file.\n\
Options:\n\
\t-o=[outputfile] : Write output to a specified file.\n\
\t-k=[clique size] : The size of the clique.\n\
\t-v : Verbose mode.\n "

//\t-w : Use weighted clique percolation.\n\
//\t-f=[weightfunction] : Specifies a weight function when using weighted clique percolation.\n "

struct Link{
  size_t source;
  size_t dest;
  float weight;
  Link(size_t source=0,size_t dest=0, float weight=0.0) : source(source), dest(dest), weight(weight) {}

};


// finds out the optimal size for the hash
size_t determineHashSize(const size_t numElements, const size_t k)
{
    size_t size_limit = 26;
    size_t t;
    if ( k < size_limit)
        t = k;
    else
        t = size_limit;
    while ( t < 10 ) t += k;
    while ( 1 << t < numElements && t <  size_limit )
    {
        t += k;
    }
    return t; // this many bits are needed
}

// determine the network size and number of links
// same link must not be twice in the network!
bool getNetSizeAndLinkNumbers(char * fileName, size_t & netSize, size_t & numLinks, std::list<Link> & linkList)
{

    std::ifstream myfile(fileName);
    std::string line;
    size_t source, dest;
    float weight;
    netSize=0;
    numLinks=0;

    if (myfile.is_open())
    {
        while (!myfile.eof())
        {
            getline(myfile, line);   // Read a line from input into a string.
            if (!line.empty())
            {
                std::istringstream is(line);  // Extract data using a stringstream.
		if ((is >> source) && (is >> dest) && (is >> weight));
		else {
		  std::cerr<<"Error reading line "<<numLinks << std::endl;
		  return false;}		

		linkList.push_back(Link(source,dest,weight));

                if (source > netSize)
                    netSize = source; //the size of the net is determined by the largest node index
                if (dest > netSize)
                    netSize = dest;
                ++numLinks;
            }
        }
        myfile.close();
    }
    ++netSize; // net size is one more than the largest index
    //std::cout << "ok\n";
    return true;
}

/*
  reads one line from the input file. The line contains the source and target nodes and weight.
*/
bool readLine(std::ifstream & myfile, size_t & source,  size_t & dest, float & weight)
{
    bool readlineok = false;
    if ( myfile.is_open())
    {

        std::string line;
        getline(myfile, line);   // Read a line from input into a string.
        if (!line.empty())
        {
            std::istringstream is(line);  // Extract data using a stringstream.
            is >> source;
            is >> dest;
            is >> weight;
            readlineok = true;
        }
    }
    else
    {
        std::cerr << "Error opening the network file!\n";
    }
    return readlineok;
}

void kCliquesFind(std::vector<weighedClique> & cliqueVector, NetType & net, size_t source, size_t dest, const float weight, const size_t k, const size_t weightFunction)
{

  // If k=2 cliques are links and the only new clique formed is the added link itself.
  if (k==2){
    std::vector<size_t> tempVector(2);
    tempVector[0] = source; tempVector[1] = dest;
    weighedClique tempClique(tempVector, net, weightFunction);
    cliqueVector.push_back(tempClique);
    net[source][dest] = weight; // add link
    return;
  }
  
  // find out degrees of source and dest
  size_t k_s, k_d;
  k_s = net(source).size(); 
  k_d = net(dest).size();
  
  // If degree of 'source' is larger than degree of 'dest', swap these. This makes it faster because we only iterate through nodes which are neighbors of 'source'.
  if (k_s > k_d)
    {
      size_t temp = source;
      source = dest;
      dest = temp;
    }
  

  if ( k_s  > k - 3 && k_d > k - 3)   // if this is not true, a new k-clique can not form
    {
      if (k == 3)
        {
	  std::vector<size_t> tempVector(3);
            tempVector[0] = source;
            tempVector[1] = dest;
            for ( NetType::const_edge_iterator i=net(source).begin(); !i.finished(); ++i)
	      {
                if ( net(*i)[dest] > 0 )
		  {
                    tempVector[2] = *i;
                    weighedClique tempClique(tempVector, net, weightFunction);
                    cliqueVector.push_back(tempClique);		    
		  }
	      }	    
        }
      else if (k == 4)
        {
	  std::vector<size_t> tempVector(4);
	  tempVector[0] = source;
	  tempVector[1] = dest;
	  for ( NetType::const_edge_iterator i=net(source).begin(); !i.finished(); ++i)
            {
	      NetType::const_edge_iterator j=i;
	      for ( ++j; !j.finished(); ++j) // makes j to point to the next iterable after i
                {
		  if ( net(*i)[dest] > 0 && net(*j)[dest] > 0 && net(*i)[*j] > 0)
                    {
		      tempVector[2] = *i;
		      tempVector[3] = *j;
		      weighedClique tempClique(tempVector, net, weightFunction);
		      cliqueVector.push_back(tempClique);
                    }
                }
            }	  
        }
      else // k>4
        {
	  nodeSet commonNeighborhood;
	  for ( NetType::const_edge_iterator i=net(source).begin(); !i.finished(); ++i)
            {
	      if ( net(*i)[dest] > 0 )
		commonNeighborhood.put(*i);
            }
	  
	  NetType subNet(commonNeighborhood.size());
	  
	  std::vector<size_t> sourceAndDest(2);
	  sourceAndDest[0] = source;
	  sourceAndDest[1] = dest;
	  
	  std::vector<weighedClique> k2cliqueVector;
	  for (nodeSet::iterator i = commonNeighborhood.begin(); !i.finished(); ++i)
            {
	      nodeSet::iterator j = i;
	      for ( ++j; !j.finished(); ++j) // makes j to point to the next iterable after i
                {
		  if (net(*i)[*j] > 0)
                    {
		      kCliquesFind(k2cliqueVector, subNet, *i, *j, net(*i)[*j], k - 2, 0);
		      for (std::vector<weighedClique>::iterator vectorIter = k2cliqueVector.begin(); vectorIter != k2cliqueVector.end(); vectorIter++)
                        {
			  weighedClique current = *vectorIter;
			  current.addNodes(sourceAndDest, net);
			  cliqueVector.push_back(current);
                        }
                    }
                }
            }	  
        }
    }

  //Finally add the new link to the network
  net[source][dest] = weight; 
}

void kCommunitiesFind(std::vector<weighedClique> & cliqueVector, KruskalTree & communities, cliqueHash & k1cliquesHash, NetType & net, const size_t k)
{
    std::vector<size_t> tempVector;
    weighedClique k1clique;
    for (std::vector<weighedClique>::iterator i = cliqueVector.begin(); i != cliqueVector.end(); ++i)
    {
        size_t rootIndex;
        for (size_t j = 0; j < k; j++)
        {
            tempVector.clear();
            for (size_t l = 0; l < k; l++)
                if (l != j)
                    tempVector.push_back(i->at(l));
            k1clique.replaceNodes(tempVector, net);

            // check if this (k-1)-clique is founded before
            int index = k1cliquesHash.getValue(k1clique);
            if (!j) // first (k-1)-clique from this k-clique
            {
                if (index >= 0) // found before
                {
                    rootIndex = index;
                }
                else
                {
                    rootIndex = communities.add();
                    k1cliquesHash.put(k1clique, rootIndex);
                }
            }
            else
            {
                if (index >= 0) // found before
                {
                    communities.connect(rootIndex, index);
                }
                else
                {
                    size_t newIndex = communities.add();
                    k1cliquesHash.put(k1clique, newIndex);
                    communities.connect(newIndex, rootIndex);
                }
            }
        }
    }
}

void outputCommunityStructure(KruskalTree & communities, cliqueHash & k1cliquesHash, std::ofstream & file)
{
    // Go through each community and put nodes from each community into a nodeSet
    std::map<size_t, nodeSet> realCommunities;
    for (std::pair<clique,size_t> currentPair = k1cliquesHash.begin(); !k1cliquesHash.finished(); currentPair = k1cliquesHash.next())
    {
        size_t community = communities.findRoot(currentPair.second);
        for (size_t i = 0; i < currentPair.first.size(); i++)
        {
            realCommunities[community].put(currentPair.first.at(i));
        }
    }

    if (file.is_open())
    {
        int communityIndex = 1;
        for (std::map<size_t, nodeSet>::iterator i = realCommunities.begin(); i != realCommunities.end(); i++)
        {
	  //file << communityIndex << ": "; // Uncomment if you want to enumerate the communities
            for (nodeSet::iterator j = i->second.begin(); !j.finished(); ++j)
                file << *j << " ";
            file << "\n";
            communityIndex++;
        }
    }
    file << "\n";
}


void unweightedSCP(NetType & net, std::list<Link> & linkList, const size_t numberOfLinks, const size_t k, std::string outputFile,bool verbose)
{
    size_t source, dest;
    float weight;
    std::vector<weighedClique> cliqueVector;
    
    //Determine the number of k-1 cliques
    size_t numberOfSmallCliques=0;
    NetType *tempNetPointer= new NetType(net.size());
    NetType &tempNet=*tempNetPointer;
    for (std::list<Link>::iterator linkIterator=linkList.begin() ; linkIterator != linkList.end(); linkIterator++ )
    {
      source=(*linkIterator).source; dest=(*linkIterator).dest;weight=(*linkIterator).weight;
      cliqueVector.clear();
      kCliquesFind(cliqueVector, tempNet, source, dest, weight, k-1, 0);
      numberOfSmallCliques+=cliqueVector.size();
    }
    delete tempNetPointer;

    //Use the number of k-1 cliques to determine the hash size
    size_t hash_bits = determineHashSize(numberOfSmallCliques, k - 1);
    size_t numSlots=1; numSlots = numSlots << hash_bits; // Number of slots is 2**hash_bits
    if (verbose){
      std::cout<< "Number of "<< k-1 <<"-cliques: " <<numberOfSmallCliques<<std::endl;
      std::cout<<"Number of bits in the hash table: "<<hash_bits<<std::endl;
      std::cout<<"Number of slots in the hash table: "<<numSlots<<std::endl;
    }
    cliqueHash k1cliquesHash(numSlots, hash_bits, k - 1);        

    KruskalTree communities;
    size_t nLinksLeft=linkList.size();
    while (nLinksLeft>0)
    {
      nLinksLeft--;
      Link link=linkList.front();linkList.pop_front();
      source=link.source;dest=link.dest;weight=link.weight;
    
      // phase I
      cliqueVector.clear();
      kCliquesFind(cliqueVector, net, source, dest, weight, k, 0);
      
      // phase II
      kCommunitiesFind(cliqueVector, communities, k1cliquesHash, net, k);
    }
    
    //communities are now detected, next we output the structure
    std::ofstream ofile(outputFile.c_str());
    outputCommunityStructure(communities, k1cliquesHash, ofile);
   
}

bool weighedCliqueCmp(const weighedClique lhs, const weighedClique rhs)
{
    return lhs.getWeight() > rhs.getWeight();
}

void kCommunitiesFindWeighted(std::vector<weighedClique> & cliqueVector, KruskalTree & communities, cliqueHash & k1cliquesHash, NetType & net, const size_t k, const float threshold)
{

    std::vector<size_t> tempVector;
    weighedClique k1clique;
    nodeCommunities nodeComs;
    Dendrogram dendrogram;
    size_t currentCliqueNumber = 0;
    CommunityTracker comTracker(k1cliquesHash, communities, nodeComs, dendrogram, net);
    for (std::vector<weighedClique>::iterator i = cliqueVector.begin(); i != cliqueVector.end(); ++i)
    {
        if (i->getWeight() < threshold)
            break;

        comTracker.addClique(*i);

        currentCliqueNumber++;

        //nodeComs.printCommunities(nodeCommunitOutputFile);
    }

    //dendrogram.printTree(dendrogramOutputFile);
}

void weightedSCP(NetType & net, std::ifstream & file, const size_t numberOfLinks, const size_t k, const float threshold, const size_t weightFunction, std::string outputFile)
{
    size_t source, dest;
    float weight;

    // store all k-cliques here and sort after that
    std::vector<weighedClique> cliqueVector;

    // phase I
    while (readLine(file, source, dest, weight))
        kCliquesFind(cliqueVector, net, source, dest, weight, k, weightFunction);

    std::sort(cliqueVector.begin(), cliqueVector.end(), weighedCliqueCmp);

    //std::cout << cliqueVector.size() << " k-cliques" << std::endl;

    // Use an upper bound for the number of k-1 cliques as hash size. Each k-clique has k k-1 cliques.
    size_t hash_bits = determineHashSize(cliqueVector.size() * k, k - 1);

    cliqueHash k1cliquesHash(1 << hash_bits, hash_bits, k - 1);
    KruskalTree communities;

    // phase II
    kCommunitiesFindWeighted(cliqueVector, communities, k1cliquesHash, net, k, threshold);

    //communities are now detected, next we output the structure
    std::ofstream ofile(outputFile.c_str());
    outputCommunityStructure(communities, k1cliquesHash, ofile);
    //std::cout << "largest: " << communities.getLargestComponentSize() << std::endl;
}

bool validateLinkList(std::list<Link> &linkList,size_t netSize,bool verbose){
  if (verbose) std::cout << "Checking that the node labels are not sparce and there are no multiedges... ";
  NetType tempNet;
  for (std::list<Link>::iterator linkIterator=linkList.begin() ; linkIterator != linkList.end(); linkIterator++ ){
    if (tempNet[linkIterator->source][linkIterator->dest]!=0){
      std::cerr <<"Error: The input file contains multi-edges."<<std::endl;
      return false;
    }
    tempNet[linkIterator->source][linkIterator->dest]=linkIterator->weight;
  }
  if (tempNet.size()!=netSize){
    std::cerr <<"Error: Node labels are sparse. Please name nodes from 0 to n-1."<<std::endl;
    return false;
  }
  if (verbose) std::cout << "Ok."<< std::endl;
  return true;
}


int percolation(char * fileName, const size_t k, const size_t weighted, const float threshold, const size_t weightFunction, std::string outputFile,bool verbose,bool sanityCheck)
{
    size_t numberOfLinks;
    size_t netSize;
    std::list<Link> linkList;
    
    // First read in the network from the file
    if (verbose) std::cout << "Reading in the network...\n";
    if (!getNetSizeAndLinkNumbers(fileName, netSize, numberOfLinks,linkList)) return EXIT_FAILURE;    
    if (verbose) std::cout<< "Number of nodes: " << netSize << "\nNumber of links: " <<numberOfLinks << "\n";

    //Check that the edge list is valid, this will waste some time
    if (sanityCheck) if (!validateLinkList(linkList,netSize,verbose)) return EXIT_FAILURE;

    // Finally, proceed with the clique percolation
    std::ifstream file(fileName);
    if (file.is_open())
    {
        NetType net(netSize);
        if (!weighted)
	  unweightedSCP(net, linkList, numberOfLinks, k, outputFile,verbose);
        if (weighted)
            weightedSCP(net, file, numberOfLinks, k, threshold, weightFunction, outputFile);
    }
    file.close();
    return EXIT_SUCCESS;
}

int main(int argc, char* argv[])
{
    size_t netSize, numberOfLinks;
    size_t k = 3;
    size_t weighted = 0;
    float threshold = 0;
    size_t weightFunction = 0;
    bool verbose=false;
    std::string outputFile;

    //-- Parse arguments
    for (size_t i = 2; i < argc; i++)
    {
      if (!strncmp(argv[i], "-k=", 3))
	k = atoi(argv[i] + 3);
      else if (!strncmp(argv[i], "-o=", 3))
	outputFile = argv[i] + 3;
      else if (!strcmp(argv[i], "-v"))
	verbose=true;
/*
      else if (!strcmp(argv[i], "-w"))
	weighted = 1;
      else if (!strncmp(argv[i], "-t=", 3))
	threshold = atof(argv[i] + 3);
      else if (!strcmp(argv[i], "-f"))
	weightFunction = atof(argv[++i]);
*/      else{
	std::cerr << "Invalid argument: "<<argv[i] <<std::endl;
	std::cerr << HELPSTR<<std::endl;
	return EXIT_FAILURE;	  
      }	        
    }

    //--- Sanity checks for the input arguments

    //Check that the input file was given
    if (argc==1){
      std::cerr << "Invalid number of arguments."<<std::endl;
      std::cerr << HELPSTR<<std::endl;
      return EXIT_FAILURE;
    }

    //Check that the clique size is valid
    if (k < 3)
    {
        std::cerr << "Invalid value of clique size k: " << k << std::endl << "The value of k must be 3 or larger." << std::endl;
        return EXIT_FAILURE;
    }
    //Check the the output file is given. If not, use "[inputfile]_output"
    if (outputFile.empty())
    {
        outputFile = argv[1];
        outputFile.append("_output");
    }


    //--- Run clique percolation    
    int exitCode=percolation(argv[1], k, weighted, threshold, weightFunction, outputFile,verbose,true);


    // calculate timings
    if (verbose)
      std::cout << "Time used: " << (double)clock() / (double)CLOCKS_PER_SEC << "s" << std::endl;

    return exitCode;
}




================================================
FILE: Algorithms/2008-CliquePercolation/src_cpp/k_clique.h
================================================
/*
scp, The sequential clique percolation algorithm.
Copyright (C) 2011  Aalto University

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*/

#ifndef H_K_CLIQUE
#define H_K_CLIQUE

#include <vector>
#include <map>
#include <cassert>
#include <iostream>
#include <vector>
#include <sstream>
#include <string>
#include <fstream>
#include <set>
#include <ctime>
#include <list>

#include "weighedClique.h"
//#include "numSet2.h"
#include "cliqueHash.h"
//#include "multiIter.h"
#include "kruskal.h"
#include "nodeCommunities.h"
#include "communityTracker.h"
#include "dendrogram.h"

// typedef float EdgeData;
// typedef  SymmNet<size_t> NetType; // needs laboratory's library
//typedef std::list<size_t> nodeList; // standard library
// typedef std::vector<numSet> vectorMap;
//typedef std::vector<clique> cliqueVector; // standard library
// typedef std::map< clique, size_t, compareIndexes > nodeCliqueMap;
// typedef std::map< clique, size_t > nodeCliqueMap;
typedef Set<size_t> nodeSet; // needs laboratory's library
//typedef std::vector<numSet2> vectorSet; // standard library
//typedef std::map< clique, size_t > nodeCliqueMap;

size_t determineHashSize(const size_t numElements, const size_t k);

void getNetSizeAndLinkNumbers(char * fileName, size_t & netSize, size_t & numLinks);

bool readLine(std::ifstream & myfile, size_t & source, size_t & dest, float & weight);

void kCliquesFind(std::vector<weighedClique> & cliqueVector, NetType & net, size_t source, size_t dest, const float weight, const size_t k, const size_t weightFunction);

void kCommunitiesFind(std::vector<weighedClique> & cliqueVector, KruskalTree & communities, cliqueHash & k1cliquesHash, NetType & net, const size_t k);

void outputCommunityStructure(KruskalTree & communities, cliqueHash & k1cliquesHash, std::ofstream & file);

void unweightedSCP(NetType & net, std::ifstream & file, const size_t numberOfLinks, const size_t k);

bool weighedCliqueCmp(weighedClique lhs, weighedClique rhs);

void kCommunitiesFindWeighted(std::vector<weighedClique> & cliqueVector, KruskalTree & communities, cliqueHash & k1cliquesHash, NetType & net, const size_t k, const float threshold);

void weightedSCP(NetType & net, std::ifstream & file, const size_t numberOfLinks, const size_t k, const float threshold, const size_t weightFunction);

void percolation(char * fileName, const size_t k, const size_t weighted, const float threshold, const size_t weightFunction);

#endif


================================================
FILE: Algorithms/2008-CliquePercolation/src_cpp/kruskal.cpp
================================================
/*
scp, The sequential clique percolation algorithm.
Copyright (C) 2011  Aalto University

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*/

#include "kruskal.h"

#include <iostream>

KruskalTree::KruskalTree() : largestComponentSize(1) {}

size_t KruskalTree::add()
{
    size_t vecSize = table.size();
    table.push_back(vecSize);
    commSizes.push_back(1);
    return vecSize;
}

size_t KruskalTree::add(const size_t root)
{
    if (root <= table.size())
    {
        table.push_back(root);
        findRoot(table[table.size() - 1]);
        commSizes.push_back(1);
    }
    else
        add();
    return table.size() - 1;
}

void KruskalTree::connect(const size_t first, const size_t second)
{
    if (first < table.size() && second < table.size() && !inSameSet(first, second)) // After the call inSameSet table[first] and table[second] point to their real roots
    {
        commSizes[table[second]] += commSizes[table[first]];
        if (commSizes[table[second]] > largestComponentSize)
            largestComponentSize = commSizes[table[second]];
        table[table[first]] = table[table[second]];
    }
}

bool KruskalTree::inSameSet(const size_t first, const size_t second)
{
    if (findRoot(first) == findRoot(second))
        return true;
    else
        return false;
}

size_t KruskalTree::findRoot(const size_t source)
{
    size_t root = table[source];
    while (root != table[root])
    {
        root = table[root];
    }
    size_t currentRoot = source;
    while (currentRoot != root)
    {
        size_t oldRoot = table[currentRoot];
        table[currentRoot] = root;
        currentRoot = oldRoot;
    }
    return root;
}

size_t KruskalTree::size(const size_t source)
{
    return commSizes[findRoot(source)];
}

size_t KruskalTree::getLargestComponentSize() const
{
    return largestComponentSize;
}

void KruskalTree::printTree(std::ostream & file) const
{
    for (int i = 0; i < table.size(); i++)
        file << i << ": " << table[i] << " s: " << commSizes[i] << std::endl;
    file << std::endl;
}


================================================
FILE: Algorithms/2008-CliquePercolation/src_cpp/kruskal.h
================================================
/*
scp, The sequential clique percolation algorithm.
Copyright (C) 2011  Aalto University

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*/

#ifndef KRUSKAL_H
#define KRUSKAL_H

#include <vector>
#include <iostream>

#include "weighedClique.h"

class KruskalTree
{
public:
    KruskalTree();

    size_t add(); // return the index where the element was added ( = table.size() - 1 )

    size_t add(const size_t root); // same as above

    void connect(const size_t first, const size_t second); // connects two sets, after the operation the first points to the root of second

    bool inSameSet(const size_t first, const size_t second); // checks if two elements belong to same set

    size_t findRoot(const size_t source); // finds the real root of an element

    size_t size(const size_t source);

    size_t getLargestComponentSize() const;

    void printTree(std::ostream & file) const;

private:

    std::vector<size_t> table; // stores the pointer to root
    std::vector<size_t> commSizes; // sizes of the sets are kept here

    size_t largestComponentSize;

};

#endif


================================================
FILE: Algorithms/2008-CliquePercolation/src_cpp/nodeCommunities.cpp
================================================
/*
scp, The sequential clique percolation algorithm.
Copyright (C) 2011  Aalto University

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*/

#include "nodeCommunities.h"

nodeCommunities::nodeCommunities() : largest(0) {}

void nodeCommunities::addClique(const size_t index, const clique & newClique)
{
    // add the nodes to the set
    for (size_t i = 0; i < newClique.size(); i++)
        communities[index].put(newClique.at(i));
    // check if this community becomes the largest
    if (communities[index].size() > largest)
    {
        largest = communities[index].size();
        largestCom = index;
    }
}

void nodeCommunities::erase(const size_t index)
{
    communities.erase(index);
    if (index == largestCom)
    {
        largest = 0;
        for (std::map<size_t, nodeSet>::iterator i = communities.begin(); i != communities.end(); i++)
            if (i->second.size() > largest)
            {
                largest = i->second.size();
                largestCom = i->first;
            }
    }
}

size_t nodeCommunities::connect(size_t first, size_t second)
{
    for (nodeSet::iterator i = communities[first].begin(); !i.finished(); ++i)
        communities[second].put(*i);

    erase(first);
    if (communities[second].size() > largest)
    {
        largest = communities[second].size();
        largestCom = second;
    }

    return second;
}

void nodeCommunities::printCommunities(std::ostream & file) const
{
    file << "largest: " << largest << std::endl;
    for (std::map<size_t, nodeSet>::const_iterator i = communities.begin(); i != communities.end(); i++)
    {
        file << i->first << ": ";
        for (nodeSet::const_iterator j = i->second.begin(); !j.finished(); ++j)
            file << *j << " ";
        file << std::endl;
    }
    file << std::endl;
}


================================================
FILE: Algorithms/2008-CliquePercolation/src_cpp/nodeCommunities.h
================================================
/*
scp, The sequential clique percolation algorithm.
Copyright (C) 2011  Aalto University

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*/

#ifndef NODECOMMUNITIES_H
#define NODECOMMUNITIES_H

#include "weighedClique.h"

#include <map>
#include <iostream>

#include "lcelib/Containers.H"

typedef Set<size_t> nodeSet;

class nodeCommunities
{
public:
    nodeCommunities();

    void addClique(const size_t index, const clique & newClique);

    size_t connect(size_t first, size_t second); // connects two communities, the smaller one is merged into the bigger one, return the index of the merged community

    size_t getLargest() const { return largest; }

    size_t getSize(const size_t comIndex) { return communities[comIndex].size(); }

    void printCommunities(std::ostream & file) const;

private:
    std::map<size_t, nodeSet> communities;

    size_t largest; // holds the size of the largest community
    size_t largestCom; // the index of the largest community

    void erase(const size_t index); // erases the community with the given index, erasing the largest community fucks up the largest counter
};

#endif


================================================
FILE: Algorithms/2008-CliquePercolation/src_cpp/script/testScp.py
================================================
import os

executable = "../k_clique"
tempDir = "../"
testDataDir = "../testData/"


def listComp(l1, l2):
    if len(l1) != len(l2):
        return cmp(len(l1), len(l2))
    for e1, e2 in zip(l1, l2):
        if e1 != e2:
            return cmp(e1, e2)
    return 0


def compareCommunities(scpComms, cfComms):
    l1 = []
    l2 = []
    for line in open(scpComms, 'r'):
        comms = map(int, line.split())
        comms.sort()
        if len(comms) > 0:
            l1.append(comms)

    for line in open(cfComms, 'r'):
        comms = map(int, line.split()[1:])
        comms.sort()
        l2.append(comms)

    l1.sort(cmp=listComp)
    l2.sort(cmp=listComp)

    l1 = tuple(map(tuple, l1))
    l2 = tuple(map(tuple, l2))
    # print l1
    # print l2
    return l1 == l2


testNets = filter(lambda x: x.endswith(".edg"), os.listdir(testDataDir))

for net in testNets:
    print "Testing ",
    print net,
    print "..."

    # find the k-values
    kvalues = []
    if os.path.exists(testDataDir + net + "_files/"):
        for file in os.listdir(testDataDir + net + "_files/"):
            if file.startswith("k="):
                kvalues.append(int(file[2:]))
    kvalues.sort()

    for k in kvalues:
        print "k=" + str(k) + ": ",
        # remove old temp file
        if os.path.exists(tempDir + "temp.txt"):
            os.remove(tempDir + "temp.txt")

        # run the k-clique percolator
        list(os.popen(executable + " " + testDataDir + net + " -k=" + str(k) + " -o=" + tempDir + "temp.txt"))

        if compareCommunities(tempDir + "temp.txt", testDataDir + net + "_files/k=" + str(k) + "/communities"):
            print "OK."
        else:
            print "FAILED!"
            break

# remove old temp file
if os.path.exists(tempDir + "temp.txt"):
    os.remove(tempDir + "temp.txt")


================================================
FILE: Algorithms/2008-CliquePercolation/src_cpp/testData/random_1000_005.edg
================================================
0	471	1.0
0	162	1.0
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0	340	1.0
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8	647	1.0
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2
Download .txt
gitextract_5m1t25tj/

├── .gitignore
├── .gitmodules
├── Algorithms/
│   ├── 2008-CliquePercolation/
│   │   ├── ReadMe.md
│   │   ├── algorithm_example.py
│   │   ├── conradlee_clique_percolation.py
│   │   ├── example_edge_list.txt
│   │   ├── src_cpp/
│   │   │   ├── CMakeLists.txt
│   │   │   ├── ReadMe.md
│   │   │   ├── cliqueHash.cpp
│   │   │   ├── cliqueHash.h
│   │   │   ├── communityTracker.cpp
│   │   │   ├── communityTracker.h
│   │   │   ├── dendrogram.cpp
│   │   │   ├── dendrogram.h
│   │   │   ├── doc/
│   │   │   │   ├── License.txt
│   │   │   │   └── makefile
│   │   │   ├── k_clique.cpp
│   │   │   ├── k_clique.h
│   │   │   ├── kruskal.cpp
│   │   │   ├── kruskal.h
│   │   │   ├── nodeCommunities.cpp
│   │   │   ├── nodeCommunities.h
│   │   │   ├── script/
│   │   │   │   └── testScp.py
│   │   │   ├── testData/
│   │   │   │   ├── random_1000_005.edg
│   │   │   │   └── random_1000_005.edg_files/
│   │   │   │       ├── k=3/
│   │   │   │       │   └── communities
│   │   │   │       ├── k=4/
│   │   │   │       │   └── communities
│   │   │   │       └── k=5/
│   │   │   │           └── communities
│   │   │   ├── weighedClique.cpp
│   │   │   └── weighedClique.h
│   │   └── src_python/
│   │       └── seq_clique_percolation.py
│   ├── 2009-Connected-Iterative-Scan/
│   │   ├── .gitignore
│   │   ├── ReadMe.md
│   │   ├── src-orginal/
│   │   │   ├── Libraries/
│   │   │   │   ├── Files/
│   │   │   │   │   ├── IOX.cc
│   │   │   │   │   ├── IOX.h
│   │   │   │   │   ├── StringEx.cc
│   │   │   │   │   ├── StringEx.h
│   │   │   │   │   ├── files.cc
│   │   │   │   │   └── makefile
│   │   │   │   ├── Network/
│   │   │   │   │   ├── Format.cc
│   │   │   │   │   ├── Format.h
│   │   │   │   │   ├── LibNetwork.cc
│   │   │   │   │   ├── Network.cc
│   │   │   │   │   ├── Network.h
│   │   │   │   │   ├── RandomNetwork.h
│   │   │   │   │   ├── TemporalNetwork.cc
│   │   │   │   │   ├── TemporalNetwork.h
│   │   │   │   │   └── makefile
│   │   │   │   └── Params/
│   │   │   │       ├── Parameters.cc
│   │   │   │       ├── Parameters.h
│   │   │   │       └── makefile
│   │   │   ├── ReadMe.md
│   │   │   ├── demo/
│   │   │   │   ├── karate_edges_input_modified.csv
│   │   │   │   ├── karate_output.csv
│   │   │   │   ├── network.cl
│   │   │   │   └── network_seeded.cl
│   │   │   ├── main.cc
│   │   │   └── makefile
│   │   └── src-refactor/
│   │       ├── CMakeLists.txt
│   │       ├── ReadMe.md
│   │       ├── dataset/
│   │       │   ├── karate_edges_input_modified.csv
│   │       │   ├── karate_output.csv
│   │       │   ├── network.cl
│   │       │   └── network_seeded.cl
│   │       ├── graph/
│   │       │   ├── network.cc
│   │       │   ├── network.h
│   │       │   ├── temporal_network.cc
│   │       │   └── temporal_network.h
│   │       ├── main.cc
│   │       ├── useless/
│   │       │   └── RandomNetwork.h
│   │       └── util/
│   │           ├── graph_io_helper.cc
│   │           ├── graph_io_helper.h
│   │           ├── io_helper.cc
│   │           ├── io_helper.h
│   │           ├── parameters_helper.cc
│   │           ├── parameters_helper.h
│   │           ├── string_helper.cc
│   │           └── string_helper.h
│   ├── 2009-EAGLE/
│   │   ├── .gitignore
│   │   ├── ReadMe.md
│   │   ├── graphs/
│   │   │   ├── eagle.edl
│   │   │   ├── eagle.graphml
│   │   │   ├── generate.sh
│   │   │   ├── originals/
│   │   │   │   └── eagle
│   │   │   └── tools/
│   │   │       ├── converter.py
│   │   │       ├── examples.py
│   │   │       ├── progressbar.py
│   │   │       └── utils.pyx
│   │   ├── relazione/
│   │   │   ├── Makefile
│   │   │   └── relazione.lyx
│   │   └── src/
│   │       ├── CMakeLists.txt
│   │       ├── ReadMe.md
│   │       ├── communities.cpp
│   │       ├── communities.h
│   │       ├── eagle.cpp
│   │       ├── eagle.h
│   │       ├── main.cpp
│   │       ├── max_cache.cpp
│   │       └── max_cache.h
│   ├── 2009-LineGraph/
│   │   ├── altix/
│   │   │   ├── axlgc.sh
│   │   │   └── axmakelgc.sh
│   │   ├── deprecated/
│   │   │   ├── LineGraphCreator.html
│   │   │   ├── lgc.bat
│   │   │   ├── makefileClever
│   │   │   ├── makefileTSE
│   │   │   └── makelgc.bat
│   │   ├── readme.txt
│   │   └── src/
│   │       ├── TseGraph.cpp
│   │       ├── TseGraph.h
│   │       └── main.cpp
│   ├── 2010-CONGA/
│   │   ├── ReadMe.md
│   │   └── conga_src/
│   │       ├── ReadMe.md
│   │       ├── dataset/
│   │       │   ├── dolphins_edges.txt
│   │       │   └── karate.txt
│   │       ├── pom.xml
│   │       └── src/
│   │           └── main/
│   │               ├── java/
│   │               │   ├── clique_modularity/
│   │               │   │   ├── CM.java
│   │               │   │   ├── algorithm/
│   │               │   │   │   ├── BK/
│   │               │   │   │   │   ├── BK.java
│   │               │   │   │   │   └── BronKerboschCFFast.java
│   │               │   │   │   ├── KJ/
│   │               │   │   │   │   └── KJ.java
│   │               │   │   │   └── MaxClique.java
│   │               │   │   ├── input_output/
│   │               │   │   │   ├── ReadEdges.java
│   │               │   │   │   └── WriteCliques.java
│   │               │   │   └── util/
│   │               │   │       ├── ARRAY2.java
│   │               │   │       ├── ARRAY_FIX.java
│   │               │   │       ├── Pair.java
│   │               │   │       ├── Tree.java
│   │               │   │       ├── benchmark/
│   │               │   │       │   ├── GG.java
│   │               │   │       │   └── GGResult.java
│   │               │   │       ├── community/
│   │               │   │       │   ├── CPP.java
│   │               │   │       │   ├── CommPair.java
│   │               │   │       │   ├── CommPairSet.java
│   │               │   │       │   ├── CompleteCliques.java
│   │               │   │       │   ├── CompleteCliques1.java
│   │               │   │       │   ├── RebuildCommunities.java
│   │               │   │       │   └── RemoveCliques.java
│   │               │   │       ├── graph/
│   │               │   │       │   └── ELEMENT.java
│   │               │   │       └── metric/
│   │               │   │           ├── Modularity.java
│   │               │   │           └── Omega.java
│   │               │   ├── conga/
│   │               │   │   ├── CONGA.java
│   │               │   │   ├── algorithm/
│   │               │   │   │   ├── Between.java
│   │               │   │   │   ├── CPP.java
│   │               │   │   │   └── PB.java
│   │               │   │   └── util/
│   │               │   │       ├── Pair.java
│   │               │   │       ├── StrPair.java
│   │               │   │       ├── Tree.java
│   │               │   │       ├── benchmark/
│   │               │   │       │   └── GResult.java
│   │               │   │       ├── community/
│   │               │   │       │   ├── BP.java
│   │               │   │       │   ├── ClusterInfo.java
│   │               │   │       │   └── Stats.java
│   │               │   │       ├── graph/
│   │               │   │       │   ├── Edge.java
│   │               │   │       │   ├── LabelledEdge.java
│   │               │   │       │   ├── Split.java
│   │               │   │       │   └── Vertex.java
│   │               │   │       └── metric/
│   │               │   │           └── ModOverlap.java
│   │               │   └── copra/
│   │               │       ├── Project.java
│   │               │       ├── algorithm/
│   │               │       │   └── COPRA.java
│   │               │       └── util/
│   │               │           ├── LabelPair.java
│   │               │           ├── SetPair.java
│   │               │           ├── VecPair.java
│   │               │           ├── Vert.java
│   │               │           ├── community/
│   │               │           │   └── ClusterLabel.java
│   │               │           └── metric/
│   │               │               └── ModOverlap.java
│   │               └── resources/
│   │                   ├── CM.jar
│   │                   ├── conga.jar
│   │                   └── copra.jar
│   ├── 2010-LinkCommunity/
│   │   ├── README.markdown
│   │   ├── cpp/
│   │   │   ├── COPYING
│   │   │   ├── README
│   │   │   ├── calcAndWrite_Jaccards.cpp
│   │   │   ├── clusterJaccsFile.cpp
│   │   │   ├── edgelist2pairs.py
│   │   │   ├── karate.pairs
│   │   │   ├── lesmis.pairs
│   │   │   ├── link_clustering.sh
│   │   │   ├── loop_thresholds.sh
│   │   │   └── partition_density.py
│   │   ├── python/
│   │   │   ├── karate.pairs
│   │   │   └── link_clustering.py
│   │   └── python_yche_refactor/
│   │       ├── ReadMe.md
│   │       ├── example_edge_list.txt
│   │       ├── graph_io_helper.py
│   │       ├── link_clustering.py
│   │       ├── link_clustering_algo.py
│   │       ├── play_ground.py
│   │       └── results_sample/
│   │           ├── example_edge_list_maxS0.166667_maxD0.703704.comm2edges.txt
│   │           ├── example_edge_list_maxS0.166667_maxD0.703704.comm2nodes.txt
│   │           ├── example_edge_list_maxS0.166667_maxD0.703704.edge2comm.txt
│   │           └── example_edge_list_thr_D.txt
│   ├── 2010-TopGC/
│   │   ├── ReadMe.md
│   │   ├── src_original/
│   │   │   ├── Graphs/
│   │   │   │   ├── graph.sample
│   │   │   │   ├── graph.sample.clusters_directed
│   │   │   │   └── original/
│   │   │   │       ├── graph.raw
│   │   │   │       ├── graph1.idx
│   │   │   │       ├── graph1.raw
│   │   │   │       ├── graph_temp.idx
│   │   │   │       ├── graph_temp.raw
│   │   │   │       ├── graph_temp2.raw
│   │   │   │       ├── mkidx
│   │   │   │       └── mkidx.c
│   │   │   ├── README
│   │   │   ├── TopGC.jar
│   │   │   ├── edgew.txt
│   │   │   ├── idxdFile
│   │   │   └── mkidx.c
│   │   └── src_refactor/
│   │       ├── pom.xml
│   │       └── src/
│   │           └── main/
│   │               ├── java/
│   │               │   ├── FindMostProm.java
│   │               │   ├── HoldBucket.java
│   │               │   ├── HoldInt.java
│   │               │   ├── IntAndDouble.java
│   │               │   ├── LSH.java
│   │               │   ├── LSHThread.java
│   │               │   ├── LSH_Cluster.java
│   │               │   ├── Look3.java
│   │               │   ├── MaxHeap.java
│   │               │   ├── MinHeap.java
│   │               │   ├── Prime.java
│   │               │   ├── TempDouble2.java
│   │               │   └── TopGC.java
│   │               └── resources/
│   │                   └── TopGC.jar
│   ├── 2010-iLCD/
│   │   ├── .gitignore
│   │   ├── ReadMe.md
│   │   ├── dataset/
│   │   │   └── exempleGraph.lnd
│   │   ├── doc/
│   │   │   └── ReadMe.rtf
│   │   ├── jars/
│   │   │   ├── iLCD-2013.jar
│   │   │   └── temporalGraphVisu.jar
│   │   └── src/
│   │       ├── pom.xml
│   │       └── src/
│   │           └── main/
│   │               └── java/
│   │                   ├── CorePackage/
│   │                   │   └── Main.java
│   │                   ├── Inputs/
│   │                   │   ├── InputCTNFhandler.java
│   │                   │   ├── InputHandlerInterface.java
│   │                   │   ├── InputNCOLhandler.java
│   │                   │   └── InputOLDLNDhandler.java
│   │                   ├── Outputs/
│   │                   │   ├── OutputCTNF.java
│   │                   │   ├── OutputHandlerInterface.java
│   │                   │   ├── OutputMultipleHandler.java
│   │                   │   ├── OutputStatic.java
│   │                   │   └── OutputSummary.java
│   │                   ├── TemporalNetworkManipulation/
│   │                   │   ├── Community.java
│   │                   │   ├── CoreProcessor.java
│   │                   │   ├── Interface.java
│   │                   │   ├── MyDate.java
│   │                   │   ├── MyDateManager.java
│   │                   │   ├── Network.java
│   │                   │   ├── Node.java
│   │                   │   ├── Operations/
│   │                   │   │   ├── AddEdgeOperation.java
│   │                   │   │   ├── BirthCommunityOperation.java
│   │                   │   │   ├── ContractCommunityOperation.java
│   │                   │   │   ├── DeathCommunityOperation.java
│   │                   │   │   ├── FusionCommunityOperation.java
│   │                   │   │   ├── GrowthCommunityOperation.java
│   │                   │   │   ├── Operation.java
│   │                   │   │   └── RemoveEdgeOperation.java
│   │                   │   └── OperationsHandler.java
│   │                   ├── communityDetectionPackage/
│   │                   │   └── ILCDMetaAlgorithm.java
│   │                   ├── implementable/
│   │                   │   ├── Implementation.java
│   │                   │   └── ImplementationRNHM.java
│   │                   └── tools/
│   │                       ├── DebugMode.java
│   │                       ├── SortEdges.java
│   │                       ├── Sorter.java
│   │                       ├── TextFileHandler.java
│   │                       └── ToolDate.java
│   ├── 2011-GCE/
│   │   ├── ReadMe.md
│   │   ├── src-original/
│   │   │   ├── Community_Finder.cpp
│   │   │   ├── Community_Finder.h
│   │   │   ├── Range.hpp
│   │   │   ├── Seed.cpp
│   │   │   ├── Seed.h
│   │   │   ├── aaron_utils.cpp
│   │   │   ├── aaron_utils.hpp
│   │   │   ├── build/
│   │   │   │   ├── .gitignore
│   │   │   │   ├── karate_edges_input.csv
│   │   │   │   ├── karate_gce_output.csv
│   │   │   │   └── makefile
│   │   │   ├── clique_percolation.hpp
│   │   │   ├── cliques.cpp
│   │   │   ├── cliques.hpp
│   │   │   ├── find_communities.cpp
│   │   │   ├── graph_analysis.hpp
│   │   │   ├── graph_loading.cpp
│   │   │   ├── graph_loading.hpp
│   │   │   ├── graph_representation.cpp
│   │   │   ├── graph_representation.hpp
│   │   │   ├── iterative.hpp
│   │   │   ├── modularity.hpp
│   │   │   └── options.hpp
│   │   └── src-refactor/
│   │       ├── CMakeLists.txt
│   │       ├── ReadMe.md
│   │       ├── algorithm/
│   │       │   ├── cliques.cpp
│   │       │   ├── cliques.hpp
│   │       │   ├── community_finder.cpp
│   │       │   ├── community_finder.h
│   │       │   ├── find_communities.cpp
│   │       │   ├── seed.cpp
│   │       │   └── seed.h
│   │       ├── useless/
│   │       │   ├── clique_percolation.hpp
│   │       │   ├── graph_analysis.hpp
│   │       │   ├── iterative.hpp
│   │       │   ├── modularity.hpp
│   │       │   └── options.hpp
│   │       └── util/
│   │           ├── aaron_utils.cpp
│   │           ├── aaron_utils.hpp
│   │           ├── graph/
│   │           │   ├── graph_loading.cpp
│   │           │   ├── graph_loading.hpp
│   │           │   ├── graph_representation.cpp
│   │           │   └── graph_representation.hpp
│   │           └── range.hpp
│   ├── 2011-MOSES/
│   │   ├── LICENSE-2.0.txt
│   │   ├── NOTICE
│   │   ├── ReadMe.md
│   │   ├── comment.txt
│   │   ├── src-original/
│   │   │   ├── Makefile
│   │   │   ├── Range.cpp
│   │   │   ├── Range.hpp
│   │   │   ├── aaron_utils.cpp
│   │   │   ├── aaron_utils.hpp
│   │   │   ├── gitstatus.cpp
│   │   │   ├── gitstatus.hpp
│   │   │   ├── graph_loading.cpp
│   │   │   ├── graph_loading.hpp
│   │   │   ├── graph_representation.cpp
│   │   │   ├── graph_representation.hpp
│   │   │   ├── groupStats.cpp
│   │   │   ├── grouping.cpp
│   │   │   ├── grouping.hpp
│   │   │   ├── iterative.hpp
│   │   │   ├── moses.cpp
│   │   │   ├── options.hpp
│   │   │   ├── overlapping.cpp
│   │   │   └── overlapping.hpp
│   │   └── src-refactor/
│   │       ├── CMakeLists.txt
│   │       ├── algorithm/
│   │       │   ├── ReadMe.md
│   │       │   ├── group_status_exec.cpp
│   │       │   ├── grouping.cpp
│   │       │   ├── grouping.hpp
│   │       │   ├── moses.cpp
│   │       │   ├── overlapping.cpp
│   │       │   └── overlapping.hpp
│   │       ├── doc/
│   │       │   ├── Makefile
│   │       │   └── comment.txt
│   │       └── util/
│   │           ├── aaron_utils.cpp
│   │           ├── aaron_utils.hpp
│   │           ├── graph/
│   │           │   ├── graph_loading.cpp
│   │           │   ├── graph_loading.hpp
│   │           │   ├── graph_representation.cpp
│   │           │   ├── graph_representation.hpp
│   │           │   └── iterative.hpp
│   │           ├── program_options/
│   │           │   └── options.hpp
│   │           ├── range.cpp
│   │           └── range.hpp
│   ├── 2011-OSLOM-v2/
│   │   ├── Sources_2_5/
│   │   │   ├── OSLOM_files/
│   │   │   │   ├── dir_weighted_tabdeg.h
│   │   │   │   ├── directed_network.h
│   │   │   │   ├── directed_oslomnet_evaluate.h
│   │   │   │   ├── egocentric_undir.h
│   │   │   │   ├── hierarchies.h
│   │   │   │   ├── log_table.h
│   │   │   │   ├── louvain_oslomnet.h
│   │   │   │   ├── louvain_oslomnet_dir.h
│   │   │   │   ├── main_body.cpp
│   │   │   │   ├── main_directed.cpp
│   │   │   │   ├── main_undirected.cpp
│   │   │   │   ├── module_collection.h
│   │   │   │   ├── oslom_net_check_overlap.cpp
│   │   │   │   ├── oslom_net_global.h
│   │   │   │   ├── oslom_net_unions.cpp
│   │   │   │   ├── set_parameters.h
│   │   │   │   ├── standard_package/
│   │   │   │   │   ├── cast.cpp
│   │   │   │   │   ├── combinatorics.cpp
│   │   │   │   │   ├── deque_numeric.cpp
│   │   │   │   │   ├── histograms.cpp
│   │   │   │   │   ├── mutual.cpp
│   │   │   │   │   ├── pajek.cpp
│   │   │   │   │   ├── partition.cpp
│   │   │   │   │   ├── print.cpp
│   │   │   │   │   ├── random.cpp
│   │   │   │   │   ├── standard_include.cpp
│   │   │   │   │   └── tabdeg.cpp
│   │   │   │   ├── try_homeless_dir.cpp
│   │   │   │   ├── try_homeless_undir.cpp
│   │   │   │   ├── undir_weighted_tabdeg.h
│   │   │   │   ├── undirected_network.h
│   │   │   │   ├── undirected_oslomnet_evaluate.h
│   │   │   │   └── wsarray.h
│   │   │   ├── ReadMe.tex
│   │   │   ├── infomap_dir/
│   │   │   │   ├── Greedy.cc
│   │   │   │   ├── Greedy.h
│   │   │   │   ├── GreedyBase.cc
│   │   │   │   ├── GreedyBase.h
│   │   │   │   ├── Makefile
│   │   │   │   ├── MersenneTwister.h
│   │   │   │   ├── Node.cc
│   │   │   │   ├── Node.h
│   │   │   │   ├── flow.net
│   │   │   │   ├── infomap.cc
│   │   │   │   ├── infomap.h
│   │   │   │   ├── infomap_scr.cpp
│   │   │   │   ├── source-sink.net
│   │   │   │   └── standard_package/
│   │   │   │       ├── cast.cpp
│   │   │   │       ├── combinatorics.cpp
│   │   │   │       ├── deque_numeric.cpp
│   │   │   │       ├── histograms.cpp
│   │   │   │       ├── mutual.cpp
│   │   │   │       ├── pajek.cpp
│   │   │   │       ├── partition.cpp
│   │   │   │       ├── print.cpp
│   │   │   │       ├── random.cpp
│   │   │   │       ├── standard_include.cpp
│   │   │   │       └── tabdeg.cpp
│   │   │   ├── infomap_undir/
│   │   │   │   ├── Greedy.cc
│   │   │   │   ├── Greedy.h
│   │   │   │   ├── GreedyBase.cc
│   │   │   │   ├── GreedyBase.h
│   │   │   │   ├── Makefile
│   │   │   │   ├── MersenneTwister.h
│   │   │   │   ├── Node.cc
│   │   │   │   ├── Node.h
│   │   │   │   ├── infomap.cc
│   │   │   │   ├── infomap.h
│   │   │   │   ├── infomap_scr.cpp
│   │   │   │   ├── karate.net
│   │   │   │   └── standard_package/
│   │   │   │       ├── cast.cpp
│   │   │   │       ├── combinatorics.cpp
│   │   │   │       ├── deque_numeric.cpp
│   │   │   │       ├── histograms.cpp
│   │   │   │       ├── mutual.cpp
│   │   │   │       ├── pajek.cpp
│   │   │   │       ├── partition.cpp
│   │   │   │       ├── print.cpp
│   │   │   │       ├── random.cpp
│   │   │   │       ├── standard_include.cpp
│   │   │   │       └── tabdeg.cpp
│   │   │   ├── louvain/
│   │   │   │   ├── Makefile
│   │   │   │   ├── a.out
│   │   │   │   ├── community.cpp
│   │   │   │   ├── community.h
│   │   │   │   ├── graph.cpp
│   │   │   │   ├── graph.h
│   │   │   │   ├── graph_binary.cpp
│   │   │   │   ├── graph_binary.h
│   │   │   │   ├── graph_binary_linux.h
│   │   │   │   ├── graph_binary_mac.h
│   │   │   │   ├── list_out
│   │   │   │   ├── main_community.cpp
│   │   │   │   ├── main_convert.cpp
│   │   │   │   ├── main_hierarchy.cpp
│   │   │   │   ├── order.cpp
│   │   │   │   ├── script_to_compile.cpp
│   │   │   │   ├── standard_package/
│   │   │   │   │   ├── cast.cpp
│   │   │   │   │   ├── combinatorics.cpp
│   │   │   │   │   ├── deque_numeric.cpp
│   │   │   │   │   ├── histograms.cpp
│   │   │   │   │   ├── mutual.cpp
│   │   │   │   │   ├── pajek.cpp
│   │   │   │   │   ├── partition.cpp
│   │   │   │   │   ├── print.cpp
│   │   │   │   │   ├── random.cpp
│   │   │   │   │   ├── standard_include.cpp
│   │   │   │   │   └── tabdeg.cpp
│   │   │   │   ├── static_network.h
│   │   │   │   └── wsarray.h
│   │   │   └── visualSources/
│   │   │       ├── hier.h
│   │   │       ├── main.cpp
│   │   │       ├── main_pajek.cpp
│   │   │       ├── main_pajek_directed.cpp
│   │   │       ├── netvi.h
│   │   │       ├── position.h
│   │   │       ├── standard_package/
│   │   │       │   ├── cast.cpp
│   │   │       │   ├── combinatorics.cpp
│   │   │       │   ├── deque_numeric.cpp
│   │   │       │   ├── histograms.cpp
│   │   │       │   ├── mutual.cpp
│   │   │       │   ├── pajek.cpp
│   │   │       │   ├── partition.cpp
│   │   │       │   ├── print.cpp
│   │   │       │   ├── random.cpp
│   │   │       │   ├── standard_include.cpp
│   │   │       │   └── tabdeg.cpp
│   │   │       ├── static_network.h
│   │   │       ├── visual_net.h
│   │   │       └── wsarray.h
│   │   ├── compile_all.sh
│   │   ├── copra.jar
│   │   └── src-refactor/
│   │       ├── CMakeLists.txt
│   │       ├── algorithm/
│   │       │   ├── infomap/
│   │       │   │   ├── dir/
│   │       │   │   │   ├── Greedy.cc
│   │       │   │   │   ├── Greedy.h
│   │       │   │   │   ├── GreedyBase.cc
│   │       │   │   │   ├── GreedyBase.h
│   │       │   │   │   ├── MersenneTwister.h
│   │       │   │   │   ├── Node.cc
│   │       │   │   │   ├── Node.h
│   │       │   │   │   ├── doc/
│   │       │   │   │   │   ├── Makefile
│   │       │   │   │   │   ├── ReadMe.md
│   │       │   │   │   │   ├── flow.net
│   │       │   │   │   │   ├── infomap_scr.cpp
│   │       │   │   │   │   └── source-sink.net
│   │       │   │   │   ├── infomap.cc
│   │       │   │   │   └── infomap.h
│   │       │   │   └── undir/
│   │       │   │       ├── Greedy.cc
│   │       │   │       ├── Greedy.h
│   │       │   │       ├── GreedyBase.cc
│   │       │   │       ├── GreedyBase.h
│   │       │   │       ├── MersenneTwister.h
│   │       │   │       ├── Node.cc
│   │       │   │       ├── Node.h
│   │       │   │       ├── doc/
│   │       │   │       │   ├── Makefile
│   │       │   │       │   ├── ReadMe.md
│   │       │   │       │   ├── infomap_scr.cpp
│   │       │   │       │   └── karate.net
│   │       │   │       ├── infomap.cc
│   │       │   │       └── infomap.h
│   │       │   ├── louvain/
│   │       │   │   ├── community.cpp
│   │       │   │   ├── community.h
│   │       │   │   ├── doc/
│   │       │   │   │   ├── Makefile
│   │       │   │   │   ├── ReadMe.md
│   │       │   │   │   ├── list_out
│   │       │   │   │   ├── order.cpp
│   │       │   │   │   ├── script_to_compile.cpp
│   │       │   │   │   └── static_network.h
│   │       │   │   ├── graph.cpp
│   │       │   │   ├── graph.h
│   │       │   │   ├── graph_binary.cpp
│   │       │   │   ├── graph_binary.h
│   │       │   │   ├── graph_binary_linux.h
│   │       │   │   ├── graph_binary_mac.h
│   │       │   │   ├── main_community.cpp
│   │       │   │   ├── main_convert.cpp
│   │       │   │   └── main_hierarchy.cpp
│   │       │   └── oslom/
│   │       │       ├── hierarchies.cpp
│   │       │       ├── hierarchies.h
│   │       │       ├── main_directed.cpp
│   │       │       └── main_undirected.cpp
│   │       ├── graph/
│   │       │   ├── directed/
│   │       │   │   ├── dir_weighted_tabdeg.cpp
│   │       │   │   ├── dir_weighted_tabdeg.h
│   │       │   │   ├── directed_network.cpp
│   │       │   │   ├── directed_network.h
│   │       │   │   ├── directed_oslomnet_evaluate.cpp
│   │       │   │   ├── directed_oslomnet_evaluate.h
│   │       │   │   ├── louvain_oslomnet_dir.cpp
│   │       │   │   ├── louvain_oslomnet_dir.h
│   │       │   │   └── try_homeless_dir.cpp
│   │       │   ├── louvain_oslomnet.cpp
│   │       │   ├── louvain_oslomnet.h
│   │       │   ├── oslom_net_global.cpp
│   │       │   ├── oslom_net_global.h
│   │       │   └── undirected/
│   │       │       ├── egocentric_undir.cpp
│   │       │       ├── egocentric_undir.h
│   │       │       ├── try_homeless_undir.cpp
│   │       │       ├── undir_weighted_tabdeg.cpp
│   │       │       ├── undir_weighted_tabdeg.h
│   │       │       ├── undirected_network.cpp
│   │       │       ├── undirected_network.h
│   │       │       ├── undirected_oslomnet_evaluate.cpp
│   │       │       └── undirected_oslomnet_evaluate.h
│   │       ├── util/
│   │       │   ├── collection/
│   │       │   │   ├── module_collection.cpp
│   │       │   │   ├── module_collection.h
│   │       │   │   ├── wsarray.cpp
│   │       │   │   └── wsarray.h
│   │       │   ├── common/
│   │       │   │   ├── cast.cpp
│   │       │   │   ├── cast.h
│   │       │   │   ├── cc.cpp
│   │       │   │   ├── cc.h
│   │       │   │   ├── combinatorics.cpp
│   │       │   │   ├── combinatorics.h
│   │       │   │   ├── deque_numeric.cpp
│   │       │   │   ├── deque_numeric.h
│   │       │   │   ├── histograms.cpp
│   │       │   │   ├── histograms.h
│   │       │   │   ├── log_table.cpp
│   │       │   │   ├── log_table.h
│   │       │   │   ├── random.cpp
│   │       │   │   └── random.h
│   │       │   ├── input_output/
│   │       │   │   ├── pajek.cpp
│   │       │   │   ├── pajek.h
│   │       │   │   ├── partition.cpp
│   │       │   │   ├── partition.h
│   │       │   │   ├── pretty_print.h
│   │       │   │   ├── tab_degree.cpp
│   │       │   │   └── tab_degree.h
│   │       │   ├── metric/
│   │       │   │   ├── mutual.cpp
│   │       │   │   └── mutual.h
│   │       │   └── program_options/
│   │       │       ├── set_parameters.cpp
│   │       │       └── set_parameters.h
│   │       └── visualization/
│   │           ├── main.cpp
│   │           ├── main_pajek.cpp
│   │           ├── main_pajek_directed.cpp
│   │           ├── unused/
│   │           │   ├── netvi.cpp
│   │           │   └── netvi.h
│   │           └── util/
│   │               ├── hier.cpp
│   │               ├── hier.h
│   │               ├── position.cpp
│   │               ├── position.h
│   │               ├── static_network.cpp
│   │               ├── static_network.h
│   │               ├── visual_net.cpp
│   │               ├── visual_net.h
│   │               ├── wsarray.cpp
│   │               └── wsarray.h
│   ├── 2011-SLPA/
│   │   ├── ReadMe.md
│   │   ├── src_original/
│   │   │   ├── GANXiS-S_v1.0/
│   │   │   │   ├── CommonFuns.cpp
│   │   │   │   ├── CommonFuns.h
│   │   │   │   ├── CommonFuns_Measure.cpp
│   │   │   │   ├── CommonFuns_Measure.h
│   │   │   │   ├── CommonFuns_TMP.h
│   │   │   │   ├── CommonFuns_TMP_Measure.h
│   │   │   │   ├── ComputeSnapshotChange.cpp
│   │   │   │   ├── ComputeSnapshotChange.h
│   │   │   │   ├── DisjointM.cpp
│   │   │   │   ├── DisjointM.h
│   │   │   │   ├── LPA.cpp
│   │   │   │   ├── LPA.h
│   │   │   │   ├── LRTPrama.cpp
│   │   │   │   ├── LRTPrama.h
│   │   │   │   ├── LabelRank.cpp
│   │   │   │   ├── LabelRank.h
│   │   │   │   ├── MersenneTwister.h
│   │   │   │   ├── NODE.cpp
│   │   │   │   ├── NODE.h
│   │   │   │   ├── Net.cpp
│   │   │   │   ├── Net.h
│   │   │   │   ├── TieLabel.cpp
│   │   │   │   ├── TieLabel.h
│   │   │   │   ├── fileOpts.cpp
│   │   │   │   ├── fileOpts.h
│   │   │   │   ├── main_LabelRank_release.cpp
│   │   │   │   ├── rndNumbers.cpp
│   │   │   │   ├── rndNumbers.h
│   │   │   │   └── test.ipairs
│   │   │   └── GANXiS_v3.0.2/
│   │   │       ├── GANXiSw.jar
│   │   │       ├── commons-collections-3.2.1.jar
│   │   │       ├── output/
│   │   │       │   ├── SLPAw_test_run1_r0.01_v3_T100.icpm
│   │   │       │   ├── SLPAw_test_run1_r0.05_v3_T100.icpm
│   │   │       │   ├── SLPAw_test_run1_r0.15_v3_T100.icpm
│   │   │       │   ├── SLPAw_test_run1_r0.1_v3_T100.icpm
│   │   │       │   ├── SLPAw_test_run1_r0.25_v3_T100.icpm
│   │   │       │   ├── SLPAw_test_run1_r0.2_v3_T100.icpm
│   │   │       │   ├── SLPAw_test_run1_r0.35_v3_T100.icpm
│   │   │       │   ├── SLPAw_test_run1_r0.3_v3_T100.icpm
│   │   │       │   ├── SLPAw_test_run1_r0.45_v3_T100.icpm
│   │   │       │   ├── SLPAw_test_run1_r0.4_v3_T100.icpm
│   │   │       │   └── SLPAw_test_run1_r0.5_v3_T100.icpm
│   │   │       ├── test.ipairs
│   │   │       ├── testLong.ipairs
│   │   │       ├── test_str.ipairs
│   │   │       └── test_w01.ipairs
│   │   ├── src_python/
│   │   │   ├── romain-fontugne/
│   │   │   │   └── slpa.py
│   │   │   └── ying_nus/
│   │   │       ├── README.md
│   │   │       ├── karate.txt
│   │   │       ├── nmi.py
│   │   │       ├── slpa.py
│   │   │       └── test_slpa.py
│   │   └── src_refactor/
│   │       ├── pom.xml
│   │       └── src/
│   │           └── main/
│   │               ├── java/
│   │               │   ├── CollectionFuns.java
│   │               │   ├── NODE.java
│   │               │   ├── Net.java
│   │               │   ├── SLPAw.java
│   │               │   └── fileOpts.java
│   │               └── resources/
│   │                   └── GANXiSw.jar
│   ├── 2012-CPMOnSteroids/
│   │   ├── ReadMe.md
│   │   ├── src_original/
│   │   │   ├── COPYING
│   │   │   ├── Makefile.in
│   │   │   ├── README
│   │   │   ├── cliques.c
│   │   │   ├── configure
│   │   │   ├── configure.in
│   │   │   ├── cos.c
│   │   │   ├── cospoc.c
│   │   │   ├── dsforest.c
│   │   │   ├── extras/
│   │   │   │   ├── Makefile.in
│   │   │   │   └── maximal_cliques.c
│   │   │   ├── include/
│   │   │   │   ├── cliques.h
│   │   │   │   ├── common.h
│   │   │   │   ├── cos.h
│   │   │   │   ├── cospoc.h
│   │   │   │   ├── debug.h
│   │   │   │   ├── dsforest.h
│   │   │   │   ├── matrix.h
│   │   │   │   └── output_communities.h
│   │   │   ├── main.c
│   │   │   ├── matrix.c
│   │   │   └── output_communities.c
│   │   └── src_refactor/
│   │       ├── doc/
│   │       │   ├── COPYING
│   │       │   └── README
│   │       └── src/
│   │           ├── CMakeLists.txt
│   │           ├── cliques.c
│   │           ├── cliques.h
│   │           ├── common.h
│   │           ├── cos.c
│   │           ├── cos.h
│   │           ├── cospoc.c
│   │           ├── cospoc.h
│   │           ├── debug.h
│   │           ├── dsforest.c
│   │           ├── dsforest.h
│   │           ├── extras/
│   │           │   └── maximal_cliques.c
│   │           ├── main.c
│   │           ├── matrix.c
│   │           ├── matrix.h
│   │           ├── output_communities.c
│   │           └── output_communities.h
│   ├── 2012-DEMON/
│   │   ├── .gitignore
│   │   ├── Demon.py
│   │   ├── HDemon.py
│   │   ├── change_input_format.py
│   │   └── test_networkx.py
│   ├── 2012-Fast-Clique-Percolation/
│   │   ├── ReadMe.md
│   │   ├── src_original/
│   │   │   ├── Makefile
│   │   │   ├── README
│   │   │   ├── cliques.cpp
│   │   │   ├── cliques.hpp
│   │   │   ├── cmdline.c
│   │   │   ├── cmdline.ggo
│   │   │   ├── cmdline.h
│   │   │   ├── gpl.txt
│   │   │   ├── graph/
│   │   │   │   ├── bloom.cpp
│   │   │   │   ├── bloom.hpp
│   │   │   │   ├── graph.cpp
│   │   │   │   ├── graph.hpp
│   │   │   │   ├── loading.cpp
│   │   │   │   ├── loading.hpp
│   │   │   │   ├── network.cpp
│   │   │   │   ├── network.hpp
│   │   │   │   ├── saving.cpp
│   │   │   │   ├── saving.hpp
│   │   │   │   ├── strings.cpp
│   │   │   │   ├── strings.hpp
│   │   │   │   ├── weights.cpp
│   │   │   │   └── weights.hpp
│   │   │   ├── percolateCliques.cpp
│   │   │   └── pp.hpp
│   │   ├── src_python/
│   │   │   ├── clique_percoaltion_naive.py
│   │   │   └── clique_percolation_fast.py
│   │   └── src_refactor/
│   │       ├── CMakeLists.txt
│   │       ├── ReadMe.md
│   │       ├── cliques.cpp
│   │       ├── cliques.hpp
│   │       ├── cmdline.c
│   │       ├── cmdline.ggo
│   │       ├── cmdline.h
│   │       ├── graph/
│   │       │   ├── bloom.cpp
│   │       │   ├── bloom.hpp
│   │       │   ├── graph.cpp
│   │       │   ├── graph.hpp
│   │       │   ├── loading.cpp
│   │       │   ├── loading.hpp
│   │       │   ├── network.cpp
│   │       │   ├── network.hpp
│   │       │   ├── saving.cpp
│   │       │   ├── saving.hpp
│   │       │   ├── strings.cpp
│   │       │   ├── strings.hpp
│   │       │   ├── weights.cpp
│   │       │   └── weights.hpp
│   │       ├── original_doc/
│   │       │   ├── Makefile
│   │       │   ├── README
│   │       │   └── gpl.txt
│   │       ├── percolateCliques.cpp
│   │       └── pp.hpp
│   ├── 2013-MSCD/
│   │   ├── MSCD.xcodeproj/
│   │   │   ├── elemarte.mode1v3
│   │   │   ├── elemarte.pbxuser
│   │   │   ├── project.pbxproj
│   │   │   ├── project.xcworkspace/
│   │   │   │   ├── contents.xcworkspacedata
│   │   │   │   └── xcuserdata/
│   │   │   │       └── elemarte.xcuserdatad/
│   │   │   │           ├── UserInterfaceState.xcuserstate
│   │   │   │           └── WorkspaceSettings.xcsettings
│   │   │   └── xcuserdata/
│   │   │       └── elemarte.xcuserdatad/
│   │   │           ├── xcdebugger/
│   │   │           │   └── Breakpoints.xcbkptlist
│   │   │           └── xcschemes/
│   │   │               ├── MSCD.xcscheme
│   │   │               └── xcschememanagement.plist
│   │   ├── Makefile
│   │   ├── ReadMe.md
│   │   ├── Readme.txt
│   │   ├── analyse.xcodeproj/
│   │   │   ├── elemarte.mode1v3
│   │   │   ├── elemarte.pbxuser
│   │   │   ├── project.pbxproj
│   │   │   ├── project.xcworkspace/
│   │   │   │   ├── contents.xcworkspacedata
│   │   │   │   └── xcuserdata/
│   │   │   │       └── elemarte.xcuserdatad/
│   │   │   │           └── UserInterfaceState.xcuserstate
│   │   │   └── xcuserdata/
│   │   │       └── elemarte.xcuserdatad/
│   │   │           └── xcschemes/
│   │   │               ├── analyse.xcscheme
│   │   │               └── xcschememanagement.plist
│   │   ├── conv.xcodeproj/
│   │   │   ├── elemarte.mode1v3
│   │   │   ├── elemarte.pbxuser
│   │   │   ├── project.pbxproj
│   │   │   ├── project.xcworkspace/
│   │   │   │   ├── contents.xcworkspacedata
│   │   │   │   └── xcuserdata/
│   │   │   │       └── elemarte.xcuserdatad/
│   │   │   │           └── UserInterfaceState.xcuserstate
│   │   │   └── xcuserdata/
│   │   │       └── elemarte.xcuserdatad/
│   │   │           └── xcschemes/
│   │   │               ├── conv.xcscheme
│   │   │               └── xcschememanagement.plist
│   │   ├── examples/
│   │   │   ├── dolphins.edges
│   │   │   ├── dolphins.qs
│   │   │   ├── dolphins_0.1.coms
│   │   │   ├── dolphins_0.2.coms
│   │   │   ├── dolphins_0.3.coms
│   │   │   ├── dolphins_0.4.coms
│   │   │   ├── dolphins_0.5.coms
│   │   │   ├── dolphins_0.6.coms
│   │   │   ├── dolphins_0.7.coms
│   │   │   ├── dolphins_0.8.coms
│   │   │   ├── dolphins_0.9.coms
│   │   │   ├── dolphins_0.coms
│   │   │   ├── dolphins_1.1.coms
│   │   │   ├── dolphins_1.2.coms
│   │   │   ├── dolphins_1.3.coms
│   │   │   ├── dolphins_1.4.coms
│   │   │   ├── dolphins_1.5.coms
│   │   │   ├── dolphins_1.6.coms
│   │   │   ├── dolphins_1.7.coms
│   │   │   ├── dolphins_1.8.coms
│   │   │   ├── dolphins_1.87905e-14.coms
│   │   │   ├── dolphins_1.9.coms
│   │   │   ├── dolphins_1.coms
│   │   │   ├── dolphins_10.coms
│   │   │   ├── dolphins_2.1.coms
│   │   │   ├── dolphins_2.2.coms
│   │   │   ├── dolphins_2.3.coms
│   │   │   ├── dolphins_2.4.coms
│   │   │   ├── dolphins_2.5.coms
│   │   │   ├── dolphins_2.6.coms
│   │   │   ├── dolphins_2.7.coms
│   │   │   ├── dolphins_2.8.coms
│   │   │   ├── dolphins_2.9.coms
│   │   │   ├── dolphins_2.coms
│   │   │   ├── dolphins_3.1.coms
│   │   │   ├── dolphins_3.2.coms
│   │   │   ├── dolphins_3.3.coms
│   │   │   ├── dolphins_3.4.coms
│   │   │   ├── dolphins_3.5.coms
│   │   │   ├── dolphins_3.6.coms
│   │   │   ├── dolphins_3.7.coms
│   │   │   ├── dolphins_3.8.coms
│   │   │   ├── dolphins_3.9.coms
│   │   │   ├── dolphins_3.coms
│   │   │   ├── dolphins_4.1.coms
│   │   │   ├── dolphins_4.2.coms
│   │   │   ├── dolphins_4.3.coms
│   │   │   ├── dolphins_4.4.coms
│   │   │   ├── dolphins_4.5.coms
│   │   │   ├── dolphins_4.6.coms
│   │   │   ├── dolphins_4.7.coms
│   │   │   ├── dolphins_4.8.coms
│   │   │   ├── dolphins_4.9.coms
│   │   │   ├── dolphins_4.coms
│   │   │   ├── dolphins_5.1.coms
│   │   │   ├── dolphins_5.2.coms
│   │   │   ├── dolphins_5.3.coms
│   │   │   ├── dolphins_5.4.coms
│   │   │   ├── dolphins_5.5.coms
│   │   │   ├── dolphins_5.6.coms
│   │   │   ├── dolphins_5.7.coms
│   │   │   ├── dolphins_5.8.coms
│   │   │   ├── dolphins_5.9.coms
│   │   │   ├── dolphins_5.coms
│   │   │   ├── dolphins_6.1.coms
│   │   │   ├── dolphins_6.2.coms
│   │   │   ├── dolphins_6.3.coms
│   │   │   ├── dolphins_6.4.coms
│   │   │   ├── dolphins_6.5.coms
│   │   │   ├── dolphins_6.6.coms
│   │   │   ├── dolphins_6.7.coms
│   │   │   ├── dolphins_6.8.coms
│   │   │   ├── dolphins_6.9.coms
│   │   │   ├── dolphins_6.coms
│   │   │   ├── dolphins_7.1.coms
│   │   │   ├── dolphins_7.2.coms
│   │   │   ├── dolphins_7.3.coms
│   │   │   ├── dolphins_7.4.coms
│   │   │   ├── dolphins_7.5.coms
│   │   │   ├── dolphins_7.6.coms
│   │   │   ├── dolphins_7.7.coms
│   │   │   ├── dolphins_7.8.coms
│   │   │   ├── dolphins_7.9.coms
│   │   │   ├── dolphins_7.coms
│   │   │   ├── dolphins_8.1.coms
│   │   │   ├── dolphins_8.2.coms
│   │   │   ├── dolphins_8.3.coms
│   │   │   ├── dolphins_8.4.coms
│   │   │   ├── dolphins_8.5.coms
│   │   │   ├── dolphins_8.6.coms
│   │   │   ├── dolphins_8.7.coms
│   │   │   ├── dolphins_8.8.coms
│   │   │   ├── dolphins_8.9.coms
│   │   │   ├── dolphins_8.coms
│   │   │   ├── dolphins_9.1.coms
│   │   │   ├── dolphins_9.2.coms
│   │   │   ├── dolphins_9.3.coms
│   │   │   ├── dolphins_9.4.coms
│   │   │   ├── dolphins_9.5.coms
│   │   │   ├── dolphins_9.6.coms
│   │   │   ├── dolphins_9.7.coms
│   │   │   ├── dolphins_9.8.coms
│   │   │   ├── dolphins_9.9.coms
│   │   │   ├── dolphins_9.coms
│   │   │   ├── football.edges
│   │   │   ├── karate.edges
│   │   │   └── miserables.edges
│   │   ├── speedtest.xcodeproj/
│   │   │   ├── project.pbxproj
│   │   │   ├── project.xcworkspace/
│   │   │   │   ├── contents.xcworkspacedata
│   │   │   │   └── xcuserdata/
│   │   │   │       └── elemarte.xcuserdatad/
│   │   │   │           └── UserInterfaceState.xcuserstate
│   │   │   └── xcuserdata/
│   │   │       └── elemarte.xcuserdatad/
│   │   │           ├── xcdebugger/
│   │   │           │   └── Breakpoints.xcbkptlist
│   │   │           └── xcschemes/
│   │   │               ├── speedtest.xcscheme
│   │   │               └── xcschememanagement.plist
│   │   └── src/
│   │       ├── analyse_main.cpp
│   │       ├── config.h
│   │       ├── conv_main.cpp
│   │       ├── mscd/
│   │       │   ├── alg/
│   │       │   │   ├── mscd_afg.cpp
│   │       │   │   ├── mscd_afg.h
│   │       │   │   ├── mscd_algorithm.h
│   │       │   │   ├── mscd_hslsw.cpp
│   │       │   │   ├── mscd_hslsw.h
│   │       │   │   ├── mscd_lfk.cpp
│   │       │   │   ├── mscd_lfk.h
│   │       │   │   ├── mscd_lfk2.cpp
│   │       │   │   ├── mscd_lfk2.h
│   │       │   │   ├── mscd_rb.cpp
│   │       │   │   ├── mscd_rb.h
│   │       │   │   ├── mscd_rn.cpp
│   │       │   │   ├── mscd_rn.h
│   │       │   │   ├── mscd_so.cpp
│   │       │   │   ├── mscd_so.h
│   │       │   │   ├── mscd_som.cpp
│   │       │   │   └── mscd_som.h
│   │       │   ├── ds/
│   │       │   │   ├── communities.h
│   │       │   │   └── graph.h
│   │       │   └── io/
│   │       │       ├── in/
│   │       │       │   ├── community_list_reader.cpp
│   │       │       │   ├── community_list_reader.h
│   │       │       │   ├── community_reader.h
│   │       │       │   ├── edge_list_graph_reader.cpp
│   │       │       │   ├── edge_list_graph_reader.h
│   │       │       │   ├── graph_reader copy.h
│   │       │       │   ├── graph_reader.h
│   │       │       │   ├── lf_community_reader.cpp
│   │       │       │   ├── lf_community_reader.h
│   │       │       │   ├── pajek_community_reader.cpp
│   │       │       │   ├── pajek_community_reader.h
│   │       │       │   ├── pajek_graph_reader.cpp
│   │       │       │   └── pajek_graph_reader.h
│   │       │       └── out/
│   │       │           ├── community_list_writer.cpp
│   │       │           ├── community_list_writer.h
│   │       │           ├── community_writer.h
│   │       │           ├── edge_list_graph_writer.cpp
│   │       │           ├── edge_list_graph_writer.h
│   │       │           ├── graph_writer.h
│   │       │           ├── lf_community_writer.cpp
│   │       │           ├── lf_community_writer.h
│   │       │           ├── pajek_community_writer.cpp
│   │       │           ├── pajek_community_writer.h
│   │       │           ├── pajek_graph_writer.cpp
│   │       │           └── pajek_graph_writer.h
│   │       ├── mscd_main.cpp
│   │       ├── speedtest_main.cpp
│   │       └── toolkit/
│   │           ├── atomic_set.h
│   │           ├── nmi.h
│   │           ├── registry.h
│   │           ├── tokeniser.cpp
│   │           ├── tokeniser.h
│   │           └── tools.h
│   ├── 2013-SVINET/
│   │   ├── ReadMe.md
│   │   ├── src-cmake/
│   │   │   ├── authors_doc/
│   │   │   │   ├── AUTHORS
│   │   │   │   ├── COPYING
│   │   │   │   ├── ChangeLog
│   │   │   │   ├── NEWS
│   │   │   │   ├── README
│   │   │   │   ├── README.md
│   │   │   │   ├── aclocal.m4
│   │   │   │   ├── detailed_readme.txt
│   │   │   │   └── validation-test-file-options-patch.txt
│   │   │   ├── example/
│   │   │   │   ├── LFR-ground-truth-n1000-k28.txt
│   │   │   │   ├── LFR-network-n1000-k28.txt
│   │   │   │   ├── assort-75-4.txt
│   │   │   │   ├── ca-AstroPh.csv
│   │   │   │   ├── n1000-k28-LFR-linksampling.tgz
│   │   │   │   ├── n17903-k20-mmsb-linksampling.tgz
│   │   │   │   └── n75-k4-mmsb-batch.tgz
│   │   │   ├── patches/
│   │   │   │   └── ammsb1.patch
│   │   │   └── src/
│   │   │       ├── CMakeLists.txt
│   │   │       ├── collection/
│   │   │       │   ├── fastqueue.hh
│   │   │       │   ├── matrix.hh
│   │   │       │   └── tsqueue.hh
│   │   │       ├── community.hh
│   │   │       ├── env.hh
│   │   │       ├── fastamm.cc
│   │   │       ├── fastamm.hh
│   │   │       ├── fastamm2.cc
│   │   │       ├── fastamm2.hh
│   │   │       ├── fastinit.cc
│   │   │       ├── fastinit.hh
│   │   │       ├── linksampling.cc
│   │   │       ├── linksampling.hh
│   │   │       ├── log.cc
│   │   │       ├── log.hh
│   │   │       ├── main.cc
│   │   │       ├── mmsbgen.cc
│   │   │       ├── mmsbgen.hh
│   │   │       ├── mmsbinfer.cc
│   │   │       ├── mmsbinfer.hh
│   │   │       ├── mmsbinferorig.cc
│   │   │       ├── mmsbinferorig.hh
│   │   │       ├── mmsborig.cc
│   │   │       ├── mmsborig.hh
│   │   │       ├── network.cc
│   │   │       ├── network.hh
│   │   │       ├── sbm.cc
│   │   │       ├── sbm.hh
│   │   │       ├── thread.cc
│   │   │       └── thread.hh
│   │   └── svinet-master/
│   │       ├── AUTHORS
│   │       ├── COPYING
│   │       ├── ChangeLog
│   │       ├── INSTALL
│   │       ├── Makefile.am
│   │       ├── Makefile.in
│   │       ├── NEWS
│   │       ├── README
│   │       ├── README.md
│   │       ├── aclocal.m4
│   │       ├── config.guess
│   │       ├── config.h.in
│   │       ├── config.sub
│   │       ├── configure
│   │       ├── configure.ac
│   │       ├── depcomp
│   │       ├── detailed_readme.txt
│   │       ├── example/
│   │       │   ├── LFR-ground-truth-n1000-k28.txt
│   │       │   ├── LFR-network-n1000-k28.txt
│   │       │   ├── assort-75-4.txt
│   │       │   ├── ca-AstroPh.csv
│   │       │   ├── n1000-k28-LFR-linksampling.tgz
│   │       │   ├── n17903-k20-mmsb-linksampling.tgz
│   │       │   └── n75-k4-mmsb-batch.tgz
│   │       ├── install-sh
│   │       ├── missing
│   │       ├── mkinstalldirs
│   │       ├── patches/
│   │       │   └── ammsb1.patch
│   │       ├── src/
│   │       │   ├── Makefile.am
│   │       │   ├── Makefile.in
│   │       │   ├── community.hh
│   │       │   ├── env.hh
│   │       │   ├── fastamm.cc
│   │       │   ├── fastamm.hh
│   │       │   ├── fastamm2.cc
│   │       │   ├── fastamm2.hh
│   │       │   ├── fastinit.cc
│   │       │   ├── fastinit.hh
│   │       │   ├── fastqueue.hh
│   │       │   ├── linksampling.cc
│   │       │   ├── linksampling.hh
│   │       │   ├── log.cc
│   │       │   ├── log.hh
│   │       │   ├── main.cc
│   │       │   ├── matrix.hh
│   │       │   ├── mmsbgen.cc
│   │       │   ├── mmsbgen.hh
│   │       │   ├── mmsbinfer.cc
│   │       │   ├── mmsbinfer.hh
│   │       │   ├── mmsbinferorig.cc
│   │       │   ├── mmsbinferorig.hh
│   │       │   ├── mmsborig.cc
│   │       │   ├── mmsborig.hh
│   │       │   ├── network.cc
│   │       │   ├── network.hh
│   │       │   ├── sbm.cc
│   │       │   ├── sbm.hh
│   │       │   ├── thread.cc
│   │       │   ├── thread.hh
│   │       │   └── tsqueue.hh
│   │       └── validation-test-file-options-patch.txt
│   ├── 2013-Seed-Set-Expansion/
│   │   ├── ReadMe.md
│   │   ├── dependencies/
│   │   │   ├── GraclusSeeds/
│   │   │   │   └── graclus1.2/
│   │   │   │       ├── Makefile
│   │   │   │       ├── Makefile.in
│   │   │   │       ├── README_Graclus
│   │   │   │       ├── graclus
│   │   │   │       ├── libmetis.a
│   │   │   │       ├── libmultilevel.a
│   │   │   │       ├── matlab/
│   │   │   │       │   ├── ComputeCenterNodes.m
│   │   │   │       │   ├── ComputeDistances.m
│   │   │   │       │   ├── GraclusImageSegmentation.m
│   │   │   │       │   ├── discretisation.m
│   │   │   │       │   ├── discretisationEigenVectorData.asv
│   │   │   │       │   ├── discretisationEigenVectorData.m
│   │   │   │       │   ├── displayLatex.m
│   │   │   │       │   ├── eigs2.m
│   │   │   │       │   ├── get_hrc_graclus_seeds.m
│   │   │   │       │   ├── graclus.m
│   │   │   │       │   ├── graclus_compile_script.m
│   │   │   │       │   ├── graclus_mex.cpp
│   │   │   │       │   ├── graclus_mex.o
│   │   │   │       │   ├── hrcGraclus.m
│   │   │   │       │   ├── io.cpp
│   │   │   │       │   ├── io.o
│   │   │   │       │   ├── mlkkm.cpp
│   │   │   │       │   ├── mlkkm.o
│   │   │   │       │   ├── ncut.asv
│   │   │   │       │   ├── ncut.m
│   │   │   │       │   ├── ncutW.asv
│   │   │   │       │   ├── ncutW.m
│   │   │   │       │   ├── readMetis.m
│   │   │   │       │   ├── wkkm.cpp
│   │   │   │       │   └── wkkm.o
│   │   │   │       ├── metisLib/
│   │   │   │       │   ├── Makefile
│   │   │   │       │   ├── balance.c
│   │   │   │       │   ├── balance.o
│   │   │   │       │   ├── bucketsort.c
│   │   │   │       │   ├── bucketsort.o
│   │   │   │       │   ├── ccgraph.c
│   │   │   │       │   ├── ccgraph.o
│   │   │   │       │   ├── coarsen.c
│   │   │   │       │   ├── coarsen.o
│   │   │   │       │   ├── compress.c
│   │   │   │       │   ├── compress.o
│   │   │   │       │   ├── debug.c
│   │   │   │       │   ├── debug.o
│   │   │   │       │   ├── defs.h
│   │   │   │       │   ├── estmem.c
│   │   │   │       │   ├── estmem.o
│   │   │   │       │   ├── fm.c
│   │   │   │       │   ├── fm.o
│   │   │   │       │   ├── fortran.c
│   │   │   │       │   ├── fortran.o
│   │   │   │       │   ├── frename.c
│   │   │   │       │   ├── frename.o
│   │   │   │       │   ├── graph.c
│   │   │   │       │   ├── graph.o
│   │   │   │       │   ├── initpart.c
│   │   │   │       │   ├── initpart.o
│   │   │   │       │   ├── kmetis.c
│   │   │   │       │   ├── kmetis.o
│   │   │   │       │   ├── kvmetis.c
│   │   │   │       │   ├── kvmetis.o
│   │   │   │       │   ├── kwayfm.c
│   │   │   │       │   ├── kwayfm.o
│   │   │   │       │   ├── kwayrefine.c
│   │   │   │       │   ├── kwayrefine.o
│   │   │   │       │   ├── kwayvolfm.c
│   │   │   │       │   ├── kwayvolfm.o
│   │   │   │       │   ├── kwayvolrefine.c
│   │   │   │       │   ├── kwayvolrefine.o
│   │   │   │       │   ├── macros.h
│   │   │   │       │   ├── match.c
│   │   │   │       │   ├── match.o
│   │   │   │       │   ├── mbalance.c
│   │   │   │       │   ├── mbalance.o
│   │   │   │       │   ├── mbalance2.c
│   │   │   │       │   ├── mbalance2.o
│   │   │   │       │   ├── mcoarsen.c
│   │   │   │       │   ├── mcoarsen.o
│   │   │   │       │   ├── memory.c
│   │   │   │       │   ├── memory.o
│   │   │   │       │   ├── mesh.c
│   │   │   │       │   ├── mesh.o
│   │   │   │       │   ├── meshpart.c
│   │   │   │       │   ├── meshpart.o
│   │   │   │       │   ├── metis.h
│   │   │   │       │   ├── mfm.c
│   │   │   │       │   ├── mfm.o
│   │   │   │       │   ├── mfm2.c
│   │   │   │       │   ├── mfm2.o
│   │   │   │       │   ├── mincover.c
│   │   │   │       │   ├── mincover.o
│   │   │   │       │   ├── minitpart.c
│   │   │   │       │   ├── minitpart.o
│   │   │   │       │   ├── minitpart2.c
│   │   │   │       │   ├── minitpart2.o
│   │   │   │       │   ├── mkmetis.c
│   │   │   │       │   ├── mkmetis.o
│   │   │   │       │   ├── mkwayfmh.c
│   │   │   │       │   ├── mkwayfmh.o
│   │   │   │       │   ├── mkwayrefine.c
│   │   │   │       │   ├── mkwayrefine.o
│   │   │   │       │   ├── mmatch.c
│   │   │   │       │   ├── mmatch.o
│   │   │   │       │   ├── mmd.c
│   │   │   │       │   ├── mmd.o
│   │   │   │       │   ├── mpmetis.c
│   │   │   │       │   ├── mpmetis.o
│   │   │   │       │   ├── mrefine.c
│   │   │   │       │   ├── mrefine.o
│   │   │   │       │   ├── mrefine2.c
│   │   │   │       │   ├── mrefine2.o
│   │   │   │       │   ├── mutil.c
│   │   │   │       │   ├── mutil.o
│   │   │   │       │   ├── myqsort.c
│   │   │   │       │   ├── myqsort.o
│   │   │   │       │   ├── ometis.c
│   │   │   │       │   ├── ometis.o
│   │   │   │       │   ├── parmetis.c
│   │   │   │       │   ├── parmetis.o
│   │   │   │       │   ├── pmetis.c
│   │   │   │       │   ├── pmetis.o
│   │   │   │       │   ├── pqueue.c
│   │   │   │       │   ├── pqueue.o
│   │   │   │       │   ├── proto.h
│   │   │   │       │   ├── refine.c
│   │   │   │       │   ├── refine.o
│   │   │   │       │   ├── rename.h
│   │   │   │       │   ├── separator.c
│   │   │   │       │   ├── separator.o
│   │   │   │       │   ├── sfm.c
│   │   │   │       │   ├── sfm.o
│   │   │   │       │   ├── srefine.c
│   │   │   │       │   ├── srefine.o
│   │   │   │       │   ├── stat.c
│   │   │   │       │   ├── stat.o
│   │   │   │       │   ├── struct.h
│   │   │   │       │   ├── subdomains.c
│   │   │   │       │   ├── subdomains.o
│   │   │   │       │   ├── timing.c
│   │   │   │       │   ├── timing.o
│   │   │   │       │   ├── util.c
│   │   │   │       │   └── util.o
│   │   │   │       ├── multilevelLib/
│   │   │   │       │   ├── Makefile
│   │   │   │       │   ├── mlkkm.c
│   │   │   │       │   ├── mlkkm.o
│   │   │   │       │   ├── wkkm.c
│   │   │   │       │   ├── wkkm.o
│   │   │   │       │   ├── wkkm_boundary_only.c
│   │   │   │       │   ├── wkkm_experiment.c
│   │   │   │       │   └── wkkm_old.c
│   │   │   │       └── programs/
│   │   │   │           ├── Makefile
│   │   │   │           ├── graclus.c
│   │   │   │           ├── graclus.o
│   │   │   │           ├── io.c
│   │   │   │           ├── io.h
│   │   │   │           └── io.o
│   │   │   └── matlab_bgl/
│   │   │       ├── .project
│   │   │       ├── @inplace/
│   │   │       │   ├── assign.m
│   │   │       │   ├── display.m
│   │   │       │   ├── double.m
│   │   │       │   ├── end.m
│   │   │       │   ├── inplace.m
│   │   │       │   ├── size.m
│   │   │       │   ├── subsasgn.m
│   │   │       │   └── subsref.m
│   │   │       ├── @ipdouble/
│   │   │       │   └── ipdouble.m
│   │   │       ├── @ipint32/
│   │   │       │   └── ipint32.m
│   │   │       ├── Contents.m
│   │   │       ├── all_shortest_paths.m
│   │   │       ├── astar_search.m
│   │   │       ├── bellman_ford_sp.m
│   │   │       ├── betweenness_centrality.m
│   │   │       ├── bfs.m
│   │   │       ├── biconnected_components.m
│   │   │       ├── boyer_myrvold_planarity_test.m
│   │   │       ├── breadth_first_search.m
│   │   │       ├── chrobak_payne_straight_line_drawing.m
│   │   │       ├── circle_graph_layout.m
│   │   │       ├── clique_graph.m
│   │   │       ├── clustering_coefficients.m
│   │   │       ├── combine_visitors.m
│   │   │       ├── components.m
│   │   │       ├── core_numbers.m
│   │   │       ├── custom/
│   │   │       │   ├── dijkstra_all_sp.m
│   │   │       │   └── path_histogram.m
│   │   │       ├── cycle_graph.m
│   │   │       ├── dag_sp.m
│   │   │       ├── depth_first_search.m
│   │   │       ├── dfs.m
│   │   │       ├── dijkstra_sp.m
│   │   │       ├── doc/
│   │   │       │   ├── changed.txt
│   │   │       │   ├── html/
│   │   │       │   │   ├── changes.html
│   │   │       │   │   ├── core_numbers_example/
│   │   │       │   │   │   └── core_numbers_example.html
│   │   │       │   │   ├── faq.html
│   │   │       │   │   ├── index.html
│   │   │       │   │   ├── new_in_3/
│   │   │       │   │   │   └── new_in_3_0.html
│   │   │       │   │   ├── new_in_4/
│   │   │       │   │   │   └── new_in_4_0.html
│   │   │       │   │   ├── old.html
│   │   │       │   │   ├── planar_graphs/
│   │   │       │   │   │   └── planar_graphs.html
│   │   │       │   │   ├── record_alg/
│   │   │       │   │   │   └── record_alg.html
│   │   │       │   │   ├── red_black/
│   │   │       │   │   │   └── red_black.html
│   │   │       │   │   ├── reweighted_graphs/
│   │   │       │   │   │   └── reweighted_graphs.html
│   │   │       │   │   ├── site.css
│   │   │       │   │   └── style.css
│   │   │       │   ├── mxdom2mbgl-html.xsl
│   │   │       │   └── write_examples_html.m
│   │   │       ├── edge_weight_index.m
│   │   │       ├── edge_weight_vector.m
│   │   │       ├── edmonds_maximum_cardinality_matching.m
│   │   │       ├── edmunds_karp_max_flow.m
│   │   │       ├── erdos_reyni.m
│   │   │       ├── examples/
│   │   │       │   ├── approx_multiway_cut.m
│   │   │       │   ├── bacon_numbers.m
│   │   │       │   ├── bfs_example.m
│   │   │       │   ├── bfs_in_mbgl.m
│   │   │       │   ├── bfs_in_mbgl_efficient.m
│   │   │       │   ├── core_numbers_example.m
│   │   │       │   ├── dfs_example.m
│   │   │       │   ├── edge_index_example.m
│   │   │       │   ├── max_flow_example.m
│   │   │       │   ├── multiway_example.m
│   │   │       │   ├── new_in_3_0.m
│   │   │       │   ├── new_in_4_0.m
│   │   │       │   ├── planar_graphs.m
│   │   │       │   ├── record_alg.m
│   │   │       │   ├── red_black.m
│   │   │       │   └── reweighted_graphs.m
│   │   │       ├── floyd_warshall_all_sp.m
│   │   │       ├── fruchterman_reingold_force_directed_layout.m
│   │   │       ├── graphs/
│   │   │       │   ├── all_shortest_paths_example.mat
│   │   │       │   ├── bfs_example.mat
│   │   │       │   ├── bgl_cities.mat
│   │   │       │   ├── clique-10.mat
│   │   │       │   ├── clr-24-1.mat
│   │   │       │   ├── clr-25-2.mat
│   │   │       │   ├── clr-26-1.mat
│   │   │       │   ├── clr-27-1.mat
│   │   │       │   ├── cores_example.mat
│   │   │       │   ├── cs-stanford.mat
│   │   │       │   ├── dfs_example.mat
│   │   │       │   ├── dominator_tree_example.mat
│   │   │       │   ├── kt-3-2.mat
│   │   │       │   ├── kt-3-7.mat
│   │   │       │   ├── kt-6-23.mat
│   │   │       │   ├── kt-7-2.mat
│   │   │       │   ├── line-7.mat
│   │   │       │   ├── matching_example.mat
│   │   │       │   ├── max_flow_example.mat
│   │   │       │   ├── minnesota.mat
│   │   │       │   ├── padgett-florentine.mat
│   │   │       │   ├── tapir.mat
│   │   │       │   └── tarjan-biconn.mat
│   │   │       ├── grid_graph.m
│   │   │       ├── gursoy_atun_layout.m
│   │   │       ├── indexed_sparse.m
│   │   │       ├── is_kuratowski_graph.m
│   │   │       ├── is_straight_line_drawing.m
│   │   │       ├── johnson_all_sp.m
│   │   │       ├── kamada_kawai_spring_layout.m
│   │   │       ├── kolmogorov_max_flow.m
│   │   │       ├── kruskal_mst.m
│   │   │       ├── kuratowski_subgraph.m
│   │   │       ├── lengauer_tarjan_dominator_tree.m
│   │   │       ├── libmbgl/
│   │   │       │   ├── ccfiles.sh
│   │   │       │   ├── compile-linux-32.sh
│   │   │       │   ├── compile-linux-64-large.sh
│   │   │       │   ├── compile-linux-64.sh
│   │   │       │   ├── compile-macosx-intel-32.sh
│   │   │       │   ├── compile-macosx-ppc-32.sh
│   │   │       │   ├── compile-win32.bat
│   │   │       │   ├── compile-win64.bat
│   │   │       │   ├── components.cc
│   │   │       │   ├── crm_graph.hpp
│   │   │       │   ├── include/
│   │   │       │   │   ├── matlab_bgl.h
│   │   │       │   │   └── matlab_bgl_types.h
│   │   │       │   ├── layouts.cc
│   │   │       │   ├── libmbgl.sln
│   │   │       │   ├── libmbgl.vcproj
│   │   │       │   ├── libmbgl_test/
│   │   │       │   │   ├── Makefile
│   │   │       │   │   ├── fr_layout_test.cc
│   │   │       │   │   ├── layout_funcs_test.cc
│   │   │       │   │   ├── libmbgl_funcs_test.cc
│   │   │       │   │   ├── libmbgl_funcs_test.h
│   │   │       │   │   ├── libmbgl_test.cc
│   │   │       │   │   ├── libmbgl_test.vcproj
│   │   │       │   │   ├── planar_funcs_test.cc
│   │   │       │   │   ├── planar_is_straight_line_test.cc
│   │   │       │   │   ├── planar_ksubgraph_test.cc
│   │   │       │   │   ├── property_map_test.cc
│   │   │       │   │   ├── simple_prop_map_test.cc
│   │   │       │   │   ├── simple_prop_map_test_2.cc
│   │   │       │   │   ├── simple_prop_map_test_3.cc
│   │   │       │   │   └── simple_prop_map_test_4.cc
│   │   │       │   ├── libmbgl_util.hpp
│   │   │       │   ├── max_flow.cc
│   │   │       │   ├── orderings.cc
│   │   │       │   ├── planar.cc
│   │   │       │   ├── searches.cc
│   │   │       │   ├── shortest_path.cc
│   │   │       │   ├── spanning_trees.cc
│   │   │       │   ├── statistics.cc
│   │   │       │   ├── stop_visitors.hpp
│   │   │       │   ├── visitor_macros.hpp
│   │   │       │   └── yasmic/
│   │   │       │       ├── .sconsign
│   │   │       │       ├── bgl_kcore.hpp
│   │   │       │       ├── binary_ifstream_graph.hpp
│   │   │       │       ├── binary_ifstream_matrix.hpp
│   │   │       │       ├── bind_utility.hpp
│   │   │       │       ├── boost_mod/
│   │   │       │       │   ├── .sconsign
│   │   │       │       │   ├── bellman_ford_shortest_paths.hpp
│   │   │       │       │   ├── betweenness_centrality.hpp
│   │   │       │       │   ├── chrobak_payne_drawing.hpp
│   │   │       │       │   ├── core_numbers.hpp
│   │   │       │       │   ├── floyd_warshall_shortest.hpp
│   │   │       │       │   ├── fruchterman_reingold.hpp
│   │   │       │       │   ├── gzip.hpp
│   │   │       │       │   ├── integer_extra.hpp
│   │   │       │       │   ├── is_straight_line_drawing.hpp
│   │   │       │       │   ├── johnson_all_pairs_shortest.hpp
│   │   │       │       │   ├── kolmogorov_max_flow.hpp
│   │   │       │       │   ├── kruskal_min_spanning_tree.hpp
│   │   │       │       │   └── zlib.cpp
│   │   │       │       ├── bvgraph_matrix.hpp
│   │   │       │       ├── cluto_ifstream_matrix.hpp
│   │   │       │       ├── compressed_row_matrix.hpp
│   │   │       │       ├── compressed_row_matrix_graph.hpp
│   │   │       │       ├── generic_matrix_operations.hpp
│   │   │       │       ├── graph_ifstream_matrix.hpp
│   │   │       │       ├── ifstream_as_matrix.hpp
│   │   │       │       ├── ifstream_matrix.hpp
│   │   │       │       ├── indexed_list.hpp
│   │   │       │       ├── indexed_list.old.hpp
│   │   │       │       ├── indexed_list_as_graph.hpp
│   │   │       │       ├── istream_as_matrix.hpp
│   │   │       │       ├── iterator_utility.hpp
│   │   │       │       ├── matrix_row_col_graph.hpp
│   │   │       │       ├── nonzero_union.hpp
│   │   │       │       ├── simple_csr_matrix.hpp
│   │   │       │       ├── simple_csr_matrix_as_graph.hpp
│   │   │       │       ├── simple_row_and_column_matrix.hpp
│   │   │       │       ├── simple_row_and_column_matrix_as_graph.hpp
│   │   │       │       ├── smatrix_traits.hpp
│   │   │       │       ├── transpose_matrix.hpp
│   │   │       │       ├── tuple_utility.hpp
│   │   │       │       ├── undir_simple_csr_matrix.hpp
│   │   │       │       ├── undir_simple_csr_matrix_as_graph.hpp
│   │   │       │       ├── util/
│   │   │       │       │   ├── .sconsign
│   │   │       │       │   ├── crm_matrix.hpp
│   │   │       │       │   ├── filtered_matrix.hpp
│   │   │       │       │   ├── load_crm_graph.hpp
│   │   │       │       │   ├── load_crm_matrix.hpp
│   │   │       │       │   ├── write_matrix.hpp
│   │   │       │       │   └── write_petsc_matrix.hpp
│   │   │       │       ├── verbose_util.hpp
│   │   │       │       ├── yasmic.cbp
│   │   │       │       ├── yasmic.layout
│   │   │       │       └── yasmic.vcproj
│   │   │       ├── make_biconnected_planar.m
│   │   │       ├── make_connected.m
│   │   │       ├── make_maximal_planar.m
│   │   │       ├── matching.m
│   │   │       ├── max_flow.m
│   │   │       ├── maximal_matching.m
│   │   │       ├── mst.m
│   │   │       ├── num_edges.m
│   │   │       ├── num_vertices.m
│   │   │       ├── path_from_pred.m
│   │   │       ├── planar_canonical_ordering.m
│   │   │       ├── prim_mst.m
│   │   │       ├── private/
│   │   │       │   ├── astar_search_mex.c
│   │   │       │   ├── betweenness_centrality_mex.c
│   │   │       │   ├── bfs_dfs_vis_mex.c
│   │   │       │   ├── bfs_mex.c
│   │   │       │   ├── biconnected_components_mex.c
│   │   │       │   ├── check_matlab_bgl.m
│   │   │       │   ├── clustering_coefficients_mex.c
│   │   │       │   ├── common_functions.h
│   │   │       │   ├── common_macros.h
│   │   │       │   ├── compile.m
│   │   │       │   ├── components_mex.c
│   │   │       │   ├── core_numbers_mex.c
│   │   │       │   ├── dfs_mex.c
│   │   │       │   ├── dominator_tree_mex.c
│   │   │       │   ├── expand_macros.h
│   │   │       │   ├── fruchterman_reingold_mex.c
│   │   │       │   ├── get_matlab_bgl_options.m
│   │   │       │   ├── gursoy_atun_mex.c
│   │   │       │   ├── kamada_kawai_spring_layout_mex.c
│   │   │       │   ├── matching_mex.c
│   │   │       │   ├── matlab_bgl_all_sp_mex.c
│   │   │       │   ├── matlab_bgl_sp_mex.c
│   │   │       │   ├── max_flow_mex.c
│   │   │       │   ├── merge_options.m
│   │   │       │   ├── merge_structs.m
│   │   │       │   ├── mst_mex.c
│   │   │       │   ├── path_from_pred_mex.c
│   │   │       │   ├── planar_drawing_mex.c
│   │   │       │   ├── planar_edges_mex.c
│   │   │       │   ├── planar_test_mex.c
│   │   │       │   ├── test_matching_mex.c
│   │   │       │   ├── todo.m
│   │   │       │   ├── todo_3_0_release.m
│   │   │       │   ├── topological_order_mex.c
│   │   │       │   └── visitor_macros.h
│   │   │       ├── push_relabel_max_flow.m
│   │   │       ├── random_graph_layout.m
│   │   │       ├── set_matlab_bgl_default.m
│   │   │       ├── shortest_paths.m
│   │   │       ├── star_graph.m
│   │   │       ├── test/
│   │   │       │   ├── assert.m
│   │   │       │   ├── rtest_1.m
│   │   │       │   ├── rtest_2.m
│   │   │       │   ├── rtest_3_cojocaru.m
│   │   │       │   ├── rtest_5_henderson.m
│   │   │       │   ├── rtest_6.m
│   │   │       │   ├── rtest_7_karsi.m
│   │   │       │   ├── rtest_all.m
│   │   │       │   ├── test_all.m
│   │   │       │   ├── test_benchmark.m
│   │   │       │   ├── test_breadth_first_search.m
│   │   │       │   ├── test_components.m
│   │   │       │   ├── test_depth_first_search.m
│   │   │       │   ├── test_examples.m
│   │   │       │   ├── test_layouts.m
│   │   │       │   ├── test_main.m
│   │   │       │   ├── test_planar.m
│   │   │       │   ├── test_searches.m
│   │   │       │   ├── test_shortest_paths.m
│   │   │       │   ├── test_spanning_trees.m
│   │   │       │   ├── test_statistics.m
│   │   │       │   └── test_trivial.m
│   │   │       ├── test_dag.m
│   │   │       ├── test_matching.m
│   │   │       ├── test_planar_graph.m
│   │   │       ├── topological_order.m
│   │   │       ├── tree_from_pred.m
│   │   │       └── wheel_graph.m
│   │   └── src/
│   │       ├── Assign_bi.m
│   │       ├── add_extra_community_data.m
│   │       ├── biconncore.m
│   │       ├── compile.m
│   │       ├── cutcond_mex.cc
│   │       ├── evaluate_clusters.m
│   │       ├── filter_community_conductance.m
│   │       ├── flip_C.m
│   │       ├── graphprep.m
│   │       ├── growclusters.m
│   │       ├── largest_component.m
│   │       ├── localEgoSeeds.m
│   │       ├── merge_community_data.m
│   │       ├── neighborhoodmin.m
│   │       ├── nise.m
│   │       ├── pprgrow.m
│   │       ├── pprgrow_mex.cc
│   │       ├── seed_report_expand.m
│   │       ├── spHubSeeds.m
│   │       ├── triangleclusters.m
│   │       ├── triangleclusters_mex.cc
│   │       ├── vpprgrow.m
│   │       └── vpprgrow_mex.cc
│   ├── 2014-Heat-Kernel/
│   │   ├── ReadMe.md
│   │   ├── authors_original_files/
│   │   │   ├── data/
│   │   │   │   ├── amazon.mat
│   │   │   │   ├── four_clusters.smat
│   │   │   │   └── netscience-cc.smat
│   │   │   ├── experiments/
│   │   │   │   ├── chirikov/
│   │   │   │   │   ├── chirikov_example.m
│   │   │   │   │   ├── chirikov_operator.m
│   │   │   │   │   ├── compile.m
│   │   │   │   │   ├── imwrite_scaled.m
│   │   │   │   │   └── pprgrow_mex.cc
│   │   │   │   ├── experimenthkgrow.m
│   │   │   │   ├── experimentpprgrow.m
│   │   │   │   ├── ground_truth/
│   │   │   │   │   ├── amazoncommunity.m
│   │   │   │   │   ├── dblpcommunity.m
│   │   │   │   │   ├── friendstercommunity.m
│   │   │   │   │   ├── ljournalcommunity.m
│   │   │   │   │   ├── orkutcommunity.m
│   │   │   │   │   └── youtubecommunity.m
│   │   │   │   ├── heavyhood.m
│   │   │   │   ├── heavyseed.m
│   │   │   │   ├── heavytwitter.m
│   │   │   │   ├── pathweights_figure.m
│   │   │   │   ├── pprfriendster.m
│   │   │   │   ├── pprheavytwitter.m
│   │   │   │   ├── pprljournal.m
│   │   │   │   ├── pprtwitter.m
│   │   │   │   ├── randhood.m
│   │   │   │   ├── randseed.m
│   │   │   │   ├── set_figure_size.m
│   │   │   │   ├── subplot3.m
│   │   │   │   ├── trials_friendster.m
│   │   │   │   ├── trials_hkgrow.m
│   │   │   │   ├── trials_ljournal.m
│   │   │   │   ├── trials_pprgrow.m
│   │   │   │   └── trials_twitter.m
│   │   │   ├── plotting/
│   │   │   │   ├── conductances.m
│   │   │   │   ├── plotconductances.m
│   │   │   │   ├── plotruntimes.m
│   │   │   │   ├── runtimes.m
│   │   │   │   └── twitcondvsclust.m
│   │   │   ├── ppr_src/
│   │   │   │   ├── compile.m
│   │   │   │   ├── pprgrow.m
│   │   │   │   └── pprgrow_mex.cc
│   │   │   └── src/
│   │   │       ├── README.md
│   │   │       ├── compile.m
│   │   │       ├── hkgrow.m
│   │   │       ├── hkgrow1.m
│   │   │       ├── hkgrow_mex.cpp
│   │   │       ├── hkgrow_mex_kdd.cpp
│   │   │       ├── load_graph.m
│   │   │       ├── normout.m
│   │   │       ├── readSMAT.m
│   │   │       ├── symmatfriend.m
│   │   │       ├── symmattwit.m
│   │   │       ├── test_hkgrow.m
│   │   │       └── test_hkgrow_mex.m
│   │   ├── src_cpp_matlab/
│   │   │   ├── hkgrow.m
│   │   │   ├── hkgrow1.m
│   │   │   ├── hkgrow_mex.cpp
│   │   │   ├── hkgrow_mex_kdd.cpp
│   │   │   ├── test_hkgrow.m
│   │   │   └── test_hkgrow_mex.m
│   │   ├── src_python/
│   │   │   ├── .gitignore
│   │   │   ├── ReadMe.md
│   │   │   ├── __init__.py
│   │   │   ├── dataset/
│   │   │   │   ├── __init__.py
│   │   │   │   ├── get_data.sh
│   │   │   │   └── graph_eval_script.txt
│   │   │   ├── demo_files/
│   │   │   │   ├── __init__.py
│   │   │   │   ├── gexpmq.py
│   │   │   │   ├── hr_relax.py
│   │   │   │   ├── yche_exp.py
│   │   │   │   └── yche_numerical_linear_algebra_exp.py
│   │   │   └── main_files/
│   │   │       ├── __init__.py
│   │   │       ├── algo_hr_grow.py
│   │   │       ├── algo_ppr.py
│   │   │       └── util_helper.py
│   │   └── yche_refactor/
│   │       ├── CMakeLists.txt
│   │       ├── ReadMe.md
│   │       ├── hkgrow_mex_kdd.cpp
│   │       └── main.cpp
│   └── 2015-LEMON/
│       ├── .gitignore
│       ├── LEMON/
│       │   └── __init__.py
│       ├── LICENSE
│       ├── README.md
│       ├── example/
│       │   └── amazon/
│       │       ├── README
│       │       ├── community
│       │       ├── graph
│       │       └── seed
│       └── python_yche_refactor/
│           ├── eval_ground_truth.txt
│           ├── io_helper.py
│           └── lemon.py
├── Benchmark/
│   └── 2009-LFR-Benchmark/
│       ├── ReadMe.md
│       ├── src_original_cpp/
│       │   ├── ReadMe.md
│       │   ├── binary_networks/
│       │   │   ├── ReadMe.txt
│       │   │   ├── Sources/
│       │   │   │   ├── benchm.cpp
│       │   │   │   ├── cast.cpp
│       │   │   │   ├── cc.cpp
│       │   │   │   ├── combinatorics.cpp
│       │   │   │   ├── histograms.cpp
│       │   │   │   ├── print.cpp
│       │   │   │   ├── random.cpp
│       │   │   │   ├── set_parameters.cpp
│       │   │   │   └── standard_include.cpp
│       │   │   ├── Thanks.txt
│       │   │   └── makefile
│       │   ├── directed_networks/
│       │   │   ├── ReadMe.txt
│       │   │   ├── Sources/
│       │   │   │   ├── benchm.cpp
│       │   │   │   ├── cast.cpp
│       │   │   │   ├── combinatorics.cpp
│       │   │   │   ├── histograms.cpp
│       │   │   │   ├── print.cpp
│       │   │   │   ├── random.cpp
│       │   │   │   ├── set_parameters.cpp
│       │   │   │   └── standard_include.cpp
│       │   │   ├── Thanks.txt
│       │   │   ├── gpl.txt
│       │   │   └── makefile
│       │   ├── hierarchical_bench2_2/
│       │   │   ├── ReadMe.txt
│       │   │   ├── Thanks.txt
│       │   │   ├── gpl.txt
│       │   │   ├── hier_ben_Sources/
│       │   │   │   ├── a.out
│       │   │   │   ├── benchm.cpp
│       │   │   │   ├── binary_benchm.cpp
│       │   │   │   ├── cc.cpp
│       │   │   │   ├── set_parameters.cpp
│       │   │   │   └── standard_package/
│       │   │   │       ├── cast.cpp
│       │   │   │       ├── combinatorics.cpp
│       │   │   │       ├── deque_numeric.cpp
│       │   │   │       ├── histograms.cpp
│       │   │   │       ├── mutual.cpp
│       │   │   │       ├── pajek.cpp
│       │   │   │       ├── partition.cpp
│       │   │   │       ├── print.cpp
│       │   │   │       ├── random.cpp
│       │   │   │       ├── standard_include.cpp
│       │   │   │       └── tabdeg.cpp
│       │   │   └── makefile
│       │   ├── weighted_directed_nets/
│       │   │   ├── ReadMe.txt
│       │   │   ├── Sources/
│       │   │   │   ├── benchm.cpp
│       │   │   │   ├── cast.cpp
│       │   │   │   ├── combinatorics.cpp
│       │   │   │   ├── dir_benchm.cpp
│       │   │   │   ├── histograms.cpp
│       │   │   │   ├── print.cpp
│       │   │   │   ├── random.cpp
│       │   │   │   ├── set_parameters.cpp
│       │   │   │   └── standard_include.cpp
│       │   │   ├── Thanks.txt
│       │   │   ├── benchmark
│       │   │   ├── gpl.txt
│       │   │   └── makefile
│       │   └── weighted_networks/
│       │       ├── ReadMe.txt
│       │       ├── Sources/
│       │       │   ├── Icon_
│       │       │   ├── benchm.cpp
│       │       │   ├── binary_benchm.cpp
│       │       │   ├── cast.cpp
│       │       │   ├── cc.cpp
│       │       │   ├── combinatorics.cpp
│       │       │   ├── histograms.cpp
│       │       │   ├── print.cpp
│       │       │   ├── random.cpp
│       │       │   ├── set_parameters.cpp
│       │       │   └── standard_include.cpp
│       │       ├── Thanks.txt
│       │       ├── gpl.txt
│       │       └── makefile
│       └── src_refactor_cpp/
│           ├── .gitignore
│           ├── CMakeLists.txt
│           ├── ReadMe.md
│           ├── benchmark_gen.py
│           ├── directed_graph/
│           │   ├── CMakeLists.txt
│           │   ├── ReadMe.md
│           │   ├── benchm.cpp
│           │   ├── doc/
│           │   │   ├── ReadMe.txt
│           │   │   ├── Thanks.txt
│           │   │   └── gpl.txt
│           │   ├── set_parameters.cpp
│           │   └── set_parameters.h
│           ├── documents/
│           │   └── ReadMe.md
│           ├── hierarchical_comm_graph/
│           │   ├── CMakeLists.txt
│           │   ├── ReadMe.md
│           │   ├── benchm.cpp
│           │   ├── binary_benchm.cpp
│           │   ├── binary_benchm.h
│           │   ├── doc/
│           │   │   ├── ReadMe.txt
│           │   │   ├── Thanks.txt
│           │   │   ├── gpl.txt
│           │   │   └── makefile
│           │   ├── set_parameters.cpp
│           │   └── set_parameters.h
│           ├── playground/
│           │   ├── CMakeLists.txt
│           │   ├── nmi_usage_demo.cpp
│           │   └── tabdeg_demo.cpp
│           ├── run_undir_gperf.sh
│           ├── run_undir_perf.sh
│           ├── undirected_graph/
│           │   ├── CMakeLists.txt
│           │   ├── ReadMe.md
│           │   ├── benchm.cpp
│           │   ├── doc/
│           │   │   ├── ReadMe.txt
│           │   │   └── Thanks.txt
│           │   ├── set_parameters.cpp
│           │   └── set_parameters.h
│           ├── util/
│           │   ├── cast.cpp
│           │   ├── cast.h
│           │   ├── cc.cpp
│           │   ├── cc.h
│           │   ├── combinatorics.cpp
│           │   ├── combinatorics.h
│           │   ├── histograms.cpp
│           │   ├── histograms.h
│           │   ├── input_output/
│           │   │   ├── tab_degree.cpp
│           │   │   └── tab_degree.h
│           │   ├── metric/
│           │   │   ├── mutual.cpp
│           │   │   └── mutual.h
│           │   ├── pretty_print.h
│           │   ├── random.cpp
│           │   ├── random.h
│           │   └── unused/
│           │       ├── deque_numeric.cpp
│           │       ├── deque_numeric.h
│           │       └── input_output/
│           │           ├── pajek.cpp
│           │           └── partition.cpp
│           ├── weighted_directed_graph/
│           │   ├── CMakeLists.txt
│           │   ├── ReadMe.md
│           │   ├── benchm.cpp
│           │   ├── dir_benchm.cpp
│           │   ├── dir_benchm.h
│           │   ├── doc/
│           │   │   ├── ReadMe.txt
│           │   │   ├── Thanks.txt
│           │   │   ├── gpl.txt
│           │   │   └── makefile
│           │   ├── set_parameters.cpp
│           │   └── set_parameters.h
│           └── weighted_graph/
│               ├── CMakeLists.txt
│               ├── ReadMe.md
│               ├── benchm.cpp
│               ├── binary_benchm.cpp
│               ├── binary_benchm.h
│               ├── doc/
│               │   ├── ReadMe.txt
│               │   ├── Thanks.txt
│               │   └── gpl.txt
│               ├── set_parameters.cpp
│               └── set_parameters.h
├── CONTRIBUTING.md
├── Datasets/
│   ├── ReadMe.md
│   ├── collaboration_edge_list.txt
│   ├── epinions_edge_list.txt
│   ├── facebook_edge_list.txt
│   ├── football_edge_list.txt
│   ├── karate_edge_list.txt
│   ├── slashdot0811_edge_list.txt
│   ├── slashdot0902_edge_list.txt
│   └── wiki_vote_edge_list.txt
├── License.md
├── Metrics/
│   ├── MultiplexNMI-Benchmark/
│   │   ├── MultiplexBenchmark/
│   │   │   ├── ReadMe.txt
│   │   │   ├── Sources/
│   │   │   │   ├── benchm.cpp
│   │   │   │   ├── cast.cpp
│   │   │   │   ├── cc.cpp
│   │   │   │   ├── combinatorics.cpp
│   │   │   │   ├── histograms.cpp
│   │   │   │   ├── print.cpp
│   │   │   │   ├── random.cpp
│   │   │   │   ├── set_parameters.cpp
│   │   │   │   ├── standard_bench.cpp
│   │   │   │   └── standard_include.cpp
│   │   │   ├── Thanks.txt
│   │   │   ├── gpl.txt
│   │   │   └── makefile
│   │   └── MultiplexNMI/
│   │       ├── ReadMe.txt
│   │       ├── clu1
│   │       ├── clu2
│   │       ├── nmi_multiplex.cpp
│   │       └── standard_package/
│   │           ├── assert.cpp
│   │           ├── cast.cpp
│   │           ├── combinatorics.cpp
│   │           ├── deque_numeric.cpp
│   │           ├── histograms.cpp
│   │           ├── map_utilities.cpp
│   │           ├── mutual.cpp
│   │           ├── pajek.cpp
│   │           ├── partition.cpp
│   │           ├── print.cpp
│   │           ├── random.cpp
│   │           ├── standard_include.cpp
│   │           └── tabdeg.cpp
│   ├── ReadMe.md
│   ├── __init__.py
│   ├── analyze_algo_quality.py
│   ├── cis_fb.out
│   ├── facebook_combined.txt
│   ├── metrics/
│   │   ├── __init__.py
│   │   ├── demo_graph.csv
│   │   ├── link_belong_modularity.py
│   │   ├── omega_idx.py
│   │   ├── overlap_nmi.py
│   │   └── util.py
│   ├── mutual3/
│   │   ├── ReadMe.txt
│   │   ├── makefile
│   │   ├── mutual
│   │   ├── mutual3.cpp
│   │   └── standard_package/
│   │       ├── Icon
│   │       ├── cast.cpp
│   │       ├── combinatorics.cpp
│   │       ├── deque_numeric.cpp
│   │       ├── histograms.cpp
│   │       ├── mutual.cpp
│   │       ├── partition.cpp
│   │       ├── print.cpp
│   │       ├── random.cpp
│   │       └── standard_include.cpp
│   └── play_ground/
│       ├── __init__.py
│       └── play_ground.py
├── NonOverlappingCodes/
│   ├── 2005-Markov-Clustering/
│   │   ├── ReadMe.md
│   │   └── mcl-14-137/
│   │       ├── AUTHORS
│   │       ├── COPYING
│   │       ├── ChangeLog
│   │       ├── INSTALL
│   │       ├── LICENSE
│   │       ├── Makefile.am
│   │       ├── Makefile.in
│   │       ├── NEWS
│   │       ├── README
│   │       ├── THANKS
│   │       ├── TODO
│   │       ├── VERSION
│   │       ├── acinclude.m4
│   │       ├── aclocal.m4
│   │       ├── autofoo/
│   │       │   ├── config.guess
│   │       │   ├── config.sub
│   │       │   ├── depcomp
│   │       │   ├── install-sh
│   │       │   └── missing
│   │       ├── bootstrap
│   │       ├── config.h.in
│   │       ├── configure
│   │       ├── configure.ac
│   │       ├── configure.ac.in
│   │       ├── doc/
│   │       │   ├── Makefile.am
│   │       │   ├── Makefile.in
│   │       │   ├── clm.1
│   │       │   ├── clm.azm
│   │       │   ├── clm.html
│   │       │   ├── clm.ps
│   │       │   ├── clmclose.1
│   │       │   ├── clmclose.azm
│   │       │   ├── clmclose.html
│   │       │   ├── clmclose.ps
│   │       │   ├── clmdist.1
│   │       │   ├── clmdist.azm
│   │       │   ├── clmdist.html
│   │       │   ├── clmdist.ps
│   │       │   ├── clmformat.1
│   │       │   ├── clmformat.azm
│   │       │   ├── clmformat.html
│   │       │   ├── clmformat.ps
│   │       │   ├── clmimac.1
│   │       │   ├── clmimac.azm
│   │       │   ├── clmimac.html
│   │       │   ├── clmimac.ps
│   │       │   ├── clminfo.1
│   │       │   ├── clminfo.azm
│   │       │   ├── clminfo.html
│   │       │   ├── clminfo.ps
│   │       │   ├── clminfo2.1
│   │       │   ├── clminfo2.azm
│   │       │   ├── clminfo2.html
│   │       │   ├── clminfo2.ps
│   │       │   ├── clmmate.1
│   │       │   ├── clmmate.azm
│   │       │   ├── clmmate.html
│   │       │   ├── clmmate.ps
│   │       │   ├── clmmeet.1
│   │       │   ├── clmmeet.azm
│   │       │   ├── clmmeet.html
│   │       │   ├── clmmeet.ps
│   │       │   ├── clmoptics.1
│   │       │   ├── clmoptics.azm
│   │       │   ├── clmoptics.html
│   │       │   ├── clmoptics.ps
│   │       │   ├── clmorder.1
│   │       │   ├── clmorder.azm
│   │       │   ├── clmorder.html
│   │       │   ├── clmorder.ps
│   │       │   ├── clmprotocols.5
│   │       │   ├── clmprotocols.azm
│   │       │   ├── clmprotocols.html
│   │       │   ├── clmprotocols.ps
│   │       │   ├── clmprotocols2.5
│   │       │   ├── clmprotocols2.azm
│   │       │   ├── clmprotocols2.html
│   │       │   ├── clmprotocols2.ps
│   │       │   ├── clmresidue.1
│   │       │   ├── clmresidue.azm
│   │       │   ├── clmresidue.html
│   │       │   ├── clmresidue.ps
│   │       │   ├── clmvol.1
│   │       │   ├── clmvol.azm
│   │       │   ├── clmvol.html
│   │       │   ├── clmvol.ps
│   │       │   ├── distindex.html
│   │       │   ├── index.html
│   │       │   ├── index.in.azm
│   │       │   ├── mcl.1
│   │       │   ├── mcl.azm
│   │       │   ├── mcl.html
│   │       │   ├── mcl.ps
│   │       │   ├── mcl.txt
│   │       │   ├── mclblastline.html
│   │       │   ├── mclblastline.ps
│   │       │   ├── mclcm.1
│   │       │   ├── mclcm.azm
│   │       │   ├── mclcm.html
│   │       │   ├── mclcm.ps
│   │       │   ├── mclcm.txt
│   │       │   ├── mclfamily.7
│   │       │   ├── mclfamily.azm
│   │       │   ├── mclfamily.html
│   │       │   ├── mclfamily.ps
│   │       │   ├── mclfaq.7
│   │       │   ├── mclfaq.azm
│   │       │   ├── mclfaq.html
│   │       │   ├── mclfaq.ps
│   │       │   ├── mclfaq.txt
│   │       │   ├── mclindex.7
│   │       │   ├── mclindex.ps
│   │       │   ├── mclmcl.txt
│   │       │   ├── mclpipeline.1
│   │       │   ├── mclpipeline.azm
│   │       │   ├── mclpipeline.html
│   │       │   ├── mclpipeline.ps
│   │       │   ├── mcx.1
│   │       │   ├── mcx.azm
│   │       │   ├── mcx.html
│   │       │   ├── mcx.ps
│   │       │   ├── mcx.zmm
│   │       │   ├── mcxalter.1
│   │       │   ├── mcxalter.azm
│   │       │   ├── mcxalter.html
│   │       │   ├── mcxalter.ps
│   │       │   ├── mcxarray.1
│   │       │   ├── mcxarray.azm
│   │       │   ├── mcxarray.html
│   │       │   ├── mcxarray.ps
│   │       │   ├── mcxassemble.1
│   │       │   ├── mcxassemble.azm
│   │       │   ├── mcxassemble.html
│   │       │   ├── mcxassemble.ps
│   │       │   ├── mcxclcf.1
│   │       │   ├── mcxclcf.azm
│   │       │   ├── mcxclcf.html
│   │       │   ├── mcxclcf.ps
│   │       │   ├── mcxconvert.1
│   │       │   ├── mcxconvert.azm
│   │       │   ├── mcxconvert.html
│   │       │   ├── mcxconvert.ps
│   │       │   ├── mcxctty.1
│   │       │   ├── mcxctty.azm
│   │       │   ├── mcxctty.html
│   │       │   ├── mcxctty.ps
│   │       │   ├── mcxdeblast.html
│   │       │   ├── mcxdeblast.ps
│   │       │   ├── mcxdiameter.1
│   │       │   ├── mcxdiameter.azm
│   │       │   ├── mcxdiameter.html
│   │       │   ├── mcxdiameter.ps
│   │       │   ├── mcxdump.1
│   │       │   ├── mcxdump.azm
│   │       │   ├── mcxdump.html
│   │       │   ├── mcxdump.ps
│   │       │   ├── mcxerdos.1
│   │       │   ├── mcxerdos.azm
│   │       │   ├── mcxerdos.html
│   │       │   ├── mcxerdos.ps
│   │       │   ├── mcxi.1
│   │       │   ├── mcxi.azm
│   │       │   ├── mcxi.html
│   │       │   ├── mcxi.ps
│   │       │   ├── mcxio.5
│   │       │   ├── mcxio.azm
│   │       │   ├── mcxio.html
│   │       │   ├── mcxio.ps
│   │       │   ├── mcxload.1
│   │       │   ├── mcxload.azm
│   │       │   ├── mcxload.html
│   │       │   ├── mcxload.ps
│   │       │   ├── mcxmap.1
│   │       │   ├── mcxmap.azm
│   │       │   ├── mcxmap.html
│   │       │   ├── mcxmap.ps
│   │       │   ├── mcxquery.1
│   │       │   ├── mcxquery.azm
│   │       │   ├── mcxquery.html
│   │       │   ├── mcxquery.ps
│   │       │   ├── mcxrand.1
│   │       │   ├── mcxrand.azm
│   │       │   ├── mcxrand.html
│   │       │   ├── mcxrand.ps
│   │       │   ├── mcxsubs.1
│   │       │   ├── mcxsubs.azm
│   │       │   ├── mcxsubs.html
│   │       │   ├── mcxsubs.ps
│   │       │   ├── minimcl
│   │       │   ├── stamp.day
│   │       │   ├── stamp.month
│   │       │   ├── stamp.stamp
│   │       │   ├── stamp.year
│   │       │   ├── tingea.log.7
│   │       │   ├── tingea.log.azm
│   │       │   ├── tingea.log.html
│   │       │   └── tingea.log.ps
│   │       ├── graphs/
│   │       │   ├── Makefile.am
│   │       │   ├── Makefile.in
│   │       │   ├── T
│   │       │   ├── Tx
│   │       │   ├── Txy
│   │       │   ├── Ty
│   │       │   ├── data.abc.hdr
│   │       │   ├── data.abc.raw
│   │       │   ├── data.hdr
│   │       │   ├── data.raw
│   │       │   ├── data.tab
│   │       │   ├── falkner.coords
│   │       │   ├── falkner.mci
│   │       │   ├── falkner2.mci
│   │       │   ├── friends
│   │       │   ├── fznyy.mci
│   │       │   ├── fznyy.tab
│   │       │   ├── honey.mci
│   │       │   ├── infinity.mci
│   │       │   ├── lattice.mci
│   │       │   ├── make-falkner.pl
│   │       │   ├── matula.mci
│   │       │   ├── petersen.mci
│   │       │   ├── proteins.mci
│   │       │   ├── seven.mci
│   │       │   ├── small.mci
│   │       │   ├── small.tab
│   │       │   ├── small64.mci
│   │       │   ├── tiny-min.mci
│   │       │   ├── tiny-nil.mci
│   │       │   ├── tiny-nilnine.mci
│   │       │   ├── tiny-ninenil.mci
│   │       │   ├── tiny-one.mci
│   │       │   └── tiny-zero.mci
│   │       ├── img/
│   │       │   ├── Makefile.am
│   │       │   ├── Makefile.in
│   │       │   ├── fa.ps
│   │       │   ├── falkner-bidi.ps
│   │       │   ├── falkner.ps
│   │       │   └── small.ps
│   │       ├── include/
│   │       │   ├── Makefile.am
│   │       │   ├── Makefile.in
│   │       │   └── include.am
│   │       ├── mkinstalldirs
│   │       ├── scripts/
│   │       │   ├── Makefile.am
│   │       │   ├── Makefile.in
│   │       │   ├── TODO
│   │       │   ├── clmsnare
│   │       │   ├── clxcoarse
│   │       │   ├── clxdo
│   │       │   ├── docme
│   │       │   ├── gengraph
│   │       │   ├── mcxplotlines.R
│   │       │   ├── minimcl
│   │       │   ├── mlm-analyze
│   │       │   ├── mlm-fifofum
│   │       │   ├── mlm-quilt
│   │       │   ├── mlm-summary
│   │       │   ├── movgraph
│   │       │   ├── packed-example.sh
│   │       │   ├── packed-example2.sh
│   │       │   ├── pichi
│   │       │   ├── piclo
│   │       │   └── tree3.pl
│   │       ├── setversion
│   │       ├── src/
│   │       │   ├── Makefile.am
│   │       │   ├── Makefile.in
│   │       │   ├── README
│   │       │   ├── alien/
│   │       │   │   ├── Makefile.am
│   │       │   │   ├── Makefile.in
│   │       │   │   └── oxygen/
│   │       │   │       ├── Makefile.am
│   │       │   │       ├── Makefile.in
│   │       │   │       ├── doc/
│   │       │   │       │   ├── Makefile.am
│   │       │   │       │   ├── Makefile.in
│   │       │   │       │   ├── mclblastline.1
│   │       │   │       │   ├── mclblastline.azm
│   │       │   │       │   ├── mclblastline.html
│   │       │   │       │   ├── mclblastline.ps
│   │       │   │       │   ├── mcxdeblast.1
│   │       │   │       │   ├── mcxdeblast.azm
│   │       │   │       │   ├── mcxdeblast.html
│   │       │   │       │   └── mcxdeblast.ps
│   │       │   │       └── src/
│   │       │   │           ├── Makefile.am
│   │       │   │           ├── Makefile.in
│   │       │   │           ├── mclblastline
│   │       │   │           └── mcxdeblast
│   │       │   ├── clew/
│   │       │   │   ├── Makefile.am
│   │       │   │   ├── Makefile.in
│   │       │   │   ├── cat.c
│   │       │   │   ├── cat.h
│   │       │   │   ├── claw.c
│   │       │   │   ├── claw.h
│   │       │   │   ├── clm.c
│   │       │   │   ├── clm.h
│   │       │   │   ├── scan.c
│   │       │   │   └── scan.h
│   │       │   ├── gryphon/
│   │       │   │   ├── Makefile.am
│   │       │   │   ├── Makefile.in
│   │       │   │   ├── path.c
│   │       │   │   └── path.h
│   │       │   ├── impala/
│   │       │   │   ├── Makefile.am
│   │       │   │   ├── Makefile.in
│   │       │   │   ├── app.c
│   │       │   │   ├── app.h
│   │       │   │   ├── compose.c
│   │       │   │   ├── compose.h
│   │       │   │   ├── edge.c
│   │       │   │   ├── edge.h
│   │       │   │   ├── iface.c
│   │       │   │   ├── iface.h
│   │       │   │   ├── io.c
│   │       │   │   ├── io.h
│   │       │   │   ├── ivp.c
│   │       │   │   ├── ivp.h
│   │       │   │   ├── ivptypes.h
│   │       │   │   ├── matrix.c
│   │       │   │   ├── matrix.h
│   │       │   │   ├── pval.c
│   │       │   │   ├── pval.h
│   │       │   │   ├── stream.c
│   │       │   │   ├── stream.h
│   │       │   │   ├── tab.c
│   │       │   │   ├── tab.h
│   │       │   │   ├── vector.c
│   │       │   │   ├── vector.h
│   │       │   │   ├── version.c
│   │       │   │   └── version.h
│   │       │   ├── mcl/
│   │       │   │   ├── Makefile.am
│   │       │   │   ├── Makefile.in
│   │       │   │   ├── alg.c
│   │       │   │   ├── alg.h
│   │       │   │   ├── dpsd.c
│   │       │   │   ├── dpsd.h
│   │       │   │   ├── expand.c
│   │       │   │   ├── expand.h
│   │       │   │   ├── inflate.c
│   │       │   │   ├── inflate.h
│   │       │   │   ├── interpret.c
│   │       │   │   ├── interpret.h
│   │       │   │   ├── proc.c
│   │       │   │   ├── proc.h
│   │       │   │   ├── procinit.c
│   │       │   │   ├── procinit.h
│   │       │   │   ├── shadow.c
│   │       │   │   ├── shadow.h
│   │       │   │   ├── transform.c
│   │       │   │   └── transform.h
│   │       │   ├── shcl/
│   │       │   │   ├── Makefile.am
│   │       │   │   ├── Makefile.in
│   │       │   │   ├── clm.c
│   │       │   │   ├── clm.h
│   │       │   │   ├── clmadjust.c
│   │       │   │   ├── clmadjust.h
│   │       │   │   ├── clmclose.c
│   │       │   │   ├── clmclose.h
│   │       │   │   ├── clmdag.c
│   │       │   │   ├── clmdist.c
│   │       │   │   ├── clmdist.h
│   │       │   │   ├── clmformat.c
│   │       │   │   ├── clmformat.zmm
│   │       │   │   ├── clmformat.zmm.h
│   │       │   │   ├── clmframe.c
│   │       │   │   ├── clmimac.c
│   │       │   │   ├── clmimac.h
│   │       │   │   ├── clminfo.c
│   │       │   │   ├── clminfo.h
│   │       │   │   ├── clminfo2.c
│   │       │   │   ├── clminfo2.h
│   │       │   │   ├── clmmate.c
│   │       │   │   ├── clmmate.h
│   │       │   │   ├── clmmeet.c
│   │       │   │   ├── clmmeet.h
│   │       │   │   ├── clmoptics.c
│   │       │   │   ├── clmoptics.h
│   │       │   │   ├── clmorder.c
│   │       │   │   ├── clmorder.h
│   │       │   │   ├── clmps.c
│   │       │   │   ├── clmps.defs
│   │       │   │   ├── clmps.defs.h
│   │       │   │   ├── clmps.h
│   │       │   │   ├── clmresidue.c
│   │       │   │   ├── clmresidue.h
│   │       │   │   ├── mclgraga
│   │       │   │   ├── mclgrep
│   │       │   │   ├── mclpipeline
│   │       │   │   ├── report.c
│   │       │   │   └── report.h
│   │       │   ├── shmcl/
│   │       │   │   ├── Makefile.am
│   │       │   │   ├── Makefile.in
│   │       │   │   ├── mcl.c
│   │       │   │   └── mclcm.c
│   │       │   ├── shmcx/
│   │       │   │   ├── Makefile.am
│   │       │   │   ├── Makefile.in
│   │       │   │   ├── TODO
│   │       │   │   ├── glob.c
│   │       │   │   ├── glob.h
│   │       │   │   ├── mcxi.c
│   │       │   │   ├── ops.c
│   │       │   │   ├── ops.h
│   │       │   │   ├── stack.c
│   │       │   │   ├── stack.h
│   │       │   │   ├── util.c
│   │       │   │   └── util.h
│   │       │   ├── shmcxquery/
│   │       │   │   ├── Makefile.am
│   │       │   │   ├── Makefile.in
│   │       │   │   ├── TODO
│   │       │   │   └── mcxquery.c
│   │       │   └── shmx/
│   │       │       ├── Makefile.am
│   │       │       ├── Makefile.in
│   │       │       ├── README
│   │       │       ├── TODO
│   │       │       ├── fake
│   │       │       ├── mcx.c
│   │       │       ├── mcx.h
│   │       │       ├── mcxalter.c
│   │       │       ├── mcxalter.h
│   │       │       ├── mcxarray.c
│   │       │       ├── mcxassemble.c
│   │       │       ├── mcxclcf.c
│   │       │       ├── mcxclcf.h
│   │       │       ├── mcxcollect.c
│   │       │       ├── mcxcollect.h
│   │       │       ├── mcxconvert.c
│   │       │       ├── mcxconvert.h
│   │       │       ├── mcxdiameter.c
│   │       │       ├── mcxdiameter.h
│   │       │       ├── mcxdump.c
│   │       │       ├── mcxerdos.c
│   │       │       ├── mcxerdos.h
│   │       │       ├── mcxfp.c
│   │       │       ├── mcxfp.h
│   │       │       ├── mcxload.c
│   │       │       ├── mcxmap.c
│   │       │       ├── mcxmetric.c
│   │       │       ├── mcxminusmeet.c
│   │       │       ├── mcxmm.c
│   │       │       ├── mcxquery.c
│   │       │       ├── mcxquery.h
│   │       │       ├── mcxrand.c
│   │       │       ├── mcxsubs.c
│   │       │       ├── mcxtab.c
│   │       │       ├── mcxtab.h
│   │       │       ├── mcxtest.c
│   │       │       └── mcxtest2.c
│   │       ├── testing/
│   │       │   ├── Makefile.am
│   │       │   ├── Makefile.in
│   │       │   ├── blast/
│   │       │   │   ├── Makefile.am
│   │       │   │   ├── Makefile.in
│   │       │   │   ├── blastfile
│   │       │   │   └── blastfile9
│   │       │   ├── setops/
│   │       │   │   ├── Makefile.am
│   │       │   │   ├── Makefile.in
│   │       │   │   └── set-test.sh
│   │       │   └── stream/
│   │       │       ├── Makefile.am
│   │       │       ├── Makefile.in
│   │       │       ├── abc-pairs.pl
│   │       │       ├── abc-test.sh
│   │       │       ├── abc.pl
│   │       │       └── az.tab
│   │       └── util/
│   │           ├── Makefile.am
│   │           ├── Makefile.in
│   │           ├── alloc.c
│   │           ├── alloc.h
│   │           ├── array.c
│   │           ├── array.h
│   │           ├── compile.h
│   │           ├── ding.c
│   │           ├── ding.h
│   │           ├── equate.c
│   │           ├── equate.h
│   │           ├── err.c
│   │           ├── err.h
│   │           ├── getpagesize.h
│   │           ├── gralloc.c
│   │           ├── gralloc.h
│   │           ├── hash.c
│   │           ├── hash.h
│   │           ├── heap.c
│   │           ├── heap.h
│   │           ├── inttypes.h
│   │           ├── io.c
│   │           ├── io.h
│   │           ├── let.c
│   │           ├── let.h
│   │           ├── list.c
│   │           ├── list.h
│   │           ├── minmax.h
│   │           ├── opt.c
│   │           ├── opt.h
│   │           ├── rand.c
│   │           ├── rand.h
│   │           ├── ting.c
│   │           ├── ting.h
│   │           ├── tok.c
│   │           ├── tok.h
│   │           ├── tr.c
│   │           ├── tr.h
│   │           ├── types.c
│   │           └── types.h
│   ├── 2008-Louvain-MultiLevel-Aggregation-Opt-Modularity/
│   │   ├── Makefile
│   │   ├── ReadMe.md
│   │   ├── community.cpp
│   │   ├── community.h
│   │   ├── graph.cpp
│   │   ├── graph.h
│   │   ├── graph_binary.cpp
│   │   ├── graph_binary.h
│   │   ├── main_community.cpp
│   │   ├── main_convert.cpp
│   │   ├── main_hierarchy.cpp
│   │   ├── main_random.cpp
│   │   └── readme.txt
│   ├── 2008-Sequential-Clique-Percolation/
│   │   ├── License.txt
│   │   ├── ReadMe.md
│   │   ├── cliqueHash.cpp
│   │   ├── cliqueHash.h
│   │   ├── communityTracker.cpp
│   │   ├── communityTracker.h
│   │   ├── dendrogram.cpp
│   │   ├── dendrogram.h
│   │   ├── k_clique.cpp
│   │   ├── k_clique.h
│   │   ├── kruskal.cpp
│   │   ├── kruskal.h
│   │   ├── lcelib/
│   │   │   ├── Containers.H
│   │   │   ├── License.txt
│   │   │   ├── Nets.H
│   │   │   ├── Neural/
│   │   │   │   └── NNet.H
│   │   │   ├── PrefetchPolicy.H
│   │   │   ├── Randgens.H
│   │   │   ├── bits/
│   │   │   │   ├── EmbBoolSelector.H
│   │   │   │   ├── FiboHeapCore.H
│   │   │   │   └── hashcore.H
│   │   │   ├── containers/
│   │   │   │   ├── ArrayBase.H
│   │   │   │   ├── ContainerPolicies.H
│   │   │   │   ├── DefaultIndexParams.H
│   │   │   │   ├── KeyPolicy.H
│   │   │   │   ├── Pair.H
│   │   │   │   ├── WeightPolicy.H
│   │   │   │   ├── indices/
│   │   │   │   │   ├── Array.H
│   │   │   │   │   ├── AutoVec.H
│   │   │   │   │   ├── HashControllers.H
│   │   │   │   │   ├── LinearHash.H
│   │   │   │   │   ├── OrderedArray.H
│   │   │   │   │   ├── TableWithStatus.H
│   │   │   │   │   └── Vector.H
│   │   │   │   └── tables/
│   │   │   │       ├── ExplSumTreeTable.H
│   │   │   │       ├── ImplSumTreeTable.H
│   │   │   │       ├── ImplTreeHelper.H
│   │   │   │       ├── StubBase.H
│   │   │   │       ├── ValueTable.H
│   │   │   │       └── WeightSumTable.H
│   │   │   ├── hashes.H
│   │   │   ├── k_clique/
│   │   │   │   ├── cliqueHash.H
│   │   │   │   ├── multiIter.H
│   │   │   │   ├── numSet.H
│   │   │   │   ├── numSet2.H
│   │   │   │   └── weighedClique.H
│   │   │   ├── misc/
│   │   │   │   ├── Bindata.H
│   │   │   │   ├── BinomialSampler.H
│   │   │   │   ├── CalQueue.H
│   │   │   │   ├── EventQueue.H
│   │   │   │   ├── FiboHeap.H
│   │   │   │   ├── KruskalTree.H
│   │   │   │   └── KruskalTree2.H
│   │   │   ├── nets/
│   │   │   │   ├── Dijkstrator.H
│   │   │   │   ├── DirNetExtras.H
│   │   │   │   ├── Distributions.H
│   │   │   │   ├── Models.H
│   │   │   │   ├── NetExtras.H
│   │   │   │   ├── NetExtras2.H
│   │   │   │   ├── OldModels.H
│   │   │   │   ├── Randomizer.H
│   │   │   │   ├── UnweightedDijk.H
│   │   │   │   └── models/
│   │   │   │       ├── BA.H
│   │   │   │       ├── BBV.H
│   │   │   │       ├── Boguna.H
│   │   │   │       ├── CommunityNet.H
│   │   │   │       ├── Davidsen.H
│   │   │   │       ├── ErdosRenyi.H
│   │   │   │       ├── HolmeKim.H
│   │   │   │       ├── Marsili.H
│   │   │   │       ├── SeedNet.H
│   │   │   │       ├── SimpleNets.H
│   │   │   │       ├── VDEB.H
│   │   │   │       └── Wong.H
│   │   │   └── packedqueue.H
│   │   ├── makefile
│   │   ├── nodeCommunities.cpp
│   │   ├── nodeCommunities.h
│   │   ├── testData/
│   │   │   ├── random_1000_005.edg
│   │   │   └── random_1000_005.edg_files/
│   │   │       ├── k=3/
│   │   │       │   └── communities
│   │   │       ├── k=4/
│   │   │       │   └── communities
│   │   │       └── k=5/
│   │   │           └── communities
│   │   ├── testScp.py
│   │   ├── weighedClique.cpp
│   │   └── weighedClique.h
│   ├── 2009-Community-Infomap-MapEquation/
│   │   ├── .gitignore
│   │   ├── .hgignore
│   │   ├── CHANGES.txt
│   │   ├── LICENSE_AGPLv3.txt
│   │   ├── Makefile
│   │   ├── README.txt
│   │   ├── ReadMe.md
│   │   ├── examples/
│   │   │   ├── R/
│   │   │   │   ├── Makefile
│   │   │   │   ├── example-igraph.R
│   │   │   │   ├── example-minimal.R
│   │   │   │   └── load-infomap.R
│   │   │   ├── cpp/
│   │   │   │   ├── Infomap-igraph-interface-library/
│   │   │   │   │   ├── Makefile
│   │   │   │   │   └── src/
│   │   │   │   │       ├── Infomap-igraph-interface.cpp
│   │   │   │   │       └── Infomap-igraph-interface.h
│   │   │   │   ├── igraph/
│   │   │   │   │   ├── Makefile
│   │   │   │   │   └── example-igraph.cpp
│   │   │   │   └── minimal/
│   │   │   │       ├── Makefile
│   │   │   │       ├── example.cpp
│   │   │   │       ├── mem-example.cpp
│   │   │   │       └── multi-example.cpp
│   │   │   ├── js/
│   │   │   │   ├── Infomap-worker.html
│   │   │   │   └── Makefile
│   │   │   └── python/
│   │   │       ├── Infomap.py
│   │   │       ├── Makefile
│   │   │       ├── example-file-io.py
│   │   │       └── example-networkx.py
│   │   ├── interfaces/
│   │   │   ├── js/
│   │   │   │   └── pre-worker-module.js
│   │   │   ├── python/
│   │   │   │   └── setup.py
│   │   │   └── swig/
│   │   │       ├── Config.i
│   │   │       ├── Date.i
│   │   │       ├── HierarchicalNetwork.i
│   │   │       ├── Infomap.i
│   │   │       └── Network.i
│   │   ├── ninetriangles.net
│   │   └── src/
│   │       ├── Infomap.cpp
│   │       ├── Infomap.h
│   │       ├── Informatter.cpp
│   │       ├── infomap/
│   │       │   ├── Edge.h
│   │       │   ├── FlowNetwork.cpp
│   │       │   ├── FlowNetwork.h
│   │       │   ├── InfomapBase.cpp
│   │       │   ├── InfomapBase.h
│   │       │   ├── InfomapContext.cpp
│   │       │   ├── InfomapContext.h
│   │       │   ├── InfomapGreedy.h
│   │       │   ├── InfomapGreedyCommon.h
│   │       │   ├── InfomapGreedySpecialized.h
│   │       │   ├── InfomapGreedyTypeSpecialized.h
│   │       │   ├── MemFlowNetwork.cpp
│   │       │   ├── MemFlowNetwork.h
│   │       │   ├── MemNetwork.cpp
│   │       │   ├── MemNetwork.h
│   │       │   ├── MemoryNetworkAdapter.cpp
│   │       │   ├── MemoryNetworkAdapter.h
│   │       │   ├── MultiplexNetwork.cpp
│   │       │   ├── MultiplexNetwork.h
│   │       │   ├── Network.cpp
│   │       │   ├── Network.h
│   │       │   ├── NetworkAdapter.cpp
│   │       │   ├── NetworkAdapter.h
│   │       │   ├── Node.cpp
│   │       │   ├── Node.h
│   │       │   ├── NodeFactory.h
│   │       │   ├── TreeData.cpp
│   │       │   ├── TreeData.h
│   │       │   ├── flowData.h
│   │       │   ├── flowData_traits.h
│   │       │   └── treeIterators.h
│   │       ├── io/
│   │       │   ├── BipartiteClusterReader.cpp
│   │       │   ├── BipartiteClusterReader.h
│   │       │   ├── ClusterReader.cpp
│   │       │   ├── ClusterReader.h
│   │       │   ├── Config.h
│   │       │   ├── HierarchicalNetwork.cpp
│   │       │   ├── HierarchicalNetwork.h
│   │       │   ├── ProgramInterface.cpp
│   │       │   ├── ProgramInterface.h
│   │       │   ├── SafeFile.h
│   │       │   ├── TreeDataWriter.cpp
│   │       │   ├── TreeDataWriter.h
│   │       │   ├── convert.h
│   │       │   ├── version.cpp
│   │       │   └── version.h
│   │       └── utils/
│   │           ├── Date.h
│   │           ├── FileURI.cpp
│   │           ├── FileURI.h
│   │           ├── Logger.cpp
│   │           ├── Logger.h
│   │           ├── MersenneTwister.h
│   │           ├── Stopwatch.h
│   │           ├── gap_iterator.h
│   │           ├── infomath.h
│   │           └── types.h
│   ├── 2014-Grappolo/
│   │   ├── Makefile
│   │   ├── README.txt
│   │   ├── RngStream.cpp
│   │   ├── RngStream.h
│   │   ├── binary/
│   │   │   └── convertFileToBinary
│   │   ├── buildNextPhase.cpp
│   │   ├── coloringDistanceOne.cpp
│   │   ├── convertFileToBinary.cpp
│   │   ├── convertFileToEdgeList.cpp
│   │   ├── convertSnapFileToBinary.cpp
│   │   ├── defs.h
│   │   ├── driverForColoringExperiments.cpp
│   │   ├── driverForGraphClustering.cpp
│   │   ├── driverForGraphClusteringBigMem.cpp
│   │   ├── driverForPartitioningWithMetis.cpp
│   │   ├── driverProcessPowerGridNetworks.cpp
│   │   ├── generateRGG.cpp
│   │   ├── generateRMAT.cpp
│   │   ├── input/
│   │   │   ├── karate.graph
│   │   │   └── west1505.gr
│   │   ├── louvainMultiPhaseRun.cpp
│   │   ├── parallelLouvainMethod.cpp
│   │   ├── parallelLouvainMethodEager.cpp
│   │   ├── parallelLouvainWithColoring.cpp
│   │   ├── parseInputFiles.cpp
│   │   ├── parseInputParameters.cpp
│   │   ├── scripts/
│   │   │   └── RunWithValgrind.sh
│   │   ├── utilityClusteringFunctions.cpp
│   │   ├── utilityClusteringFunctions.h
│   │   ├── utilityFunctions.cpp
│   │   ├── utilityGraphPartitioner.cpp
│   │   ├── utilityGraphPartitioner.h
│   │   ├── utilityParseInputParameters.hpp
│   │   ├── utilityStringTokenizer.hpp
│   │   ├── vertexFollowing.cpp
│   │   └── writeGraphDimacsFormat.cpp
│   └── ReadMe.md
├── Prensentation/
│   ├── ReadMe.md
│   ├── __init__.py
│   ├── algorithms/
│   │   ├── clique_percolation/
│   │   │   ├── community_result_visualization.py
│   │   │   ├── conradlee_clique_percolation.py
│   │   │   ├── example_edge_list.txt
│   │   │   └── problem_vis.py
│   │   ├── dynamics/
│   │   │   ├── async_lp_res0.txt
│   │   │   ├── example_edge_list.txt
│   │   │   ├── label_propagation.py
│   │   │   ├── label_propagation_yche.py
│   │   │   ├── others/
│   │   │   │   ├── aync_vs_sync.py
│   │   │   │   ├── copra_lpa.py
│   │   │   │   └── lpa.py
│   │   │   ├── prev/
│   │   │   │   ├── disjoint_community.txt
│   │   │   │   └── disjoint_visualization.py
│   │   │   ├── problem_vis.py
│   │   │   └── sync_lp_res0.txt
│   │   ├── link_partition/
│   │   │   ├── example_edge_list.txt
│   │   │   ├── graph_io_helper.py
│   │   │   ├── input/
│   │   │   │   └── get_karate_edge_list.py
│   │   │   ├── link_clustering.py
│   │   │   ├── link_clustering_algo.py
│   │   │   ├── result/
│   │   │   │   ├── example_edge_list_dendro.cid2edge.txt
│   │   │   │   ├── example_edge_list_dendro.linkage.txt
│   │   │   │   ├── example_edge_list_maxS0.250000_maxD0.777778.comm2edges.txt
│   │   │   │   ├── example_edge_list_maxS0.250000_maxD0.777778.comm2nodes.txt
│   │   │   │   ├── example_edge_list_maxS0.250000_maxD0.777778.edge2comm.txt
│   │   │   │   ├── example_edge_list_thr_D.txt
│   │   │   │   ├── karate_edge_list_maxS0.333333_maxD0.284758.comm2edges.txt
│   │   │   │   ├── karate_edge_list_maxS0.333333_maxD0.284758.comm2nodes.txt
│   │   │   │   ├── karate_edge_list_maxS0.333333_maxD0.284758.edge2comm.txt
│   │   │   │   └── karate_edge_list_thr_D.txt
│   │   │   └── visualization/
│   │   │       ├── dendrogram/
│   │   │       │   ├── dendrogram_vis.py
│   │   │       │   ├── radial_demo.py
│   │   │       │   ├── radial_grouper.py
│   │   │       │   ├── radial_support.py
│   │   │       │   └── radial_visualizer.py
│   │   │       └── link_clustering_visualization.py
│   │   ├── local_expansion/
│   │   │   ├── cis_algo.py
│   │   │   ├── cis_algo_output.txt
│   │   │   ├── cis_algo_res.txt
│   │   │   ├── cis_algo_visualization.py
│   │   │   ├── example_edge_list.txt
│   │   │   ├── karate_edge_list.txt
│   │   │   ├── problem_vis.py
│   │   │   ├── result_for_vis.txt
│   │   │   └── src/
│   │   │       ├── CMakeLists.txt
│   │   │       ├── cis_algo_output.txt
│   │   │       ├── cis_sequential_algorithm.cpp
│   │   │       ├── cis_sequential_algorithm.h
│   │   │       ├── demo_cis.cpp
│   │   │       └── util/
│   │   │           ├── ReadMe.md
│   │   │           ├── basic_io_helper.h
│   │   │           ├── graph_io_helper.cpp
│   │   │           ├── graph_io_helper.h
│   │   │           └── pretty_print.h
│   │   └── statistical_inference/
│   │       └── block_model_demo.py
│   ├── graph_serialization/
│   │   ├── __init__.py
│   │   ├── graph_formats.py
│   │   ├── input/
│   │   │   ├── __init__.py
│   │   │   └── example_graph.edgelist
│   │   ├── output_json/
│   │   │   ├── adjacency.json
│   │   │   └── node_link.json
│   │   ├── output_other/
│   │   │   ├── example_graph.gml
│   │   │   └── example_graph.pajek
│   │   ├── output_raw/
│   │   │   ├── __init__.py
│   │   │   ├── example_graph.adjlist
│   │   │   ├── example_graph.edgelist
│   │   │   └── example_graph.multiline_adjlist
│   │   ├── output_serialization/
│   │   │   ├── __init__.py
│   │   │   ├── example_graph.graph6
│   │   │   ├── example_graph.pickle
│   │   │   └── example_graph.yaml
│   │   └── output_xml/
│   │       ├── __init__.py
│   │       ├── example_graph.gexf
│   │       └── example_graph.graphml
│   ├── graph_tool_usage/
│   │   ├── intro_graph_tool/
│   │   │   ├── .gitignore
│   │   │   ├── begining.py
│   │   │   ├── draw_pie_graph.py
│   │   │   ├── graph_creation_basics.py
│   │   │   ├── graph_notations.md
│   │   │   └── nx2gt.py
│   │   └── play.py
│   ├── jupter_playground/
│   │   ├── .gitignore
│   │   ├── .ipynb_checkpoints/
│   │   │   ├── graph_draw_study0-checkpoint.ipynb
│   │   │   └── pie_graph-checkpoint.ipynb
│   │   ├── graph_draw_study0.ipynb
│   │   └── pie_graph.ipynb
│   ├── metrics/
│   │   ├── ReadMe.md
│   │   ├── __init__.py
│   │   ├── demo_graph.csv
│   │   ├── link_belong_modularity.py
│   │   ├── omega_idx.py
│   │   ├── overlap_nmi.py
│   │   ├── rand_idx_example.py
│   │   └── util.py
│   ├── problem_definition/
│   │   ├── demo_cis_output_result.txt
│   │   ├── demo_input_graph.txt
│   │   └── problem_vis.py
│   ├── social_network/
│   │   ├── disjoint_community_detection.py
│   │   ├── others/
│   │   │   └── visualization_different_colors.py
│   │   ├── visualization_karate.py
│   │   └── zachary_karate_club/
│   │       ├── __init__.py
│   │       ├── gml_formatter.py
│   │       ├── gml_parser.py
│   │       ├── karate.gml
│   │       ├── karate.txt
│   │       └── karate_new.gml
│   └── test.gml
├── README.md
├── Scripts/
│   └── dataset_aggragation.py
├── SubModules/
│   └── ReadMe.md
└── Survey/
    ├── Community-Detection-New-Findings.md
    ├── Community-Detection-Reading-List.md
    ├── Community-Detection-Survey.md
    ├── Community-Search-Survey.md
    ├── Conference-Papers-About-Graph/
    │   └── VLDB.md
    ├── Overlapping-Community-Detection-Codes.md
    ├── ReadMe.md
    └── Social-Media-Recommendation.md
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SYMBOL INDEX (9797 symbols across 1202 files)

FILE: Algorithms/2008-CliquePercolation/conradlee_clique_percolation.py
  function get_percolated_cliques (line 5) | def get_percolated_cliques(G, k):

FILE: Algorithms/2008-CliquePercolation/src_cpp/cliqueHash.h
  function class (line 27) | class cliqueHash

FILE: Algorithms/2008-CliquePercolation/src_cpp/communityTracker.h
  function class (line 33) | class CommunityTracker

FILE: Algorithms/2008-CliquePercolation/src_cpp/dendrogram.h
  function class (line 30) | class Dendrogram
  function compareNodes (line 67) | static bool compareNodes(DendrogramNode * first, DendrogramNode * second...

FILE: Algorithms/2008-CliquePercolation/src_cpp/k_clique.cpp
  type Link (line 50) | struct Link{
    method Link (line 54) | Link(size_t source=0,size_t dest=0, float weight=0.0) : source(source)...
  function determineHashSize (line 60) | size_t determineHashSize(const size_t numElements, const size_t k)
  function getNetSizeAndLinkNumbers (line 78) | bool getNetSizeAndLinkNumbers(char * fileName, size_t & netSize, size_t ...
  function readLine (line 120) | bool readLine(std::ifstream & myfile, size_t & source,  size_t & dest, f...
  function kCliquesFind (line 144) | void kCliquesFind(std::vector<weighedClique> & cliqueVector, NetType & n...
  function kCommunitiesFind (line 248) | void kCommunitiesFind(std::vector<weighedClique> & cliqueVector, Kruskal...
  function outputCommunityStructure (line 294) | void outputCommunityStructure(KruskalTree & communities, cliqueHash & k1...
  function unweightedSCP (line 323) | void unweightedSCP(NetType & net, std::list<Link> & linkList, const size...
  function weighedCliqueCmp (line 374) | bool weighedCliqueCmp(const weighedClique lhs, const weighedClique rhs)
  function kCommunitiesFindWeighted (line 379) | void kCommunitiesFindWeighted(std::vector<weighedClique> & cliqueVector,...
  function weightedSCP (line 403) | void weightedSCP(NetType & net, std::ifstream & file, const size_t numbe...
  function validateLinkList (line 434) | bool validateLinkList(std::list<Link> &linkList,size_t netSize,bool verb...
  function percolation (line 453) | int percolation(char * fileName, const size_t k, const size_t weighted, ...
  function main (line 481) | int main(int argc, char* argv[])

FILE: Algorithms/2008-CliquePercolation/src_cpp/k_clique.h
  type Set (line 51) | typedef Set<size_t> nodeSet;

FILE: Algorithms/2008-CliquePercolation/src_cpp/kruskal.h
  function class (line 28) | class KruskalTree

FILE: Algorithms/2008-CliquePercolation/src_cpp/nodeCommunities.h
  type Set (line 30) | typedef Set<size_t> nodeSet;
  function class (line 32) | class nodeCommunities

FILE: Algorithms/2008-CliquePercolation/src_cpp/script/testScp.py
  function listComp (line 8) | def listComp(l1, l2):
  function compareCommunities (line 17) | def compareCommunities(scpComms, cfComms):

FILE: Algorithms/2008-CliquePercolation/src_cpp/weighedClique.h
  function class (line 29) | class clique
  type SymmNet (line 82) | typedef  SymmNet<float> NetType;
  function class (line 86) | class weighedClique: public clique

FILE: Algorithms/2008-CliquePercolation/src_python/seq_clique_percolation.py
  class Net (line 22) | class Net(object):
    method __init__ (line 25) | def __init__(self):
    method _legaledge (line 28) | def _legaledge(self, src, dst):
    method _intsetedge (line 32) | def _intsetedge(self, src, dst, val):
    method _setedge (line 46) | def _setedge(self, src, dst, val):
    method __getitem__ (line 51) | def __getitem__(self, args):
    method __setitem__ (line 64) | def __setitem__(self, key, val):
    method __delitem__ (line 85) | def __delitem__(self, args):
    method __iter__ (line 95) | def __iter__(self):
    method isSymmetric (line 98) | def isSymmetric(self):
    method __len__ (line 101) | def __len__(self):
  class Node (line 105) | class Node(object):
    method __init__ (line 106) | def __init__(self, net, index):
    method __iter__ (line 110) | def __iter__(self):
    method __getitem__ (line 116) | def __getitem__(self, index):
    method __setitem__ (line 119) | def __setitem__(self, index, val):
    method deg (line 123) | def deg(self):
  class SymmNet (line 127) | class SymmNet(Net):
    method _legaledge (line 130) | def _legaledge(self, src, dst):
    method _intsetedge (line 139) | def _intsetedge(self, src, dst, val):
    method isSymmetric (line 144) | def isSymmetric(self):
  class Net_edges (line 149) | class Net_edges:
    method __init__ (line 150) | def __init__(self, net):
    method __iter__ (line 153) | def __iter__(self):
    method __len__ (line 160) | def __len__(self):
    method __str__ (line 169) | def __str__(self):
  function getSubnet (line 176) | def getSubnet(net, nodes):
  function loadNet_edg (line 197) | def loadNet_edg(input, mutualEdges=False, splitterChar=None, symmetricNe...
  class Enumerator (line 245) | class Enumerator:
    method __init__ (line 261) | def __init__(self):
    method _addItem (line 265) | def _addItem(self, item):
    method __getitem__ (line 271) | def __getitem__(self, item):
    method getReverse (line 277) | def getReverse(self, number):
    method __iter__ (line 280) | def __iter__(self):
    method __len__ (line 283) | def __len__(self):
  class NodeFamily (line 287) | class NodeFamily:
    method __init__ (line 292) | def __init__(self, cmap={}, inputFile=None):
    method _parseStrings (line 300) | def _parseStrings(self, input):
    method __str__ (line 306) | def __str__(self):
    method _sortBySize (line 314) | def _sortBySize(self):
    method _addCommunity (line 317) | def _addCommunity(self, newCommunity):
    method __getitem__ (line 320) | def __getitem__(self, index):
    method __len__ (line 323) | def __len__(self):
    method getSizeDist (line 326) | def getSizeDist(self):
    method getGiant (line 339) | def getGiant(self):
    method getGiantSize (line 352) | def getGiantSize(self):
    method getSusceptibility (line 362) | def getSusceptibility(self, size=None):
    method getCollapsed (line 402) | def getCollapsed(self):
    method getNew (line 421) | def getNew(self, newNodes):
    method getSetsForNodes (line 441) | def getSetsForNodes(self):
  class KtreeInteger (line 456) | class KtreeInteger:
    method __init__ (line 461) | def __init__(self, size=0):
    method __getRealParent (line 468) | def __getRealParent(self, node):
    method __setRealParent (line 478) | def __setRealParent(self, node, newParent):
    method getParent (line 488) | def getParent(self, node):
    method setParent (line 494) | def setParent(self, node, newParent):
    method __iter__ (line 497) | def __iter__(self):
    method getCommStruct (line 501) | def getCommStruct(self, separateElements=True):
    method __len__ (line 518) | def __len__(self):
    method mergeSetsWithElements (line 521) | def mergeSetsWithElements(self, elements):
    method addEdge (line 526) | def addEdge(self, edge):
    method setSize (line 529) | def setSize(self, newSize):
  class Ktree (line 534) | class Ktree(KtreeInteger):
    method __init__ (line 540) | def __init__(self, size=0):
    method getParent (line 545) | def getParent(self, node):
    method setParent (line 548) | def setParent(self, node, newParent):
    method __iter__ (line 551) | def __iter__(self):
    method getCommStruct (line 554) | def getCommStruct(self):
  class EvaluationList (line 565) | class EvaluationList:
    method __init__ (line 571) | def __init__(self, thelist, weightFunction=lambda x: x[2]):
    method setEvaluations (line 578) | def setEvaluations(self, evaluationPoints):
    method setLinearEvaluations (line 581) | def setLinearEvaluations(self, first, last, numberOfEvaluationPoints):
    method setStrengthEvaluations (line 592) | def setStrengthEvaluations(self):
    method setLastEvaluation (line 596) | def setLastEvaluation(self):
    method __iter__ (line 599) | def __iter__(self):
  function getKCliqueComponents (line 629) | def getKCliqueComponents(net, k):
  class KClique (line 646) | class KClique(object):
    method __init__ (line 652) | def __init__(self, nodelist, notSorted=True):
    method __hash__ (line 658) | def __hash__(self):
    method __iter__ (line 663) | def __iter__(self):
    method __cmp__ (line 667) | def __cmp__(self, kclique):
    method __add__ (line 673) | def __add__(self, kclique):
    method getSubcliques (line 676) | def getSubcliques(self):
    method __str__ (line 680) | def __str__(self):
    method getEdges (line 683) | def getEdges(self):
    method getK (line 689) | def getK(self):
  function getIntensity (line 693) | def getIntensity(kclique, net):
  class EvaluationEvent (line 700) | class EvaluationEvent:
    method __init__ (line 701) | def __init__(self, threshold=None, addedElements=None):
  function kcliquesAtSubnet (line 706) | def kcliquesAtSubnet(nodes, net, k):
  function kcliquesByEdges (line 727) | def kcliquesByEdges(edges, k):
  function kcliquesWeight (line 757) | def kcliquesWeight(net, k, weightFunction):
  function communitiesByKCliques (line 764) | def communitiesByKCliques(kcliques):
  function kcliquePercolator (line 783) | def kcliquePercolator(net, k, start, stop, evaluations, reverse=False, w...

FILE: Algorithms/2009-Connected-Iterative-Scan/src-orginal/Libraries/Files/IOX.cc
  function fline_tr (line 15) | bool fline_tr(ifstream* fin, vector<string>* fields, string delim)
  function split_tr (line 52) | void split_tr(string input, vector < string >* fields, string delim){
  function openFile (line 87) | bool openFile(ifstream* fin, string filename)
  function openFileHarsh (line 108) | void openFileHarsh(ifstream* fin, string filename)
  function FileError (line 119) | void FileError(const string& filename){

FILE: Algorithms/2009-Connected-Iterative-Scan/src-orginal/Libraries/Files/StringEx.cc
  function trim (line 12) | const std::string trim(const std::string& pString,
  function replaceAll (line 34) | void replaceAll(string& str, const char& x, const char& y){
  function string (line 50) | string replaceStrChar(string str, const string& replace, char ch)

FILE: Algorithms/2009-Connected-Iterative-Scan/src-orginal/Libraries/Network/Format.cc
  function ChangeDelimiter (line 16) | void ChangeDelimiter ( const string& filein, const string& fileout, cons...
  function EncodeNetwork (line 50) | void EncodeNetwork ( const string& filein, const string& fileout, const ...
  function DecodeCommunities (line 99) | void DecodeCommunities ( const string& filein, const string& fileout, co...

FILE: Algorithms/2009-Connected-Iterative-Scan/src-orginal/Libraries/Network/Network.h
  type cmp_str_ptr (line 9) | struct cmp_str_ptr{
  type cmp_set_str (line 15) | struct cmp_set_str{
  function class (line 31) | class Network {

FILE: Algorithms/2009-Connected-Iterative-Scan/src-orginal/Libraries/Network/RandomNetwork.h
  function RandomNetwork (line 7) | void RandomNetwork ( const int& V, const double& dist, const int& min_de...

FILE: Algorithms/2009-Connected-Iterative-Scan/src-orginal/Libraries/Network/TemporalNetwork.h
  type set (line 16) | typedef set < shared_ptr < string >, cmp_str_ptr > community;
  function class (line 22) | class TemporalNetwork{

FILE: Algorithms/2009-Connected-Iterative-Scan/src-orginal/Libraries/Params/Parameters.h
  type sui (line 20) | typedef short unsigned int sui;
  type lui (line 21) | typedef long unsigned int lui;
  function class (line 28) | class Parameters {

FILE: Algorithms/2009-Connected-Iterative-Scan/src-orginal/main.cc
  function Print (line 16) | void Print( const set < shared_ptr < string >, cmp_str_ptr >& seed ){
  function CalcDensity (line 37) | double CalcDensity( const int& size, const double& Win, const double& Wo...
  function Components (line 60) | map < double, set < shared_ptr < string >, cmp_str_ptr > > Components ( ...
  function ExpandSeed (line 115) | void ExpandSeed ( set < shared_ptr < string >, cmp_str_ptr >& seed, shar...
  function Print (line 306) | void Print( const set < shared_ptr < string >, cmp_str_ptr >& seed, ofst...
  function main (line 323) | int main ( int argc, char** argv ){

FILE: Algorithms/2009-Connected-Iterative-Scan/src-refactor/graph/network.h
  type cmp_str_ptr (line 11) | struct cmp_str_ptr {
  type cmp_set_str (line 17) | struct cmp_set_str {
  function class (line 34) | class network {

FILE: Algorithms/2009-Connected-Iterative-Scan/src-refactor/graph/temporal_network.h
  type set (line 16) | typedef set<shared_ptr<string>, cmp_str_ptr> community;
  function class (line 22) | class temporal_network {

FILE: Algorithms/2009-Connected-Iterative-Scan/src-refactor/main.cc
  function Print (line 15) | void Print(const set<shared_ptr<string>, cmp_str_ptr> &seed) {
  function CalcDensity (line 36) | double CalcDensity(const int &size, const double &Win, const double &Wou...
  function Components (line 59) | map<double, set<shared_ptr<string>, cmp_str_ptr> >
  function ExpandSeed (line 117) | void ExpandSeed(set<shared_ptr<string>, cmp_str_ptr> &seed, shared_ptr<n...
  function Print (line 316) | void Print(const set<shared_ptr<string>, cmp_str_ptr> &seed, ofstream &f...
  function main (line 333) | int main(int argc, char **argv) {

FILE: Algorithms/2009-Connected-Iterative-Scan/src-refactor/useless/RandomNetwork.h
  function RandomNetwork (line 7) | void RandomNetwork ( const int& V, const double& dist, const int& min_de...

FILE: Algorithms/2009-Connected-Iterative-Scan/src-refactor/util/graph_io_helper.cc
  function ChangeDelimiter (line 16) | void ChangeDelimiter(const string &filein, const string &fileout, const ...
  function EncodeNetwork (line 51) | void EncodeNetwork(const string &filein, const string &fileout, const ch...
  function DecodeCommunities (line 102) | void DecodeCommunities(const string &filein, const string &fileout, cons...

FILE: Algorithms/2009-Connected-Iterative-Scan/src-refactor/util/io_helper.cc
  function fline_tr (line 15) | bool fline_tr(ifstream *fin, vector<string> *fields, string delim) {
  function split_tr (line 49) | void split_tr(string input, vector<string> *fields, string delim) {
  function openFile (line 82) | bool openFile(ifstream *fin, string filename) {
  function openFileHarsh (line 101) | void openFileHarsh(ifstream *fin, string filename) {
  function FileError (line 110) | void FileError(const string &filename) {

FILE: Algorithms/2009-Connected-Iterative-Scan/src-refactor/util/parameters_helper.h
  type sui (line 22) | typedef short unsigned int sui;
  type lui (line 23) | typedef long unsigned int lui;
  function class (line 30) | class parameters_helper {

FILE: Algorithms/2009-Connected-Iterative-Scan/src-refactor/util/string_helper.cc
  function trim (line 12) | const std::string trim(const std::string& pString,
  function replaceAll (line 34) | void replaceAll(string& str, const char& x, const char& y){
  function string (line 50) | string replaceStrChar(string str, const string& replace, char ch)

FILE: Algorithms/2009-EAGLE/graphs/tools/converter.py
  function asdot (line 18) | def asdot(AS):
  function select (line 25) | def select(x):
  class Converter (line 28) | class Converter:
    method reg (line 34) | def reg(self, v):
    method add (line 43) | def add(self, data, mv):
    method toFileAs (line 67) | def toFileAs(self, path):
    method toGraph (line 75) | def toGraph(self):

FILE: Algorithms/2009-EAGLE/graphs/tools/examples.py
  function example0 (line 7) | def example0():
  function example1 (line 15) | def example1():
  function example2 (line 25) | def example2():
  function example3 (line 45) | def example3():
  function example4 (line 54) | def example4():
  function example5 (line 66) | def example5():
  function example6 (line 74) | def example6():
  function example7 (line 82) | def example7():
  function example8 (line 88) | def example8():

FILE: Algorithms/2009-EAGLE/graphs/tools/progressbar.py
  class ProgressBarWidget (line 62) | class ProgressBarWidget(object):
    method update (line 69) | def update(self, pbar):
  class ProgressBarWidgetHFill (line 79) | class ProgressBarWidgetHFill(object):
    method update (line 88) | def update(self, pbar, width):
  class ETA (line 100) | class ETA(ProgressBarWidget):
    method format_time (line 102) | def format_time(self, seconds):
    method update (line 104) | def update(self, pbar):
  class FileTransferSpeed (line 114) | class FileTransferSpeed(ProgressBarWidget):
    method __init__ (line 116) | def __init__(self, unit='B'):
    method update (line 120) | def update(self, pbar):
  class RotatingMarker (line 132) | class RotatingMarker(ProgressBarWidget):
    method __init__ (line 134) | def __init__(self, markers='|/-\\'):
    method update (line 137) | def update(self, pbar):
  class Percentage (line 143) | class Percentage(ProgressBarWidget):
    method update (line 145) | def update(self, pbar):
  class SimpleProgress (line 148) | class SimpleProgress(ProgressBarWidget):
    method __init__ (line 150) | def __init__(self, sep=' of '):
    method update (line 152) | def update(self, pbar):
  class Bar (line 155) | class Bar(ProgressBarWidgetHFill):
    method __init__ (line 157) | def __init__(self, marker='#', left='|', right='|'):
    method _format_marker (line 161) | def _format_marker(self, pbar):
    method update (line 166) | def update(self, pbar, width):
  class ReverseBar (line 174) | class ReverseBar(Bar):
    method update (line 176) | def update(self, pbar, width):
  class ProgressBar (line 185) | class ProgressBar(object):
    method __init__ (line 233) | def __init__(self, maxval=None, widgets=default_widgets, term_width=None,
    method __call__ (line 258) | def __call__(self, iterable):
    method __iter__ (line 271) | def __iter__(self):
    method next (line 274) | def next(self):
    method _handle_resize (line 283) | def _handle_resize(self, signum, frame):
    method percentage (line 287) | def percentage(self):
    method _format_widgets (line 291) | def _format_widgets(self):
    method _format_line (line 313) | def _format_line(self):
    method _next_update (line 316) | def _next_update(self):
    method _need_update (line 321) | def _need_update(self):
    method update (line 341) | def update(self, value):
    method start (line 355) | def start(self):
    method finish (line 378) | def finish(self):

FILE: Algorithms/2009-EAGLE/src/communities.cpp
  function BOOST_FOREACH (line 73) | BOOST_FOREACH(CID c, keys) {
  function BOOST_FOREACH (line 84) | BOOST_FOREACH(CID c, toDelete) {
  function BOOST_FOREACH (line 190) | BOOST_FOREACH(unsigned int i, keys) {
  function CID (line 267) | CID Communities::registerCommunity(CommunityPtr c) {
  function CID (line 275) | CID Communities::addCommunity(NodeSet *s) {
  function CID (line 295) | CID Communities::addCommunity(igraph_vector_t *vector) {
  function CID (line 315) | CID Communities::addCommunity(unsigned int i) {

FILE: Algorithms/2009-EAGLE/src/communities.h
  type Community (line 27) | struct Community
  type Node (line 29) | typedef unsigned int Node;
  type CID (line 30) | typedef unsigned int CID;
  type Community (line 32) | typedef Community *CommunityPtr;
  type std (line 33) | typedef std::set<Node> NodeSet;
  type NodeSet (line 34) | typedef const NodeSet *NodeSetPtr;
  type boost (line 36) | typedef boost::unordered_map<CID, CommunityPtr> CommunitiesMap;
  type boost (line 37) | typedef boost::unordered_map<Node, std::set<CID> > MembershipMap;
  type Community (line 53) | struct Community {
  function update (line 155) | inline
  function degrees (line 184) | inline
  function CommunityPtr (line 192) | inline
  function CommunityPtr (line 203) | inline
  function igraph_vector_t (line 213) | inline
  function igraph_vs_t (line 226) | inline
  function CommunityPtr (line 234) | inline
  function class (line 250) | class Communities {
  function size (line 412) | inline
  function getDegree (line 418) | inline
  function areConnected (line 423) | inline
  function getCommunitySize (line 431) | inline
  function ownership (line 436) | inline
  function CommunityPtr (line 441) | inline
  function conductance (line 460) | inline
  function expansion (line 467) | inline
  function internalDensity (line 474) | inline
  function cutRatio (line 481) | inline
  function normalizedCut (line 488) | inline
  function linkDensity (line 497) | inline
  function scaledLinkDensity (line 504) | inline
  function maxODF (line 511) | inline
  function avgODF (line 545) | inline
  function flakeODF (line 580) | inline
  function EQ (line 614) | inline
  function similarity (line 648) | inline
  function NodeSetPtr (line 665) | inline

FILE: Algorithms/2009-EAGLE/src/eagle.cpp
  function Communities (line 67) | Communities *EAGLE::run() {

FILE: Algorithms/2009-EAGLE/src/eagle.h
  function class (line 10) | class EAGLE {

FILE: Algorithms/2009-EAGLE/src/main.cpp
  function main (line 6) | int main(int argc, char *argv[]) {

FILE: Algorithms/2009-EAGLE/src/max_cache.cpp
  function Max (line 60) | Max MaxCache::get() {

FILE: Algorithms/2009-EAGLE/src/max_cache.h
  type Max (line 14) | struct Max {
  function class (line 45) | class MaxCache {

FILE: Algorithms/2009-LineGraph/src/TseGraph.h
  function class (line 39) | class TseGraph {

FILE: Algorithms/2009-LineGraph/src/main.cpp
  function printLineGraphTypes (line 27) | void
  function printFileFormats (line 36) | void
  function usage (line 63) | void
  function usage (line 80) | void
  function parse_args (line 88) | void
  function display_time (line 137) | void
  function makeLineGraph (line 158) | void
  function main (line 261) | int main(int argc, char **argv) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/CM.java
  class CM (line 19) | public class CM {
    method CM (line 24) | public CM() {
    method main (line 27) | public static void main(String[] var0) {
    method realGraph (line 58) | private static void realGraph(String var0, String var1, int var2) {
    method benchmarkGraph (line 91) | private static void benchmarkGraph(int var0, int var1, int var2, doubl...
    method omegaResult (line 129) | private static void omegaResult(String var0, String var1, int var2) {
    method omegaBGLL (line 140) | private static double omegaBGLL(String var0, String var1, int var2) {
    method modularityResult (line 149) | private static void modularityResult(String var0, String var1) {
    method printOmega (line 155) | private static void printOmega() {
    method avgOmegaOthers (line 163) | private static void avgOmegaOthers(int var0) {
    method avgOmegaCM (line 188) | private static void avgOmegaCM(int var0) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/algorithm/BK/BK.java
  class BK (line 18) | public class BK {
    method BK (line 27) | public BK() {
    method main (line 30) | public static void main(String[] var0) throws FileNotFoundException {
    method communityResults (line 50) | public static long communityResults(String var0, String var1, int var2...
    method saveCliques (line 78) | private static void saveCliques(ArrayList var0) {
    method printGraph (line 90) | private static void printGraph(ArrayList<HashSet<Integer>> var0) {
    method calculate (line 107) | private static void calculate(ArrayList<HashSet<Integer>> var0) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/algorithm/BK/BronKerboschCFFast.java
  class BronKerboschCFFast (line 13) | public class BronKerboschCFFast {
    method BronKerboschCFFast (line 17) | public BronKerboschCFFast(ArrayList<HashSet<Integer>> var1) {
    method getBiggestMaximalCliques (line 21) | public Collection<Set<Integer>> getBiggestMaximalCliques() {
    method getAllMaximalCliques (line 47) | public Collection<Set<Integer>> getAllMaximalCliques() {
    method findCliques (line 63) | private Set<Integer> findCliques(List<Integer> var1, List<Integer> var...
    method check (line 129) | private void check(String var1, Set<Integer> var2, List<Integer> var3) {
    method end (line 139) | private boolean end(List<Integer> var1, List<Integer> var2) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/algorithm/KJ/KJ.java
  class KJ (line 22) | public class KJ {
    method KJ (line 31) | public KJ() {
    method main (line 34) | public static void main(String[] var0) throws FileNotFoundException {
    method communityResults (line 54) | public static long communityResults(String var0, String var1, int var2...
    method saveCliques (line 101) | private static void saveCliques(ArrayList var0) {
    method converseTolist (line 113) | private static ArrayList converseTolist(HashSet<Integer> var0) {
    method printGraph (line 125) | private static void printGraph(ArrayList<HashSet<Integer>> var0) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/algorithm/MaxClique.java
  class MaxClique (line 19) | public class MaxClique {
    method MaxClique (line 29) | public MaxClique() {
    method main (line 32) | public static void main(String[] var0) {
    method mcq (line 39) | public static HashSet<Integer> mcq(String var0) {
    method mcq (line 45) | public static HashSet<Integer> mcq(ArrayList<HashSet<Integer>> var0, i...
    method mcq (line 51) | public static HashSet<Integer> mcq(ArrayList<HashSet<Integer>> var0, A...
    method readGraph (line 66) | private static int readGraph(String var0, ArrayList<HashSet<Integer>> ...
    method convert_V (line 108) | public static ARRAY2 convert_V(int var0) {
    method convert_e (line 120) | public static boolean[][] convert_e(ArrayList<HashSet<Integer>> var0) {
    method MCQ (line 134) | private static long MCQ(ArrayList<HashSet<Integer>> var0, ARRAY2 var1,...
    method vSort (line 156) | private static void vSort(ARRAY2 var0, TreeSet<ELEMENT> var1, ArrayLis...
    method initVerts (line 170) | public static TreeSet<ELEMENT> initVerts(ARRAY2 var0, ArrayList<HashSe...
    method EXPAND (line 188) | private static void EXPAND(ARRAY2 var0, boolean[][] var1, int var2) {
    method CUT2 (line 213) | private static boolean CUT2(int var0, ARRAY2 var1, ARRAY2 var2, boolea...
    method COLOR_SORT (line 227) | private static void COLOR_SORT(ARRAY2 var0, boolean[][] var1, int var2) {
    method CUT1 (line 286) | private static boolean CUT1(int var0, ARRAY_FIX var1, boolean[][] var2) {
    method COPY (line 295) | private static void COPY(ARRAY_FIX var0, ARRAY_FIX var1) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/input_output/ReadEdges.java
  class ReadEdges (line 12) | public class ReadEdges {
    method ReadEdges (line 13) | public ReadEdges() {
    method readGraph (line 16) | public ArrayList<HashSet<Integer>> readGraph(String var1, int var2) th...

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/input_output/WriteCliques.java
  class WriteCliques (line 12) | public class WriteCliques {
    method WriteCliques (line 13) | public WriteCliques() {
    method saveGraphfile (line 16) | public static void saveGraphfile(ArrayList<HashSet<Integer>> var0, Str...

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/ARRAY2.java
  class ARRAY2 (line 8) | public class ARRAY2 {
    method ARRAY2 (line 12) | public ARRAY2() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/ARRAY_FIX.java
  class ARRAY_FIX (line 8) | public class ARRAY_FIX {
    method ARRAY_FIX (line 12) | public ARRAY_FIX(int var1) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/Pair.java
  class Pair (line 6) | public class Pair {
    method Pair (line 10) | public Pair(int var1, int var2) {
    method toString (line 15) | public String toString() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/Tree.java
  class Tree (line 8) | public class Tree {
    method Tree (line 14) | public Tree(HashSet<Integer> var1) {
    method Tree (line 19) | public Tree(Tree var1, Tree var2) {
    method add (line 25) | public void add(Tree var1) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/benchmark/GG.java
  class GG (line 26) | public class GG {
    method GG (line 32) | public GG() {
    method main (line 35) | public static void main(String[] var0) {
    method gen_benchmark (line 202) | public static int gen_benchmark(int var0, int var1, int var2, double v...
    method run_command (line 233) | private static long run_command(String var0, boolean var1) {
    method convert_bm_network (line 257) | public static void convert_bm_network(String var0, String var1) {
    method convert_bm_community (line 280) | public static int convert_bm_community(String var0, String var1) {
    method generate (line 327) | public static GGResult generate(int var0, int var1, int var2, double v...
    method gen (line 336) | private static GGResult gen(int var0, int var1, int var2, double var3,...
    method pruneGraph (line 420) | private static void pruneGraph(ArrayList<HashSet<Integer>> var0, HashS...
    method showStatsBi (line 437) | private static void showStatsBi(String var0, ArrayList<HashSet<Integer...
    method nVertices (line 506) | private static int nVertices(ArrayList<HashSet<Integer>> var0) {
    method sameGroup (line 518) | private static boolean sameGroup(int var0, int var1, ArrayList<TreeSet...
    method checkSaveGraph (line 528) | private static GGResult checkSaveGraph(ArrayList<HashSet<Integer>> var...
    method invert (line 539) | public static ArrayList<HashSet<Integer>> invert(ArrayList<HashSet<Int...
    method project (line 558) | public static ArrayList<HashSet<Integer>> project(ArrayList<HashSet<In...
    method weightedProject (line 576) | public static ArrayList<HashMap<Integer, Integer>> weightedProject(Arr...
    method averageDiameter (line 604) | private static GGResult averageDiameter(ArrayList<TreeSet<Integer>> va...
    method diameter (line 625) | private static int diameter(TreeSet<Integer> var0, ArrayList<HashSet<I...
    method maxDist (line 640) | private static int maxDist(int var0, TreeSet<Integer> var1, ArrayList<...
    method saveGroups (line 672) | private static void saveGroups(ArrayList<TreeSet<Integer>> var0, int v...
    method saveGraph (line 705) | private static void saveGraph(ArrayList<HashSet<Integer>> var0, int va...
    method saveWGraph (line 741) | private static void saveWGraph(ArrayList<HashMap<Integer, Integer>> va...
    method saveGraphCSV (line 777) | private static void saveGraphCSV(ArrayList<HashSet<Integer>> var0, int...
    method randName (line 804) | private static String randName(int var0, int var1, double var2, double...
    method minSize (line 814) | private static int minSize(ArrayList<TreeSet<Integer>> var0, int var1) {
    method makeArrayList (line 827) | private static ArrayList<HashSet<Integer>> makeArrayList(HashMap<Integ...
    method makeEdgesPA (line 847) | private static ArrayList<HashSet<Integer>> makeEdgesPA(ArrayList<TreeS...
    method randInt (line 961) | private static int randInt(double var0, Random var2) {
    method findInitVertex (line 970) | private static int findInitVertex(int var0, int var1, ArrayList<ArrayL...
    method findVertex (line 985) | private static int findVertex(int var0, int var1, ArrayList<TreeSet<In...
    method makeEdgesOld (line 1017) | private static ArrayList<HashSet<Integer>> makeEdgesOld(HashMap<Intege...
    method makeEdges (line 1055) | private static ArrayList<HashSet<Integer>> makeEdges(ArrayList<TreeSet...
    method makeEdgesBi (line 1059) | private static ArrayList<HashSet<Integer>> makeEdgesBi(ArrayList<TreeS...
    method findVertex1 (line 1159) | private static int findVertex1(int var0, double var1, TreeSet<Integer>...
    method inVertex (line 1175) | private static int inVertex(Integer[] var0, Random var1) {
    method outVertex (line 1180) | private static int outVertex(int var0, TreeSet<Integer> var1, Random v...
    method makeEdges (line 1189) | private static void makeEdges(int var0, HashSet<Integer> var1, ArrayLi...
    method makeEdge (line 1198) | private static boolean makeEdge(double var0, int var2, int var3, Array...
    method makeEdge (line 1207) | private static boolean makeEdge(int var0, int var1, ArrayList<HashSet<...
    method makeEdgesPref (line 1220) | private static HashMap<Integer, HashSet<Integer>> makeEdgesPref(HashMa...
    method makeEdgesFlat (line 1299) | private static boolean[][] makeEdgesFlat(HashSet<Pair> var0, int var1,...
    method randIntFromDouble (line 1354) | private static int randIntFromDouble(double var0, Random var2) {
    method randBoolean (line 1363) | private static boolean randBoolean(double var0, Random var2) {
    method makeSameGroup (line 1367) | private static HashMap<Integer, HashSet<Integer>> makeSameGroup(int va...
    method makeGroups (line 1394) | private static ArrayList<TreeSet<Integer>> makeGroups(int var0, int va...
    method individualName (line 1502) | private static int individualName(int var0) {
    method printBoolean (line 1506) | private static void printBoolean(boolean[][] var0, int var1) {
    method componentOf (line 1521) | private static HashSet<Integer> componentOf(int var0, ArrayList<HashSe...
    method printUsageAndExit (line 1543) | private static void printUsageAndExit() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/benchmark/GGResult.java
  class GGResult (line 6) | class GGResult {
    method GGResult (line 14) | public GGResult(int var1, double var2, double var4, double var6) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/community/CPP.java
  class CPP (line 23) | public class CPP {
    method CPP (line 24) | public CPP() {
    method main (line 27) | public static void main(String[] var0) {
    method preprocess (line 57) | public static int preprocess(String var0, String var1, String var2) {
    method process (line 69) | public static void process(String var0, String var1, String var2) {
    method convert_wakita_clusters (line 118) | public static void convert_wakita_clusters(String var0, String var1, i...
    method convert_cnm_clusters (line 186) | public static void convert_cnm_clusters(String var0, String var1) {
    method convert_cnm (line 192) | private static void convert_cnm(String var0, String var1) {
    method convert_pons_clusters (line 223) | public static void convert_pons_clusters(String var0, String var1) {
    method convert_blondel_clusters (line 260) | public static boolean convert_blondel_clusters(String var0, String var...
    method printUsageAndExit (line 312) | private static void printUsageAndExit() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/community/CommPair.java
  class CommPair (line 6) | public class CommPair {
    method CommPair (line 11) | public CommPair(int var1, int var2, double var3) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/community/CommPairSet.java
  class CommPairSet (line 12) | public class CommPairSet {
    method compare (line 15) | public int compare(CommPair var1, CommPair var2) {
    method CommPairSet (line 20) | public CommPairSet(int var1) {
    method add (line 27) | public boolean add(CommPair var1) {
    method remove (line 33) | public void remove(int var1) {
    method best (line 49) | public CommPair best() {
    method toString (line 53) | public String toString() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/community/CompleteCliques.java
  class CompleteCliques (line 13) | public class CompleteCliques {
    method CompleteCliques (line 16) | public CompleteCliques() {
    method completeCliques (line 19) | public static ArrayList<HashSet<Integer>> completeCliques(ArrayList<Ha...

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/community/CompleteCliques1.java
  class CompleteCliques1 (line 13) | public class CompleteCliques1 {
    method CompleteCliques1 (line 14) | public CompleteCliques1() {
    method completeCliques1 (line 17) | public static ArrayList<HashSet<Integer>> completeCliques1(ArrayList<H...

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/community/RebuildCommunities.java
  class RebuildCommunities (line 17) | public class RebuildCommunities {
    method RebuildCommunities (line 20) | public RebuildCommunities() {
    method rebuildCommunities (line 23) | public static ArrayList<HashSet<Integer>> rebuildCommunities(int var0,...
    method compareCliques_mod_fast (line 102) | private static double compareCliques_mod_fast(int var0, int var1, int[...
    method collect (line 106) | private static void collect(Tree var0, HashSet<Integer> var1) {
    method modularity (line 118) | private static double modularity(ArrayList<HashSet<Integer>> var0, int...
    method show (line 177) | public static void show(int[][] var0, ArrayList<HashSet<Integer>> var1...
    method detcomp (line 190) | public static int detcomp(double var0, int var2, int var3, double var4...
    method updateMod (line 194) | private static double updateMod(int var0, int var1, int[][] var2, Arra...
    method compareCliques_missing (line 221) | static double compareCliques_missing(int var0, int var1, ArrayList<Has...
    method compareCliques_missing2 (line 232) | static double compareCliques_missing2(int var0, int var1, ArrayList<Ha...
    method compareCliques_edgeCount (line 241) | static double compareCliques_edgeCount(int var0, int var1, ArrayList<H...
    method edgeCount (line 248) | static int edgeCount(HashSet<Integer> var0, HashSet<Integer> var1, Arr...
    method compareCliques_mod (line 267) | static double compareCliques_mod(int var0, int var1, ArrayList<HashSet...
    method getMod (line 276) | static double getMod(String var0, ArrayList<HashSet<Integer>> var1, in...
    method writeCom (line 305) | static void writeCom(HashSet<Integer> var0, PrintStream var1) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/community/RemoveCliques.java
  class RemoveCliques (line 15) | public class RemoveCliques {
    method RemoveCliques (line 16) | public RemoveCliques() {
    method removeCliques (line 19) | public static ArrayList<HashSet<Integer>> removeCliques(ArrayList<Hash...
    method saveNewedges (line 35) | public static void saveNewedges(ArrayList<HashSet<Integer>> var0, Stri...
    method saveUndirected (line 57) | public static void saveUndirected(ArrayList<HashSet<Integer>> var0) {
    method printGraph (line 83) | private static void printGraph(ArrayList<HashSet<Integer>> var0) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/graph/ELEMENT.java
  class ELEMENT (line 6) | public class ELEMENT {
    method ELEMENT (line 10) | public ELEMENT() {
    method ELEMENT (line 13) | public ELEMENT(int var1, int var2) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/metric/Modularity.java
  class Modularity (line 19) | public class Modularity {
    method Modularity (line 22) | public Modularity() {
    method main (line 25) | public static void main(String[] var0) {
    method modularity (line 33) | public static double modularity(String var0, String var1) {
    method modularity (line 58) | private static double modularity(int var0, List<Integer> var1, List<Pa...
    method readClusters (line 95) | private static int readClusters(List<Integer> var0, String var1, HashM...
    method numVertex (line 130) | private static int numVertex(String var0, HashMap<String, Integer> var...

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/metric/Omega.java
  class Omega (line 12) | public class Omega {
    method Omega (line 13) | public Omega() {
    method main (line 16) | public static void main(String[] var0) {
    method readCount (line 29) | public static int readCount(Vector<HashMap<Integer, Integer>> var0, St...
    method evaluateOmega (line 91) | public static double evaluateOmega(Vector<HashMap<Integer, Integer>> v...

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/CONGA.java
  class CONGA (line 39) | public class CONGA {
    method CONGA (line 64) | public CONGA() {
    method main (line 67) | public static void main(String[] var0) {
    method clusterGraph (line 202) | public static Stats clusterGraph(int var0, HashSet<String> var1, Strin...
    method clusterGraph1 (line 212) | private static Stats clusterGraph1(int var0, String var1, int var2, Ha...
    method getSplitWeight (line 318) | private static float getSplitWeight(String var0, HashMap<String, HashM...
    method showOption (line 360) | private static void showOption(int var0, String var1, String var2) {
    method sameCluster (line 369) | private static boolean sameCluster(String var0, String var1, HashSet<H...
    method checkGraph (line 384) | private static int checkGraph(HashMap<String, HashSet<String>> var0) t...
    method statsGraph (line 410) | private static void statsGraph(List<HashSet<Integer>> var0) {
    method readGraphEdges (line 452) | public static HashMap<String, HashSet<String>> readGraphEdges(String v...
    method addWeight (line 538) | public static void addWeight(String var0, String var1, float var2, Has...
    method readGraph (line 554) | public static HashMap<String, HashSet<String>> readGraph(String var0, ...
    method vertex (line 633) | private static void vertex(String var0, HashMap<String, HashSet<String...
    method neighbour (line 640) | private static void neighbour(String var0, String var1, HashMap<String...
    method compactGraph (line 654) | public static void compactGraph(HashMap<String, HashSet<String>> var0,...
    method findClusters (line 713) | private static void findClusters(HashMap<String, HashSet<String>> var0...
    method writeSplitGraph (line 744) | public static void writeSplitGraph(List<HashSet<Integer>> var0, List<H...
    method sb_vs_vb (line 853) | private static float sb_vs_vb(int var0) {
    method cluster (line 877) | private static void cluster(List<HashSet<Integer>> var0, List<HashMap<...
    method wEdgeBetweenness (line 1056) | private static float wEdgeBetweenness(Edge var0, List<HashMap<Integer,...
    method wVertexBetweenness (line 1073) | private static float wVertexBetweenness(Vertex var0, float var1) {
    method updatePhase (line 1077) | private static boolean updatePhase(int var0, float var1, float var2, b...
    method addNewEdges (line 1100) | private static void addNewEdges(List<HashSet<Integer>> var0, List<Hash...
    method showStep (line 1165) | private static void showStep(int var0, int var1, int var2, float var3,...
    method setSizes (line 1204) | private static void setSizes(int var0, Between var1, List<HashSet<Inte...
    method update2Comps (line 1225) | private static boolean update2Comps(int var0, int var1, Between var2, ...
    method updateComps (line 1250) | private static void updateComps(HashSet<Integer> var0, Between var1, L...
    method compBetweenness (line 1261) | private static void compBetweenness(Between var0, List<HashSet<Integer...
    method betweenness (line 1272) | private static void betweenness(int var0, Between var1, List<HashSet<I...
    method compVertices (line 1373) | private static void compVertices(TreeSet<Integer> var0, Between var1, ...
    method detLess (line 1394) | public static boolean detLess(float var0, float var1) {
    method detLess (line 1398) | public static boolean detLess(float var0, float var1, int var2, int va...
    method detLess (line 1402) | public static boolean detLess(float var0, float var1, int var2, int va...
    method removeEdge (line 1406) | private static void removeEdge(int var0, int var1, Between var2, List<...
    method splitVertex (line 1420) | private static int splitVertex(int var0, Split var1, Between var2, Lis...
    method replaceWeight (line 1455) | private static void replaceWeight(int var0, int var1, int var2, List<H...
    method nameVertex (line 1473) | private static String nameVertex(List<String> var0, HashSet<Integer> v...
    method rootName (line 1481) | public static String rootName(String var0) {
    method compVertex (line 1486) | private static void compVertex(Integer var0, Between var1, List<HashSe...
    method tempMatrixCopy (line 1601) | private static float[][] tempMatrixCopy(float[][] var0, int var1) {
    method componentOf (line 1616) | public static TreeSet<Integer> componentOf(int var0, List<HashSet<Inte...
    method regionOf (line 1620) | private static TreeSet<Integer> regionOf(int var0, int var1, List<Hash...
    method regionOf (line 1626) | private static List<Integer> regionOf(int var0, int var1, List<HashSet...
    method smallRegion (line 1652) | private static boolean smallRegion(List<Integer> var0, TreeSet<Integer...
    method constructShowClusters (line 1675) | private static void constructShowClusters(String var0, int var1, Strin...
    method showClusters (line 1761) | private static void showClusters(List<Pair> var0, List<Pair> var1, Lis...
    method vad (line 1969) | private static double vad(HashMap<Integer, HashMap<String, Double>> va...
    method makeClusters (line 1989) | private static int makeClusters(int[] var0, HashMap<Integer, HashMap<S...
    method incWeight (line 2015) | private static void incWeight(HashMap<String, Double> var0, String var...
    method averageDiameter (line 2023) | private static GResult averageDiameter(HashMap<Integer, HashMap<String...
    method diameter (line 2047) | private static int diameter(HashMap<String, Double> var0, HashMap<Stri...
    method maxDist (line 2062) | private static int maxDist(String var0, HashMap<String, Double> var1, ...
    method modularity (line 2094) | private static double modularity(int var0, int[] var1, List<Pair> var2) {
    method rootOf (line 2131) | private static Tree rootOf(Tree var0) {
    method makeTree (line 2139) | private static Tree makeTree(Tree var0, Tree var1) {
    method clusterId (line 2149) | private static int clusterId(Tree var0) {
    method dispTree (line 2153) | private static void dispTree(Tree var0) {
    method flattenTree (line 2168) | private static HashSet<Integer> flattenTree(Tree var0) {
    method flattenTree (line 2174) | private static void flattenTree(Tree var0, HashSet<Integer> var1) {
    method printDegree (line 2184) | public static void printDegree(TreeSet<Integer> var0, List<HashSet<Int...
    method printUsageAndExit (line 2194) | private static void printUsageAndExit() {
    method cSplit (line 2219) | private static void cSplit(int var0, int var1, PrintStream var2, Clust...
    method cEdge (line 2229) | private static void cEdge(int var0, int var1, PrintStream var2, Cluste...
    method dOutput (line 2238) | private static void dOutput(String var0) {
    method sOutputN (line 2245) | private static void sOutputN(String var0) {
    method sOutput (line 2252) | private static void sOutput(String var0) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/algorithm/Between.java
  class Between (line 20) | public class Between {
    method compare (line 25) | public int compare(Edge var1, Edge var2) {
    method compare (line 36) | public int compare(Vertex var1, Vertex var2) {
    method Between (line 41) | public Between(List<HashSet<Integer>> var1, HashSet<String> var2, List...
    method getPB (line 66) | public PB getPB(int var1) {
    method setSize (line 70) | public void setSize(int var1) {
    method bestEdge (line 83) | public Edge bestEdge() {
    method bestVertex (line 87) | public Vertex bestVertex() {
    method initComp (line 91) | public void initComp(TreeSet<Integer> var1, List<HashSet<Integer>> var...
    method removeEdge (line 103) | public void removeEdge(int var1, int var2) {
    method splitVertex (line 109) | public void splitVertex(int var1, int var2, HashSet<Integer> var3, Has...
    method putEdge (line 131) | public void putEdge(int var1, int var2) {
    method putVertex (line 144) | public void putVertex(int var1, float var2, Split var3) {
    method putVertex (line 148) | public void putVertex(int var1, float var2, Split var3, float var4) {
    method getVertex (line 159) | public Vertex getVertex(int var1) {
    method wBetweenness (line 164) | private float wBetweenness(Edge var1, List<HashMap<Integer, Float>> va...
    method replaceEdges (line 179) | private void replaceEdges(int var1, HashSet<Integer> var2) {
    method replaceEdge (line 203) | private void replaceEdge(int var1, int var2, int var3) {
    method deleteEdge (line 218) | private void deleteEdge(int var1, int var2) {
    method addEdge (line 232) | private void addEdge(int var1, int var2) {
    method reduceVertex (line 242) | private void reduceVertex(int var1, int var2) {
    method deleteVertex (line 250) | private void deleteVertex(int var1) {
    method addVertex (line 260) | private void addVertex(int var1, HashSet<Integer> var2) {
    method printBetweenness (line 269) | public void printBetweenness(int var1, List<String> var2) {
    method checkConsistency (line 287) | public void checkConsistency(int var1, List<HashSet<Integer>> var2) {
    method getSplitBetweenness (line 384) | public ArrayList<Float> getSplitBetweenness(List<String> var1) {
    method getVertexBetweenness (line 410) | public ArrayList<Float> getVertexBetweenness(TreeSet<Integer> var1, Li...

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/algorithm/CPP.java
  class CPP (line 23) | public class CPP {
    method CPP (line 24) | public CPP() {
    method main (line 27) | public static void main(String[] var0) {
    method preprocessDir (line 91) | public static void preprocessDir(String var0, String var1, String var2) {
    method preprocess (line 165) | public static int preprocess(String var0, String var1, String var2, bo...
    method alspac (line 181) | public static void alspac(String var0, String var1) {
    method process (line 214) | public static void process(String var0, String var1, String var2) {
    method convert_wakita_clusters (line 270) | public static void convert_wakita_clusters(String var0, String var1, i...
    method convert_cnm_clusters (line 338) | public static void convert_cnm_clusters(String var0, String var1) {
    method convert_cnm_network (line 344) | public static void convert_cnm_network(String var0, String var1) {
    method convert_cnm (line 366) | private static void convert_cnm(String var0, String var1) {
    method convert_pons_clusters (line 397) | public static void convert_pons_clusters(String var0, String var1) {
    method convert_lfm_clusters (line 433) | public static void convert_lfm_clusters(String var0, String var1) {
    method convert_fc_clusters (line 475) | public static void convert_fc_clusters(String var0, String var1) {
    method convert_nmf_clusters (line 534) | public static void convert_nmf_clusters(String var0, String var1) {
    method convert_eagle_clusters (line 585) | public static void convert_eagle_clusters(String var0, String var1) {
    method convert_im_clusters (line 611) | public static void convert_im_clusters(String var0, String var1) {
    method convert_oslom_clusters (line 669) | public static void convert_oslom_clusters(String var0, String var1) {
    method convert_nmf_graph (line 690) | public static int convert_nmf_graph(String var0, String var1) {
    method convert_eagle_graph (line 748) | public static void convert_eagle_graph(String var0, String var1, Strin...
    method convert_im_graph (line 784) | public static void convert_im_graph(String var0, String var1) {
    method convert_blondel_clusters (line 841) | public static boolean convert_blondel_clusters(String var0, String var...
    method printUsageAndExit (line 893) | private static void printUsageAndExit() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/algorithm/PB.java
  class PB (line 13) | public class PB {
    method PB (line 21) | public PB(HashSet<Integer> var1, Vertex var2) {
    method replace (line 37) | public void replace(int var1, int var2) {
    method remove (line 43) | public int remove(int var1) {
    method print (line 70) | public void print(String var1) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/Pair.java
  class Pair (line 6) | public class Pair {
    method Pair (line 10) | public Pair(int var1, int var2) {
    method toString (line 15) | public String toString() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/StrPair.java
  class StrPair (line 6) | public class StrPair {
    method StrPair (line 10) | public StrPair(String var1, String var2) {
    method toString (line 15) | public String toString() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/Tree.java
  class Tree (line 6) | public class Tree {
    method Tree (line 12) | public Tree(int var1) {
    method Tree (line 19) | public Tree(Tree var1) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/benchmark/GResult.java
  class GResult (line 6) | public class GResult {
    method GResult (line 11) | public GResult(double var1, double var3, double var5) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/community/BP.java
  class BP (line 6) | public class BP {
    method BP (line 10) | public BP(float var1, float var2) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/community/ClusterInfo.java
  class ClusterInfo (line 10) | public class ClusterInfo {
    method ClusterInfo (line 16) | public ClusterInfo() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/community/Stats.java
  class Stats (line 12) | public class Stats {
    method Stats (line 43) | public Stats() {
    method showStats (line 46) | public void showStats(String var1) throws Exception {
    method splitVertex (line 59) | public void splitVertex(String var1, Split var2) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/graph/Edge.java
  class Edge (line 6) | public class Edge {
    method Edge (line 11) | public Edge(int var1, int var2) {
    method Edge (line 17) | public Edge(int var1, int var2, float var3) {
    method toString (line 23) | public String toString() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/graph/LabelledEdge.java
  class LabelledEdge (line 6) | public class LabelledEdge {
    method LabelledEdge (line 11) | public LabelledEdge(float var1, int var2, int var3) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/graph/Split.java
  class Split (line 8) | public class Split {
    method Split (line 12) | public Split(HashSet<Integer> var1, HashSet<Integer> var2) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/graph/Vertex.java
  class Vertex (line 6) | public class Vertex {
    method Vertex (line 12) | public Vertex(int var1) {
    method Vertex (line 19) | public Vertex(int var1, float var2, Split var3, float var4) {
    method toString (line 26) | public String toString() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/metric/ModOverlap.java
  class ModOverlap (line 15) | public class ModOverlap {
    method ModOverlap (line 18) | public ModOverlap() {
    method main (line 21) | public static void main(String[] var0) {
    method modOverlap (line 29) | public static double modOverlap(String var0, String var1) {
    method showClusters (line 45) | private static void showClusters(HashMap<Integer, HashMap<String, Doub...
    method invertClusters (line 51) | private static HashMap<String, HashMap<Integer, Double>> invertCluster...
    method readClusters (line 72) | private static HashMap<Integer, HashMap<String, Double>> readClusters(...
    method readGraphEdges (line 124) | public static HashMap<String, HashSet<String>> readGraphEdges(String v...
    method normalize (line 178) | public static void normalize(HashMap<Integer, HashMap<String, Double>>...
    method modOverlap (line 193) | public static double modOverlap(HashMap<Integer, HashMap<String, Doubl...
    method beta_out (line 258) | private static double beta_out(String var0, int var1, double var2, Has...
    method beta_in (line 278) | private static double beta_in(String var0, int var1, double var2, Hash...
    method F (line 298) | private static double F(String var0, String var1, int var2, HashMap<In...
    method f (line 305) | private static double f(double var0) {
    method alpha (line 309) | private static double alpha(String var0, int var1, HashMap<Integer, Ha...

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/copra/Project.java
  class Project (line 18) | public class Project {
    method Project (line 19) | public Project() {
    method main (line 22) | public static void main(String[] var0) {
    method project (line 71) | private static List<HashSet<Integer>> project(List<HashSet<Integer>> v...
    method weightedProject (line 89) | private static List<HashMap<Integer, Float>> weightedProject(List<Hash...
    method writeGraphEdges (line 117) | private static void writeGraphEdges(String var0, List<HashSet<Integer>...
    method writeWeightedEdges (line 139) | private static void writeWeightedEdges(String var0, List<HashMap<Integ...
    method printUsageAndExit (line 163) | private static void printUsageAndExit() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/copra/algorithm/COPRA.java
  class COPRA (line 30) | public class COPRA {
    method COPRA (line 39) | public COPRA() {
    method main (line 42) | public static void main(String[] var0) {
    method showOptions (line 219) | private static void showOptions(int var0, int var1, int var2, boolean ...
    method clusterGraph (line 305) | public static VecPair clusterGraph(int var0, String var1, String var2,...
    method clusterGraph (line 314) | public static VecPair clusterGraph(int var0, String var1, String var2,...
    method clusterGraph1 (line 337) | private static VecPair clusterGraph1(int var0, String var1, List<HashS...
    method nEdges (line 515) | private static int nEdges(List<HashSet<Integer>> var0) {
    method stdDev (line 525) | private static double stdDev(double var0, int var2, double var3) {
    method minSummary (line 537) | private static Map<Integer, Float> minSummary(Map<Integer, Float> var0...
    method clusteringSummary1 (line 553) | private static Map<Integer, Float> clusteringSummary1(List<ClusterLabe...
    method clusteringSummary2 (line 572) | private static Map<Integer, Float> clusteringSummary2(List<ClusterLabe...
    method propagate (line 593) | public static void propagate(String var0, int var1, String var2, Strin...
    method propagateClusters (line 606) | private static List<ClusterLabel> propagateClusters(List<ClusterLabel>...
    method reportRes (line 629) | private static void reportRes(Vector<Double> var0, Vector<String> var1...
    method sumRes (line 640) | private static Vector<Double> sumRes(Vector<Double> var0, Vector<Doubl...
    method report (line 656) | private static void report(double var0, double var2, double var4, doub...
    method readBiGraphEdges (line 673) | public static void readBiGraphEdges(String var0, List<HashSet<Integer>...
    method copyFile (line 679) | private static void copyFile(String var0, String var1) {
    method readBiGraphEdges (line 700) | private static int readBiGraphEdges(String var0, List<HashSet<Integer>...
    method nameInt (line 768) | private static int nameInt(String var0, List<String> var1, Map<String,...
    method outputClusters (line 784) | private static Vector<Double> outputClusters(List<ClusterLabel> var0, ...
    method totSize (line 852) | private static int totSize(List<TreeSet<Integer>> var0) {
    method filterClusters (line 862) | private static List<TreeSet<Integer>> filterClusters(List<TreeSet<Inte...
    method combineGraphs (line 891) | private static List<HashSet<Integer>> combineGraphs(List<HashSet<Integ...
    method combineClusters (line 916) | private static void combineClusters(List<TreeSet<Integer>> var0, List<...
    method addSingletons (line 923) | private static void addSingletons(List<TreeSet<Integer>> var0, HashSet...
    method flatten (line 938) | private static HashSet<Integer> flatten(List<TreeSet<Integer>> var0) {
    method writeClusters (line 948) | private static void writeClusters(List<TreeSet<Integer>> var0, String ...
    method convertClusters (line 965) | private static List<TreeSet<Integer>> convertClusters(List<ClusterLabe...
    method removeEmpty (line 992) | private static List<TreeSet<Integer>> removeEmpty(List<TreeSet<Integer...
    method simpleSimplifyClusters (line 1005) | private static void simpleSimplifyClusters(List<TreeSet<Integer>> var0...
    method deletable (line 1016) | private static boolean deletable(int var0, List<TreeSet<Integer>> var1) {
    method simplifyClusters (line 1032) | private static void simplifyClusters(List<TreeSet<Integer>> var0) {
    method contiguous (line 1066) | private static List<TreeSet<Integer>> contiguous(List<TreeSet<Integer>...
    method contiguous (line 1082) | private static TreeSet<Integer> contiguous(int var0, TreeSet<Integer> ...
    method writeBiClusters (line 1100) | private static void writeBiClusters(List<TreeSet<Integer>> var0, Strin...
    method writeClusters (line 1135) | private static void writeClusters(List<TreeSet<Integer>> var0, PrintSt...
    method writeCluster (line 1147) | private static void writeCluster(TreeSet<Integer> var0, PrintStream va...
    method simpleClustering (line 1171) | private static List<ClusterLabel> simpleClustering(int var0, float var...
    method printUsageAndExit (line 1182) | private static void printUsageAndExit() {
    method readClusters (line 1198) | private static List<ClusterLabel> readClusters(String var0, int var1, ...

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/copra/util/LabelPair.java
  class LabelPair (line 6) | public class LabelPair {
    method LabelPair (line 10) | public LabelPair(float var1, int var2) {
    method toString (line 15) | public String toString() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/copra/util/SetPair.java
  class SetPair (line 8) | public class SetPair implements Comparable<SetPair> {
    method SetPair (line 12) | public SetPair(int var1, TreeSet<Integer> var2) {
    method compareTo (line 17) | public int compareTo(SetPair var1) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/copra/util/VecPair.java
  class VecPair (line 8) | public class VecPair {
    method VecPair (line 12) | public VecPair(Vector<String> var1, Vector<Double> var2) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/copra/util/Vert.java
  class Vert (line 6) | public class Vert implements Comparable<Vert> {
    method Vert (line 10) | public Vert(int var1, int var2) {
    method compareTo (line 15) | @Override

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/copra/util/community/ClusterLabel.java
  class ClusterLabel (line 14) | public class ClusterLabel {
    method ClusterLabel (line 20) | public ClusterLabel(int var1, float var2) {
    method ClusterLabel (line 24) | public ClusterLabel(int var1, float var2, int var3, boolean var4) {
    method initialize (line 33) | private void initialize(int var1, float var2) {
    method getLabel (line 45) | public Map<Integer, Float> getLabel() {
    method getWeight (line 49) | public float getWeight() {
    method labelSet (line 53) | public TreeSet<Integer> labelSet() {
    method labelMap (line 57) | public Map<Integer, Float> labelMap() {
    method add (line 61) | public void add(int var1) {
    method sameAs (line 71) | public boolean sameAs(ClusterLabel var1) {
    method neighbour (line 100) | public void neighbour(ClusterLabel var1, float var2) {
    method noMore (line 119) | public void noMore() {
    method reduce (line 124) | private void reduce() {
    method normalize (line 174) | public void normalize() {
    method toString (line 188) | public String toString() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/copra/util/metric/ModOverlap.java
  class ModOverlap (line 15) | public class ModOverlap {
    method ModOverlap (line 18) | public ModOverlap() {
    method main (line 21) | public static void main(String[] var0) {
    method modOverlap (line 29) | public static double modOverlap(String var0, String var1) {
    method showClusters (line 45) | private static void showClusters(HashMap<Integer, HashMap<String, Doub...
    method invertClusters (line 51) | private static HashMap<String, HashMap<Integer, Double>> invertCluster...
    method readClusters (line 72) | private static HashMap<Integer, HashMap<String, Double>> readClusters(...
    method readGraphEdges (line 124) | public static HashMap<String, HashSet<String>> readGraphEdges(String v...
    method normalize (line 178) | public static void normalize(HashMap<Integer, HashMap<String, Double>>...
    method modOverlap (line 193) | public static double modOverlap(HashMap<Integer, HashMap<String, Doubl...
    method beta_out (line 258) | private static double beta_out(String var0, int var1, double var2, Has...
    method beta_in (line 278) | private static double beta_in(String var0, int var1, double var2, Hash...
    method F (line 298) | private static double F(String var0, String var1, int var2, HashMap<In...
    method f (line 305) | private static double f(double var0) {
    method alpha (line 309) | private static double alpha(String var0, int var1, HashMap<Integer, Ha...

FILE: Algorithms/2010-LinkCommunity/cpp/calcAndWrite_Jaccards.cpp
  function intersection_size (line 56) | int intersection_size( const set<int> &A, const set<int> &B ) {
  function main (line 76) | int main (int argc, char const *argv[]){

FILE: Algorithms/2010-LinkCommunity/cpp/clusterJaccsFile.cpp
  function main (line 65) | int main (int argc, char const *argv[]){

FILE: Algorithms/2010-LinkCommunity/cpp/edgelist2pairs.py
  function getDelimiter (line 46) | def getDelimiter(infile, expectedLength=2):

FILE: Algorithms/2010-LinkCommunity/cpp/partition_density.py
  function load_cluster_stats (line 29) | def load_cluster_stats(filename):
  function partition_density (line 33) | def partition_density(list_mc_nc):
  function partition_density_from_file (line 42) | def partition_density_from_file(filename):

FILE: Algorithms/2010-LinkCommunity/python/link_clustering.py
  function swap (line 42) | def swap(a, b):
  function Dc (line 48) | def Dc(m, n):
  class HLC (line 56) | class HLC:
    method __init__ (line 57) | def __init__(self, adj, edges):
    method initialize_edges (line 70) | def initialize_edges(self):
    method merge_comms (line 79) | def merge_comms(self, edge1, edge2, S, dendro_flag=False):
    method single_linkage (line 117) | def single_linkage(self, threshold=None, w=None, dendro_flag=False):
  function similarities_unweighted (line 156) | def similarities_unweighted(adj):
  function similarities_weighted (line 173) | def similarities_weighted(adj, ij2wij):
  function read_edgelist_unweighted (line 202) | def read_edgelist_unweighted(filename, delimiter=None, nodetype=str):
  function read_edgelist_weighted (line 218) | def read_edgelist_weighted(filename, delimiter=None, nodetype=str, weigh...
  function write_edge2cid (line 238) | def write_edge2cid(e2c, filename, delimiter="\t"):
  function write_dendro (line 271) | def write_dendro(filename, orig_cid2edge, linkage):
  class MyParser (line 283) | class MyParser(OptionParser):
    method format_epilog (line 284) | def format_epilog(self, formatter):

FILE: Algorithms/2010-LinkCommunity/python_yche_refactor/graph_io_helper.py
  function get_sorted_edge (line 9) | def get_sorted_edge(a, b):
  function read_edge_list_unweighted (line 13) | def read_edge_list_unweighted(filename, node_type=str):
  function read_edge_list_weighted (line 32) | def read_edge_list_weighted(filename, node_type=str, weight_type=float):
  function write_edge2cid (line 48) | def write_edge2cid(e2c, filename, delimiter="\t"):
  function write_dendro (line 74) | def write_dendro(filename, orig_cid2edge, linkage):

FILE: Algorithms/2010-LinkCommunity/python_yche_refactor/link_clustering.py
  class MyParser (line 10) | class MyParser(OptionParser):
    method format_epilog (line 11) | def format_epilog(self, formatter):

FILE: Algorithms/2010-LinkCommunity/python_yche_refactor/link_clustering_algo.py
  class HLC (line 10) | class HLC:
    method get_sorted_pair (line 12) | def get_sorted_pair(a, b):
    method sort_edge_pairs_by_similarity (line 16) | def sort_edge_pairs_by_similarity(adj_list_dict):
    method sort_edge_pairs_by_similarity_weighted (line 31) | def sort_edge_pairs_by_similarity_weighted(adj_list_dict, edge_weight_...
    method __init__ (line 57) | def __init__(self, adj_list_dict, edges):
    method single_linkage (line 85) | def single_linkage(self, threshold=None, w=None, dendro_flag=False):

FILE: Algorithms/2010-TopGC/src_original/Graphs/original/mkidx.c
  type list (line 7) | struct list {
  type list (line 13) | struct list
  type list (line 14) | struct list
  type list (line 21) | struct list
  function add (line 72) | void
  function dowrite (line 92) | void dowrite() {
  function outInt (line 106) | void outInt(long data) {

FILE: Algorithms/2010-TopGC/src_original/mkidx.c
  type list (line 7) | struct list
  type list (line 14) | struct list
  type list (line 15) | struct list
  type list (line 22) | struct list
  function add (line 91) | void
  function dowrite (line 114) | void
  function outInt (line 130) | void

FILE: Algorithms/2010-TopGC/src_refactor/src/main/java/FindMostProm.java
  class FindMostProm (line 16) | public class FindMostProm implements Runnable {
    method FindMostProm (line 50) | public FindMostProm(int start, int end, int threadNum, String graphFil...
    method run (line 76) | public void run() {
    method getScore2 (line 163) | public double getScore2(int currentNode, ArrayList<TempDouble2> neighb...
    method makeAndStoreWords (line 344) | public void makeAndStoreWords(int topN, ArrayList<TempDouble2> neighbo...
    method convertToList (line 441) | public LinkedList<TempDouble2> convertToList(Hashtable<Integer, Double...
    method getNumNeighborsCutoffs (line 464) | public HashSet<Integer> getNumNeighborsCutoffs(ArrayList<TempDouble2> ...
    method findIndex (line 486) | public int findIndex(double guess, TempDouble2[] neighbors) {
    method setLSH (line 503) | public void setLSH() {
    method setLSH2 (line 528) | public void setLSH2() {

FILE: Algorithms/2010-TopGC/src_refactor/src/main/java/HoldBucket.java
  class HoldBucket (line 9) | public class HoldBucket implements Comparable<HoldBucket> {
    method HoldBucket (line 13) | public HoldBucket(double score, Hashtable<Integer, Integer> bin) {
    method compareTo (line 18) | public int compareTo(HoldBucket other) {

FILE: Algorithms/2010-TopGC/src_refactor/src/main/java/HoldInt.java
  class HoldInt (line 6) | public class HoldInt {
    method HoldInt (line 9) | public HoldInt(int[] m) {

FILE: Algorithms/2010-TopGC/src_refactor/src/main/java/IntAndDouble.java
  class IntAndDouble (line 6) | public class IntAndDouble implements Comparable<IntAndDouble> {
    method IntAndDouble (line 10) | public IntAndDouble(int i, double d) {
    method compareTo (line 15) | public int compareTo(IntAndDouble other) {
    method toString (line 19) | public String toString() {

FILE: Algorithms/2010-TopGC/src_refactor/src/main/java/LSH.java
  class LSH (line 14) | public class LSH {
    method LSH (line 34) | public LSH(HashSet<Integer> bestNodes, String graphFileName, int m2, i...
    method setLSH (line 126) | public void setLSH() {
    method setLSH2 (line 151) | public void setLSH2() {
    method findLessBins (line 175) | public int findLessBins(double mult, int numToFind) {
    method findBins3 (line 245) | public int findBins3(double mult) {
    method findBins2 (line 307) | public int findBins2(double mult) {
    method findBins (line 367) | public int findBins(double mult) {
    method getCutoff (line 427) | public double getCutoff(double mult, double averageNumNeighbors) {
    method clearMem (line 436) | public void clearMem() {

FILE: Algorithms/2010-TopGC/src_refactor/src/main/java/LSHThread.java
  class LSHThread (line 14) | public class LSHThread implements Runnable {
    method LSHThread (line 39) | public LSHThread(int start2, int cutKey, String graphFileName, int tri...
    method run (line 66) | public void run() {
    method getNeighbors (line 113) | public LinkedList<TempDouble2> getNeighbors(Look3 look, int currentNod...
    method getNumNeighborsCutoffs (line 148) | public HashSet<Integer> getNumNeighborsCutoffs(LinkedList<TempDouble2>...
    method findIndex (line 170) | public int findIndex(double guess, TempDouble2[] neighbors) {
    method makeAndStoreWords (line 197) | public void makeAndStoreWords(int topN, LinkedList<TempDouble2> neighb...

FILE: Algorithms/2010-TopGC/src_refactor/src/main/java/LSH_Cluster.java
  class LSH_Cluster (line 11) | public class LSH_Cluster implements Comparable<LSH_Cluster> {
    method LSH_Cluster (line 18) | public LSH_Cluster(String l, Hashtable<Integer, Integer> n, Hashtable<...
    method LSH_Cluster (line 31) | public LSH_Cluster(String l, HashSet<Integer> n, Hashtable<Integer, Ha...
    method LSH_Cluster (line 44) | public LSH_Cluster(String l, HashSet<String> n, Hashtable<String, Hash...
    method compareTo (line 57) | public int compareTo(LSH_Cluster other) {
    method size (line 61) | public int size() {
    method getScore (line 65) | double getScore(Hashtable<Integer, Hashtable<Integer, Double>> smallGr...
    method getScore2 (line 94) | double getScore2(Hashtable<String, Hashtable<String, Double>> smallGra...

FILE: Algorithms/2010-TopGC/src_refactor/src/main/java/Look3.java
  class Look3 (line 10) | public class Look3 {
    method Look3 (line 24) | public Look3(String filename) throws Exception {
    method setCache (line 32) | public void setCache(int size) {
    method look (line 43) | public int[] look(int node) throws Exception {
    method getNEdges (line 86) | public int getNEdges() {
    method getNNodes (line 90) | public int getNNodes() {
    method hasWeights (line 94) | public boolean hasWeights() {
    method cacheLook (line 98) | private int[] cacheLook(int key) {
    method addCache (line 109) | public void addCache(int key, int[] entry) {
    method printCacheStats (line 120) | public static void printCacheStats() {
    method main (line 125) | public static void main(String[] args) {

FILE: Algorithms/2010-TopGC/src_refactor/src/main/java/MaxHeap.java
  class MaxHeap (line 8) | public class MaxHeap {
    method main (line 13) | public static void main(String[] args) {
    method MaxHeap (line 25) | public MaxHeap() {
    method MaxHeap (line 29) | public MaxHeap(int max) {
    method leftchild (line 36) | private int leftchild(int pos) {
    method rightchild (line 40) | private int rightchild(int pos) {
    method parent (line 44) | private int parent(int pos) {
    method isleaf (line 48) | private boolean isleaf(int pos) {
    method swap (line 52) | private void swap(int pos1, int pos2) {
    method insert (line 58) | public void insert(HoldBucket elem) {
    method doubleSize (line 72) | public void doubleSize() {
    method print (line 83) | public void print() {
    method peek (line 91) | public HoldBucket peek() {
    method removeMin (line 95) | public HoldBucket removeMin() {
    method pushdown (line 105) | private void pushdown(int position) {
    method size (line 122) | public int size() {

FILE: Algorithms/2010-TopGC/src_refactor/src/main/java/MinHeap.java
  class MinHeap (line 6) | public class MinHeap {
    method main (line 11) | public static void main(String[] args) {
    method MinHeap (line 29) | public MinHeap() {
    method MinHeap (line 33) | public MinHeap(int max) {
    method leftchild (line 40) | private int leftchild(int pos) {
    method rightchild (line 44) | private int rightchild(int pos) {
    method parent (line 48) | private int parent(int pos) {
    method isleaf (line 52) | private boolean isleaf(int pos) {
    method swap (line 56) | private void swap(int pos1, int pos2) {
    method insert (line 62) | public void insert(IntAndDouble elem) {
    method doubleSize (line 76) | public void doubleSize() {
    method print (line 87) | public void print() {
    method peek (line 95) | public IntAndDouble peek() {
    method removeMin (line 99) | public IntAndDouble removeMin() {
    method pushdown (line 109) | private void pushdown(int position) {
    method size (line 126) | public int size() {

FILE: Algorithms/2010-TopGC/src_refactor/src/main/java/Prime.java
  class Prime (line 6) | public class Prime {
    method Prime (line 7) | public Prime() {
    method isPrime (line 10) | boolean isPrime(int n) {
    method getPrime (line 28) | int getPrime(int n) {

FILE: Algorithms/2010-TopGC/src_refactor/src/main/java/TempDouble2.java
  class TempDouble2 (line 6) | class TempDouble2 implements Comparable<TempDouble2> {
    method TempDouble2 (line 11) | public TempDouble2(int n, double w) {
    method compareTo (line 16) | public int compareTo(TempDouble2 other) {

FILE: Algorithms/2010-TopGC/src_refactor/src/main/java/TopGC.java
  class TopGC (line 20) | public class TopGC {
    method main (line 45) | public static void main(String[] argv) throws FileNotFoundException, I...
    method TopGC (line 49) | public TopGC(String[] argv) {
    method setDefaultArgs (line 329) | public void setDefaultArgs() {
    method overlapCluster (line 368) | public boolean overlapCluster(LSH_Cluster cluster, LinkedList<HashSet<...
    method getScore (line 397) | public double getScore(int currentNode, Hashtable<Integer, Double> nei...
    method checkArgsFirst (line 425) | public void checkArgsFirst(String[] argv) {
    method checkArgs (line 478) | public void checkArgs(String[] argv) {
    method makeLine (line 575) | public String makeLine(Hashtable<Integer, Integer> cluster) {
    method makeLine (line 594) | public String makeLine(HashSet<Integer> cluster) {
    method removeDupes (line 613) | public ArrayList<Hashtable<Integer, Integer>> removeDupes(ArrayList<Ha...
    method intersect (line 776) | public int intersect(HashSet<Integer> compare1, HashSet<Integer> compa...
    method overlapTooMuch (line 789) | public boolean overlapTooMuch(HashSet<Integer> compare1, HashSet<Integ...
    method convertClust (line 811) | public Hashtable<Integer, Integer> convertClust(HashSet<Integer> nodes...
    method shouldCombine (line 835) | public boolean shouldCombine(double overlapRemove, TopGC.TempCluster b...
    method removeOverlap (line 887) | public boolean removeOverlap(double overlapRemove, ArrayList<Hashtable...
    method combineBuckets (line 946) | public void combineBuckets(Hashtable<Integer, Integer> bucket1, Hashta...
    method split (line 961) | public String[] split(String str, char delim) {
    class IterateSet (line 981) | private class IterateSet {
      method IterateSet (line 986) | public IterateSet(LinkedList<Integer> var1) {
      method almostDone (line 995) | public boolean almostDone() {
      method hasNext (line 1007) | public boolean hasNext() {
      method next (line 1011) | public HashSet<Integer> next() {
      method incr (line 1024) | public void incr() {
    class TempCluster (line 1042) | private class TempCluster {
      method TempCluster (line 1054) | private TempCluster(HashSet<Integer> var1, HashSet<Integer> nodes) {
      method TempCluster (line 1060) | private TempCluster(TopGC.TempCluster clust1, TopGC.TempCluster clus...

FILE: Algorithms/2010-iLCD/src/src/main/java/CorePackage/Main.java
  class Main (line 29) | public class Main {
    method main (line 93) | public static void main(String args[]) {
    method argumentsHandling (line 132) | private void argumentsHandling(String args[]) {

FILE: Algorithms/2010-iLCD/src/src/main/java/Inputs/InputCTNFhandler.java
  class InputCTNFhandler (line 16) | public class InputCTNFhandler extends InputHandlerInterface{
    method InputCTNFhandler (line 18) | public InputCTNFhandler(Network net) {
    method operationFromLine (line 25) | public Operation operationFromLine(String line){

FILE: Algorithms/2010-iLCD/src/src/main/java/Inputs/InputHandlerInterface.java
  class InputHandlerInterface (line 6) | public abstract class InputHandlerInterface {
    method InputHandlerInterface (line 9) | InputHandlerInterface(Network net){
    method operationFromLine (line 12) | public abstract Operation operationFromLine(String line);

FILE: Algorithms/2010-iLCD/src/src/main/java/Inputs/InputNCOLhandler.java
  class InputNCOLhandler (line 10) | public class InputNCOLhandler extends InputHandlerInterface{
    method InputNCOLhandler (line 12) | public InputNCOLhandler(Network net) {
    method operationFromLine (line 19) | public Operation operationFromLine(String line){

FILE: Algorithms/2010-iLCD/src/src/main/java/Inputs/InputOLDLNDhandler.java
  class InputOLDLNDhandler (line 17) | public class InputOLDLNDhandler extends InputHandlerInterface{
    method InputOLDLNDhandler (line 19) | public InputOLDLNDhandler(Network net) {
    method operationFromLine (line 26) | public Operation operationFromLine(String line){

FILE: Algorithms/2010-iLCD/src/src/main/java/Outputs/OutputCTNF.java
  class OutputCTNF (line 31) | public class OutputCTNF implements OutputHandlerInterface{
    method OutputCTNF (line 41) | public OutputCTNF(MyDateManager dateManager, Network theNetwork) {
    method initialise (line 46) | public void initialise(String outputFile){
    method terminate (line 56) | public void terminate(){
    method printLine (line 60) | public void printLine(String line){
    method handleGrowth (line 71) | public void handleGrowth(Node n, Community c){
    method handleGrowth (line 75) | public void handleGrowth(Community initialCommunity, Community resulti...
    method handleBirth (line 84) | public void handleBirth(Community c) {
    method handleDeath (line 90) | public void handleDeath(Community c) {
    method handleContraction (line 106) | public void handleContraction(Node n, Community c) {
    method handleNewEdge (line 110) | public void handleNewEdge(Node n, Node n2) {
    method handleRemoveEdge (line 114) | public void handleRemoveEdge(Node n, Node n2) {
    method handleFusion (line 118) | public void handleFusion(Community resultingCommunity, Community suppr...
    method handleDateChange (line 123) | public void handleDateChange(String date) {

FILE: Algorithms/2010-iLCD/src/src/main/java/Outputs/OutputHandlerInterface.java
  type OutputHandlerInterface (line 15) | public interface OutputHandlerInterface {
    method initialise (line 20) | public void initialise(String outputFile);
    method terminate (line 23) | public void terminate();
    method handleGrowth (line 28) | public void handleGrowth(Node n, Community c);
    method handleGrowth (line 30) | public void handleGrowth(Community initialCommunity, Community resulti...
    method handleBirth (line 32) | public void handleBirth(Community c);
    method handleDeath (line 34) | public void handleDeath(Community c);
    method handleContraction (line 38) | public void handleContraction(Node n, Community c);
    method handleNewEdge (line 40) | public void handleNewEdge(Node n, Node n2);
    method handleRemoveEdge (line 42) | public void handleRemoveEdge(Node n, Node n2);
    method handleFusion (line 44) | public void handleFusion(Community resultingCommunity, Community suppr...
    method handleDateChange (line 45) | public void handleDateChange(String date);

FILE: Algorithms/2010-iLCD/src/src/main/java/Outputs/OutputMultipleHandler.java
  class OutputMultipleHandler (line 18) | public class OutputMultipleHandler implements OutputHandlerInterface{
    method OutputMultipleHandler (line 29) | public OutputMultipleHandler() {
    method addOutputHandler (line 32) | public void addOutputHandler(OutputHandlerInterface oh){
    method initialise (line 35) | public void initialise(String outputFile){
    method terminate (line 41) | public void terminate(){
    method handleGrowth (line 47) | public void handleGrowth(Node n, Community c){
    method handleGrowth (line 53) | public void handleGrowth(Community initialCommunity, Community resulti...
    method handleBirth (line 60) | public void handleBirth(Community c) {
    method handleDeath (line 68) | public void handleDeath(Community c) {
    method handleContraction (line 81) | public void handleContraction(Node n, Community c) {
    method handleNewEdge (line 86) | public void handleNewEdge(Node n, Node n2) {
    method handleRemoveEdge (line 91) | public void handleRemoveEdge(Node n, Node n2) {
    method handleFusion (line 96) | public void handleFusion(Community resultingCommunity, Community suppr...
    method handleDateChange (line 102) | public void handleDateChange(String date) {

FILE: Algorithms/2010-iLCD/src/src/main/java/Outputs/OutputStatic.java
  class OutputStatic (line 26) | public class OutputStatic implements OutputHandlerInterface{
    method OutputStatic (line 37) | public OutputStatic(MyDateManager dateManager, Network theNetwork) {
    method initialise (line 41) | public void initialise(String outputFile){
    method terminate (line 51) | public void terminate(){
    method printLine (line 70) | public void printLine(String line){
    method handleGrowth (line 78) | public void handleGrowth(Node n, Community c){
    method handleGrowth (line 82) | public void handleGrowth(Community initialCommunity, Community resulti...
    method handleBirth (line 86) | public void handleBirth(Community c) {
    method handleDeath (line 92) | public void handleDeath(Community c) {
    method handleContraction (line 105) | public void handleContraction(Node n, Community c) {
    method handleNewEdge (line 109) | public void handleNewEdge(Node n, Node n2) {
    method handleRemoveEdge (line 113) | public void handleRemoveEdge(Node n, Node n2) {
    method handleFusion (line 117) | public void handleFusion(Community resultingCommunity, Community suppr...
    method handleDateChange (line 121) | public void handleDateChange(String date) {

FILE: Algorithms/2010-iLCD/src/src/main/java/Outputs/OutputSummary.java
  class OutputSummary (line 27) | public class OutputSummary implements OutputHandlerInterface{
    method OutputSummary (line 42) | public OutputSummary(MyDateManager dateManager, Network theNetwork) {
    method initialise (line 47) | public void initialise(String outputFile){
    method terminate (line 57) | public void terminate(){
    method printACommunity (line 78) | private void printACommunity(CommunityToPrint ctp){
    method printLine (line 93) | public void printLine(String line){
    method handleGrowth (line 104) | public void handleGrowth(Node n, Community c){
    method handleGrowth (line 111) | public void handleGrowth(Community initialCommunity, Community resulti...
    method handleBirth (line 120) | public void handleBirth(Community c) {
    method handleDeath (line 135) | public void handleDeath(Community c) {
    method handleContraction (line 158) | public void handleContraction(Node n, Community c) {
    method handleNewEdge (line 162) | public void handleNewEdge(Node n, Node n2) {
    method handleRemoveEdge (line 166) | public void handleRemoveEdge(Node n, Node n2) {
    method handleFusion (line 170) | public void handleFusion(Community resultingCommunity, Community suppr...
    method handleDateChange (line 177) | public void handleDateChange(String date) {
    class CommunityToPrint (line 182) | private class CommunityToPrint implements Comparable<CommunityToPrint>{
      method compareTo (line 188) | @Override

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/Community.java
  class Community (line 12) | public class Community implements Comparable<Community>{
    method Community (line 22) | public Community(Community c) {
    method Community (line 26) | public Community(){
    method Community (line 31) | public Community(int ID){
    method addNode (line 35) | private void addNode(Node node1) {
    method addNodeToCommunity (line 46) | public void addNodeToCommunity(Node n){
    method removeNodeFromCommunity (line 52) | protected void removeNodeFromCommunity(Node n){
    method removeNode (line 58) | protected void removeNode(Node n) {
    method getID (line 67) | public int getID() {
    method isDifferent (line 72) | public boolean isDifferent(Community otherCom) {
    method setBirthDate (line 92) | protected void setBirthDate(MyDate date){
    method getComponents (line 97) | public THashSet<Node> getComponents() {
    method youngerThan (line 101) | public boolean youngerThan(Community c2) {
    method compareTo (line 105) | @Override
    method getCommonNodes (line 110) | public THashSet<Node> getCommonNodes(Community cTested) {

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/CoreProcessor.java
  class CoreProcessor (line 19) | public class CoreProcessor {
    method CoreProcessor (line 28) | public CoreProcessor(Network mainNetwork) {
    method setOperationHandler (line 32) | public void setOperationHandler(OperationsHandler opHandler){
    method setInputHandler (line 36) | public void setInputHandler(InputHandlerInterface inputHandler){
    method initializeReading (line 40) | public void initializeReading(String file){
    method readALine (line 50) | public void readALine(String line){
    method readOperationStream (line 59) | public void readOperationStream(String file){
    method getOperation (line 80) | public Operation getOperation(String line){

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/Interface.java
  class Interface (line 13) | public class Interface {
    type PossibleOutputFormat (line 25) | public static enum PossibleOutputFormat{CTNF,SUMMARY,STATIC}
    type PossibleInputFormat (line 26) | public enum PossibleInputFormat {UNKNOWN, NCOL, TNF, CTNF, LND}
    method Interface (line 29) | public Interface(String inputFile, String inputDateF){
    method addOutput (line 61) | public void addOutput(PossibleOutputFormat format, String outputFile, ...
    method setOperationHandler (line 86) | public void setOperationHandler(OperationsHandler operationHandler){
    method readOperationStream (line 94) | public void readOperationStream() {
    method processALine (line 103) | public String processALine(String line) {
    method terminate (line 113) | public void terminate() {
    method getFileType (line 118) | public static PossibleInputFormat getFileType(String file){
    method getCurrentDate (line 138) | public String getCurrentDate(){
    method getInputFileType (line 142) | public PossibleInputFormat getInputFileType(){

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/MyDate.java
  class MyDate (line 3) | public class MyDate implements Comparable{
    type dateType (line 5) | public enum dateType {YYYYMMDD,YYYYMMDDHHMMSS,NONE}
    method MyDate (line 11) | public MyDate(String date, dateType type){
    method MyDate (line 24) | public MyDate(MyDate currentTime) {
    method writeDate (line 29) | public String writeDate(dateType type){
    method before (line 42) | public boolean before(MyDate toCompare){
    method after (line 46) | public boolean after(MyDate toCompare){
    method sameDateAs (line 50) | public boolean sameDateAs(MyDate toCompare){
    method beginningOfTheUniverse (line 55) | public static MyDate beginningOfTheUniverse(){
    method increment (line 60) | public MyDate increment() {
    method compareTo (line 70) | @Override

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/MyDateManager.java
  class MyDateManager (line 5) | public class MyDateManager {
    method MyDateManager (line 12) | public MyDateManager(String inputFormat){
    method setOutputDateFormat (line 17) | public void setOutputDateFormat(String outputFormat){
    method getDate (line 22) | public MyDate getDate(String date){
    method writeDate (line 34) | public String writeDate(MyDate aDate){
    method convertDateFormat (line 38) | private MyDate.dateType convertDateFormat(String stringFormat){

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/Network.java
  class Network (line 17) | public class Network {
    method Network (line 26) | public Network(MyDateManager dateManager, OutputHandlerInterface outpu...
    method getNode (line 32) | public Node getNode(String nodeName) {
    method doOperation (line 43) | public void doOperation(Operation currentOperation) {
    method changeTime (line 91) | public void changeTime(MyDate newDate) {
    method getCurrentTime (line 100) | public MyDate getCurrentTime() {
    method createCommunity (line 105) | public void createCommunity(Integer c) {
    method getCommunity (line 114) | public Community getCommunity(Integer com) {
    method removeCommunity (line 122) | public void removeCommunity(Community c) {
    method addCommunity (line 131) | public void addCommunity(Community c) {
    method getCommunities (line 139) | public THashSet<Community> getCommunities() {

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/Node.java
  class Node (line 10) | public class Node {
    method Node (line 18) | public Node(String nodeName) {
    method getCommunities (line 22) | public THashSet<Community> getCommunities(){
    method addCommunity (line 26) | protected void addCommunity(Community c) {
    method getName (line 35) | public String getName() {
    method removeCommunity (line 39) | protected void removeCommunity(Community c) {
    method getNeighbors (line 47) | public THashSet<Node> getNeighbors() {
    method getNeighborsInCommunity (line 51) | public THashSet<Node> getNeighborsInCommunity(Community c){
    method addNeighbor (line 58) | protected void addNeighbor(Node node2) {
    method removeNeighbor (line 68) | protected void removeNeighbor(Node node2) {

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/Operations/AddEdgeOperation.java
  class AddEdgeOperation (line 6) | public class AddEdgeOperation extends Operation{
    method AddEdgeOperation (line 8) | public AddEdgeOperation(Node n1, Node n2) {

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/Operations/BirthCommunityOperation.java
  class BirthCommunityOperation (line 9) | public class BirthCommunityOperation extends Operation{
    method BirthCommunityOperation (line 13) | public BirthCommunityOperation(Community c) {

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/Operations/ContractCommunityOperation.java
  class ContractCommunityOperation (line 7) | public class ContractCommunityOperation extends Operation{
    method ContractCommunityOperation (line 9) | public ContractCommunityOperation(Community c, Node n) {

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/Operations/DeathCommunityOperation.java
  class DeathCommunityOperation (line 6) | public class DeathCommunityOperation extends Operation{
    method DeathCommunityOperation (line 8) | public DeathCommunityOperation(Community c) {

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/Operations/FusionCommunityOperation.java
  class FusionCommunityOperation (line 6) | public class FusionCommunityOperation extends Operation{
    method FusionCommunityOperation (line 8) | public FusionCommunityOperation(Community absorb, Community mergedIn) {

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/Operations/GrowthCommunityOperation.java
  class GrowthCommunityOperation (line 7) | public class GrowthCommunityOperation extends Operation{
    method GrowthCommunityOperation (line 9) | public GrowthCommunityOperation(Community c, Node n) {

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/Operations/Operation.java
  class Operation (line 8) | public class Operation {
    type OperationType (line 26) | public enum OperationType { ADD, REMOVE,BIRTH,DEATH,FUSION,GROWTH,CONT...
    method Operation (line 29) | public Operation(Node n1, Node n2, Community c1, Community c2, Communi...
    method getNode1 (line 37) | public Node getNode1(){
    method getNode2 (line 41) | public Node getNode2(){
    method getCommunity1 (line 45) | public Community getCommunity1(){
    method getCommunity2 (line 49) | public Community getCommunity2(){
    method getCommunity3 (line 53) | public Community getCommunity3(){
    method getNodes (line 57) | public HashSet<Node> getNodes(){

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/Operations/RemoveEdgeOperation.java
  class RemoveEdgeOperation (line 6) | public class RemoveEdgeOperation extends Operation{
    method RemoveEdgeOperation (line 8) | public RemoveEdgeOperation(Node n1, Node n2) {

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/OperationsHandler.java
  type OperationsHandler (line 5) | public interface OperationsHandler {
    method handle (line 7) | public void handle(Operation currentOperation);

FILE: Algorithms/2010-iLCD/src/src/main/java/communityDetectionPackage/ILCDMetaAlgorithm.java
  class ILCDMetaAlgorithm (line 44) | public class ILCDMetaAlgorithm implements OperationsHandler {
    method ILCDMetaAlgorithm (line 56) | public ILCDMetaAlgorithm(Implementation implementationToUse, Network n...
    method handle (line 61) | public void handle(Operation currentOperation) {
    method addNodeToCommunity (line 248) | public void addNodeToCommunity(Node node, Community c) {
    method fusion (line 256) | private void fusion(Community resultingCommunity, Community c1, Commun...
    method deathOf (line 275) | private void deathOf(Community c) {
    method contract (line 297) | public void contract(Node n, Community community) {
    method diviseCommunity (line 308) | private void diviseCommunity(Community tempSavedCom, ArrayList<Communi...
    method addCommunity (line 315) | public void addCommunity(Community c) {

FILE: Algorithms/2010-iLCD/src/src/main/java/implementable/Implementation.java
  class Implementation (line 22) | public abstract class Implementation {
    method GROWTH (line 30) | public abstract boolean GROWTH(Node candidate, Community com);
    method BIRTH (line 40) | public abstract ArrayList<Community> BIRTH(Node n1, Node n2);
    method CONTRACTION_DIVISION (line 54) | public abstract ArrayList<Community> CONTRACTION_DIVISION(Community af...
    method DEATH (line 61) | public abstract boolean DEATH(Community testedCom);
    method FUSION (line 71) | public abstract ArrayList<Community> FUSION(Community c1, Community c2...
    method getCommunitiesForWhichIsRepresentative (line 78) | public THashSet<Community> getCommunitiesForWhichIsRepresentative(Node...

FILE: Algorithms/2010-iLCD/src/src/main/java/implementable/ImplementationRNHM.java
  class ImplementationRNHM (line 21) | public class ImplementationRNHM extends Implementation {
    method ImplementationRNHM (line 32) | public ImplementationRNHM(int intialComSize, float integrateParameter,...
    method GROWTH (line 38) | @Override
    method BIRTH (line 53) | @Override
    method CONTRACTION_DIVISION (line 80) | @Override
    method DEATH (line 118) | @Override
    method FUSION (line 128) | @Override
    method getRepresentativity (line 167) | private float getRepresentativity(Node n, Community c) {
    method getIdRelation (line 180) | private String getIdRelation(Node n, Community c) {
    method getBelongingStrength (line 184) | private float getBelongingStrength(Node n, Community c) {
    method getIntrinsicCohesion (line 204) | private float getIntrinsicCohesion(Community c) {
    method birthCase3 (line 229) | private ArrayList<Community> birthCase3(ArrayList<Community> newCommun...
    method birthCase4 (line 258) | private ArrayList<Community> birthCase4(ArrayList<Community> newCommun...

FILE: Algorithms/2010-iLCD/src/src/main/java/tools/DebugMode.java
  class DebugMode (line 5) | public class DebugMode {
    method printDebug (line 9) | public static void printDebug(String s){
    method printBasic (line 24) | public static void printBasic(String s){

FILE: Algorithms/2010-iLCD/src/src/main/java/tools/SortEdges.java
  class SortEdges (line 8) | public class SortEdges {
    method sort (line 12) | public static void sort(String input, String output){
    method main (line 47) | public static void main(String args[]){

FILE: Algorithms/2010-iLCD/src/src/main/java/tools/Sorter.java
  class Sorter (line 7) | public class Sorter<T> {
    method Sorter (line 11) | public Sorter(){
    method add (line 16) | public void add(T el, Double val){
    method getSortedValues (line 33) | public ArrayList<T> getSortedValues(){
    method getElts (line 44) | public ArrayList<T> getElts(){
    class Element (line 50) | public class Element<T> implements Comparable{
      method compareTo (line 54) | @Override
    method modVal (line 62) | public void modVal(T el, Double val){
    method getHigher (line 68) | public T getHigher(){

FILE: Algorithms/2010-iLCD/src/src/main/java/tools/TextFileHandler.java
  class TextFileHandler (line 14) | public class TextFileHandler {
    method loadDictionary (line 19) | public static HashMap<String,String> loadDictionary(String fileName,St...
    method readFirstLine (line 53) | public static String readFirstLine(String fileName){
    method loadFile (line 74) | public static ArrayList<String> loadFile(String fileName){
    method printFile (line 97) | public static void printFile(String fileName,ArrayList<String> lines){
    method splitLine (line 117) | public static Vector<String> splitLine(String line, String separator){
    method main (line 125) | public static void main(String args[]){
    method cleanNodeName (line 158) | public static String cleanNodeName(String nodeName){

FILE: Algorithms/2010-iLCD/src/src/main/java/tools/ToolDate.java
  class ToolDate (line 7) | public class ToolDate {
    method timInDaySince (line 11) | public static long timInDaySince(Date d){
    method timInDayBetween (line 15) | public static long timInDayBetween(Date beginning, Date end){
    method dateFromString (line 19) | public static Date dateFromString(String date, String format){

FILE: Algorithms/2011-GCE/src-original/Community_Finder.cpp
  function sizeSortFunctionLargestFirst (line 26) | bool sizeSortFunctionLargestFirst (Seed * two,  Seed * one)
  function sizeSortFunctionSmallestFirst (line 31) | bool sizeSortFunctionSmallestFirst (Seed * one,  Seed * two)
  function vectorSizeSortFunctionLargestFirst (line 36) | bool vectorSizeSortFunctionLargestFirst (vector <V> two,  vector <V> one)
  function vectorSizeSortFunctionSmallestFirst (line 40) | bool vectorSizeSortFunctionSmallestFirst (vector <V> one,  vector <V> two)

FILE: Algorithms/2011-GCE/src-original/Community_Finder.h
  function class (line 26) | class Community_Finder {

FILE: Algorithms/2011-GCE/src-original/Range.hpp
  class IteratorRange (line 13) | class IteratorRange {
    method IteratorRange (line 20) | IteratorRange(const Iterator & _begin, const Iterator & _end) : curren...
    method IteratorRange (line 21) | IteratorRange(std::pair<Iterator,Iterator> be) : current(be.first), en...
    method empty (line 23) | bool empty() const { return current == end; }
    method Iterated (line 24) | Iterated & front() const { return *current; }
    method Iterator (line 25) | Iterator   frontIterator() const { return  current; }
    method popFront (line 26) | void popFront() { ++current; }
  class ContainerProperties (line 30) | class ContainerProperties {
  class ContainerRange (line 37) | class ContainerRange : public IteratorRange< typename ContainerPropertie...
    method ContainerRange (line 39) | ContainerRange(Container &c) : IteratorRange< typename ContainerProper...
  class ContainerRangeReverse (line 42) | class ContainerRangeReverse : public IteratorRange< typename ContainerPr...
    method ContainerRangeReverse (line 44) | ContainerRangeReverse(Container &c) : IteratorRange< typename Containe...
  class RangeTypes (line 50) | class RangeTypes {
  class ChainedRange (line 57) | class ChainedRange { // Chain Two together
    method ChainedRange (line 61) | ChainedRange(const Range &_first, const Range &_second) : first(_first...
    method empty (line 62) | bool empty() const { return first.empty() && second.empty(); }
    method firstEmpty (line 63) | bool firstEmpty() const { return first.empty(); }
    method front (line 64) | typename RangeTypes<Range>::ElementType front() const { return first.e...
    method popFront (line 65) | void popFront() { if (first.empty()) second.popFront(); else first.pop...

FILE: Algorithms/2011-GCE/src-original/Seed.h
  function class (line 19) | class Seed {

FILE: Algorithms/2011-GCE/src-original/aaron_utils.cpp
  function testForError (line 2) | int testForError(FILE * x) { return x==NULL; }
  function testForError (line 3) | int testForError(int x) { return x==-1; }
  function string (line 5) | string show(long x) { ostringstream s; s << x; return s.str(); }
  function string (line 6) | string show(const char * x) { ostringstream s; s << x; return s.str(); }
  function string (line 7) | string show(const string &s) { return s; }
  function string (line 15) | string runningAverage::operator() (void) const {
  function DummyOutputStream (line 21) | DummyOutputStream& DummyOutputStream::operator << (int) { return *this; }
  function DummyOutputStream (line 22) | DummyOutputStream& DummyOutputStream::operator << (const char*) { return...

FILE: Algorithms/2011-GCE/src-original/aaron_utils.hpp
  function string (line 24) | static string thousandsSeparated(unsigned long x) {
  class runningAverage (line 57) | class runningAverage {
  type RefPair (line 68) | struct RefPair {
    method RefPair (line 71) | RefPair(T1 &in1, T2 &in2) : e1(in1), e2(in2) { }
  function make_refpair (line 75) | RefPair<T1, T2> make_refpair(T1 &e1, T2 &e2) {
  type DummyOutputStream (line 80) | struct DummyOutputStream {
  type StopWatch (line 86) | struct StopWatch { // TODO: put the stopWatch in another file?
    type timeval (line 87) | struct timeval
    type timeval (line 88) | struct timeval
    method StopWatch (line 89) | StopWatch() {
    method laptime (line 93) | void laptime(void) { laptime(""); }
    method laptime (line 94) | void laptime(const string &tag) {

FILE: Algorithms/2011-GCE/src-original/cliques.cpp
  type cliques (line 3) | namespace cliques {
    function cliquesForOneNode (line 8) | void cliquesForOneNode(const SimpleIntGraph &g, CliqueFunctionAdaptor ...
    function tryCandidate (line 26) | static inline void tryCandidate (const SimpleIntGraph & g, CliqueFunct...
    function cliquesWorker (line 42) | void cliquesWorker(const SimpleIntGraph & g, CliqueFunctionAdaptor &cl...
    function create_directory (line 120) | void create_directory(const string& directory) throw() {
    function cliquesToDirectory (line 130) | void cliquesToDirectory(const bloomGraph<int> &g_, const string &outpu...

FILE: Algorithms/2011-GCE/src-original/cliques.hpp
  type cliques (line 15) | namespace cliques {
    type CliqueFunctionAdaptor (line 17) | struct CliqueFunctionAdaptor {
    function findCliques (line 30) | void findCliques(const SimpleIntGraph &g, T & cliquesOut, unsigned int...
    function findCliquesJustIDs (line 54) | void findCliquesJustIDs            (const bloomGraph<int> &g, T &cliqu...
    function findCliquesOriginalVertexNames (line 55) | void findCliquesOriginalVertexNames(const bloomGraph<int> &g, T &cliqu...
    type CliqueSink (line 57) | struct CliqueSink { // Dump the cliques to a file in the CFinder format
      method CliqueSink (line 61) | CliqueSink(const bloomGraph<int> &_g, const string& fileName) : g(_g...
      method ForeachContainer (line 65) | ForeachContainer(V v, Compsub) {

FILE: Algorithms/2011-GCE/src-original/find_communities.cpp
  function main (line 19) | int main (int argc, char **argv) {

FILE: Algorithms/2011-GCE/src-original/graph_analysis.hpp
  type graph_analysis (line 3) | namespace graph_analysis {

FILE: Algorithms/2011-GCE/src-original/graph_loading.cpp
  type graph_loading (line 15) | namespace graph_loading {
    type readEdgeInvalidLineInDataException (line 16) | struct readEdgeInvalidLineInDataException : public exception { }
    class RangeOfEdges (line 19) | class RangeOfEdges {
      method read_a_row (line 25) | void read_a_row() { updating_p = readEdge(p, l, r); }
      method RangeOfEdges (line 27) | RangeOfEdges(const char* b, const char* e) : p(b), fileEnd(e) { if(p...
      method front (line 28) | pair<Name, Name> front() { return make_pair(l,r); }
      method empty (line 29) | bool empty() { return p == fileEnd; }
      method popFront (line 30) | void popFront() { p = updating_p ; if(p!=fileEnd) read_a_row(); }
    function loadSimpleIntGraphFromFile (line 43) | void loadSimpleIntGraphFromFile(SimpleIntGraph &bg, const char *fileNa...
    function loadBloomGraphMMAP (line 46) | void loadBloomGraphMMAP(SimpleIntGraph &bg, const char *fileName) {
    function loadBloomGraphMMAPFastButFussy (line 110) | void loadBloomGraphMMAPFastButFussy(SimpleIntGraph &bg, const char *fi...
    function findDistinctVertices (line 151) | void findDistinctVertices(RangeOfEdges<SimpleIntGraph::Name> roe, Simp...
    function countDegrees (line 219) | void countDegrees(RangeOfEdges<SimpleIntGraph::Name> roe, SimpleIntGra...
    function convertDegreesToOffsets (line 230) | void convertDegreesToOffsets(SimpleIntGraph &bg) {
    function populateNameToIDHash (line 251) | void populateNameToIDHash(SimpleIntGraph &bg) {
    function addNeighbour (line 267) | static void addNeighbour(VertexIDType edge_source, VertexIDType edge_t...
    function loadEdges (line 294) | void loadEdges(RangeOfEdges<SimpleIntGraph::Name> roe, SimpleIntGraph ...
    function mmapFile (line 314) | pair<const char *, const char *> mmapFile(const char *fileName) {

FILE: Algorithms/2011-GCE/src-original/graph_loading.hpp
  type graph_loading (line 5) | namespace graph_loading {

FILE: Algorithms/2011-GCE/src-original/graph_representation.cpp
  function string (line 26) | string VertexNameToString (const int &l) {

FILE: Algorithms/2011-GCE/src-original/graph_representation.hpp
  type bloomGraph (line 14) | struct bloomGraph
    method bloomGraph (line 34) | bloomGraph(void) : vertex_count(0), edge_count(0) {}
    method vcount (line 36) | long unsigned int vcount(void) const { return vertex_count ; }
    method ecount (line 37) | long unsigned int ecount(void) const { return edge_count / 2; }
    method degree (line 38) | inline long unsigned int degree(long int v) const { return degrees.at(...
    method VertexNameType (line 39) | VertexNameType name_of_one_node(long int v) const { return vertex_mapp...
    method string (line 40) | string name_of_one_node_asString(long int v) const { return VertexName...
    method are_connected (line 42) | bool are_connected(const EdgeType &e) const {
    method neighbours (line 48) | pair<const VertexIDType*,const VertexIDType*> neighbours(VertexIDType ...
    method neighbours (line 54) | pair<VertexIDType*,VertexIDType*> neighbours(VertexIDType i) {
  function H (line 19) | H hash_integer( // This is used in populateHash and key_for_vertexName f...
  type bloomGraph (line 27) | struct bloomGraph {
    method bloomGraph (line 34) | bloomGraph(void) : vertex_count(0), edge_count(0) {}
    method vcount (line 36) | long unsigned int vcount(void) const { return vertex_count ; }
    method ecount (line 37) | long unsigned int ecount(void) const { return edge_count / 2; }
    method degree (line 38) | inline long unsigned int degree(long int v) const { return degrees.at(...
    method VertexNameType (line 39) | VertexNameType name_of_one_node(long int v) const { return vertex_mapp...
    method string (line 40) | string name_of_one_node_asString(long int v) const { return VertexName...
    method are_connected (line 42) | bool are_connected(const EdgeType &e) const {
    method neighbours (line 48) | pair<const VertexIDType*,const VertexIDType*> neighbours(VertexIDType ...
    method neighbours (line 54) | pair<VertexIDType*,VertexIDType*> neighbours(VertexIDType i) {

FILE: Algorithms/2011-GCE/src-original/iterative.hpp
  type iterative (line 3) | namespace iterative {

FILE: Algorithms/2011-GCE/src-original/modularity.hpp
  type modularity (line 4) | namespace modularity {

FILE: Algorithms/2011-GCE/src-refactor/algorithm/cliques.cpp
  type cliques (line 3) | namespace cliques {
    function cliquesForOneNode (line 9) | void cliquesForOneNode(const SimpleIntGraph &g, CliqueFunctionAdaptor ...
    function tryCandidate (line 27) | static inline void
    function cliquesWorker (line 44) | void cliquesWorker(const SimpleIntGraph &g, CliqueFunctionAdaptor &cli...
    function create_directory (line 127) | void create_directory(const string &directory) throw() {
    function cliquesToDirectory (line 137) | void

FILE: Algorithms/2011-GCE/src-refactor/algorithm/cliques.hpp
  type cliques (line 16) | namespace cliques {
    type CliqueFunctionAdaptor (line 18) | struct CliqueFunctionAdaptor {
    function findCliques (line 41) | void findCliques(const SimpleIntGraph &g, T &cliquesOut, unsigned int ...
    function findCliquesJustIDs (line 68) | void findCliquesJustIDs(const bloomGraph<int> &g, T &cliquesOut, unsig...
    function findCliquesOriginalVertexNames (line 73) | void findCliquesOriginalVertexNames(const bloomGraph<int> &g, T &cliqu...
    type CliqueSink (line 76) | struct CliqueSink { // Dump the cliques to a file in the CFinder format
      method CliqueSink (line 81) | CliqueSink(const bloomGraph<int> &_g, const string &fileName) : g(_g...
      method ForeachContainer (line 86) | ForeachContainer(V v, Compsub) {

FILE: Algorithms/2011-GCE/src-refactor/algorithm/community_finder.cpp
  function sizeSortFunctionLargestFirst (line 27) | bool sizeSortFunctionLargestFirst(Seed *two, Seed *one) {
  function sizeSortFunctionSmallestFirst (line 31) | bool sizeSortFunctionSmallestFirst(Seed *one, Seed *two) {
  function vectorSizeSortFunctionLargestFirst (line 35) | bool vectorSizeSortFunctionLargestFirst(vector<V> two, vector<V> one) {
  function vectorSizeSortFunctionSmallestFirst (line 39) | bool vectorSizeSortFunctionSmallestFirst(vector<V> one, vector<V> two) {

FILE: Algorithms/2011-GCE/src-refactor/algorithm/community_finder.h
  function class (line 29) | class community_finder {

FILE: Algorithms/2011-GCE/src-refactor/algorithm/find_communities.cpp
  function main (line 17) | int main(int argc, char **argv) {

FILE: Algorithms/2011-GCE/src-refactor/algorithm/seed.h
  function class (line 22) | class Seed {

FILE: Algorithms/2011-GCE/src-refactor/useless/graph_analysis.hpp
  type graph_analysis (line 3) | namespace graph_analysis {

FILE: Algorithms/2011-GCE/src-refactor/useless/iterative.hpp
  type iterative (line 3) | namespace iterative {

FILE: Algorithms/2011-GCE/src-refactor/useless/modularity.hpp
  type modularity (line 3) | namespace modularity {

FILE: Algorithms/2011-GCE/src-refactor/util/aaron_utils.cpp
  function testForError (line 3) | int testForError(FILE *x) { return x == NULL; }
  function testForError (line 5) | int testForError(int x) { return x == -1; }
  function string (line 7) | string show(long x) {
  function string (line 13) | string show(const char *x) {
  function string (line 19) | string show(const string &s) { return s; }
  function string (line 29) | string runningAverage::operator()(void) const {
  function DummyOutputStream (line 35) | DummyOutputStream &DummyOutputStream::operator<<(int) { return *this; }
  function DummyOutputStream (line 37) | DummyOutputStream &DummyOutputStream::operator<<(const char *) { return ...

FILE: Algorithms/2011-GCE/src-refactor/util/aaron_utils.hpp
  function string (line 28) | static string thousandsSeparated(unsigned long x) {
  class runningAverage (line 65) | class runningAverage {
  type RefPair (line 79) | struct RefPair {
    method RefPair (line 83) | RefPair(T1 &in1, T2 &in2) : e1(in1), e2(in2) {}
  function make_refpair (line 92) | RefPair<T1, T2> make_refpair(T1 &e1, T2 &e2) {
  type DummyOutputStream (line 97) | struct DummyOutputStream {
  type StopWatch (line 105) | struct StopWatch { // TODO: put the stopWatch in another file?
    type timeval (line 106) | struct timeval
    type timeval (line 107) | struct timeval
    method StopWatch (line 109) | StopWatch() {
    method laptime (line 114) | void laptime(void) { laptime(""); }
    method laptime (line 116) | void laptime(const string &tag) {

FILE: Algorithms/2011-GCE/src-refactor/util/graph/graph_loading.cpp
  type graph_loading (line 15) | namespace graph_loading {
    type readEdgeInvalidLineInDataException (line 16) | struct readEdgeInvalidLineInDataException : public exception {
    class RangeOfEdges (line 21) | class RangeOfEdges {
      method read_a_row (line 28) | void read_a_row() { updating_p = readEdge(p, l, r); }
      method RangeOfEdges (line 31) | RangeOfEdges(const char *b, const char *e) : p(b), fileEnd(e) { if (...
      method front (line 33) | pair<Name, Name> front() { return make_pair(l, r); }
      method empty (line 35) | bool empty() { return p == fileEnd; }
      method popFront (line 37) | void popFront() {
    function loadSimpleIntGraphFromFile (line 61) | void loadSimpleIntGraphFromFile(SimpleIntGraph &bg, const char *fileNa...
    function loadBloomGraphMMAP (line 65) | void loadBloomGraphMMAP(SimpleIntGraph &bg, const char *fileName) {
    function loadBloomGraphMMAPFastButFussy (line 133) | void loadBloomGraphMMAPFastButFussy(SimpleIntGraph &bg, const char *fi...
    function findDistinctVertices (line 174) | void findDistinctVertices(RangeOfEdges<SimpleIntGraph::Name> roe, Simp...
    function countDegrees (line 248) | void countDegrees(RangeOfEdges<SimpleIntGraph::Name> roe, SimpleIntGra...
    function convertDegreesToOffsets (line 259) | void convertDegreesToOffsets(SimpleIntGraph &bg) {
    function populateNameToIDHash (line 281) | void populateNameToIDHash(SimpleIntGraph &bg) {
    function addNeighbour (line 298) | static void
    function loadEdges (line 330) | void loadEdges(RangeOfEdges<SimpleIntGraph::Name> roe, SimpleIntGraph ...
    function mmapFile (line 351) | pair<const char *, const char *> mmapFile(const char *fileName) {

FILE: Algorithms/2011-GCE/src-refactor/util/graph/graph_loading.hpp
  type graph_loading (line 5) | namespace graph_loading {

FILE: Algorithms/2011-GCE/src-refactor/util/graph/graph_representation.cpp
  function string (line 28) | string VertexNameToString(const int &l) {

FILE: Algorithms/2011-GCE/src-refactor/util/graph/graph_representation.hpp
  type bloomGraph (line 14) | struct bloomGraph
    method bloomGraph (line 35) | bloomGraph(void) : vertex_count(0), edge_count(0) {}
    method vcount (line 37) | long unsigned int vcount(void) const { return vertex_count; }
    method ecount (line 39) | long unsigned int ecount(void) const {
    method degree (line 42) | inline long unsigned int degree(long int v) const { return degrees.at(...
    method VertexNameType (line 44) | VertexNameType name_of_one_node(long int v) const { return vertex_mapp...
    method string (line 46) | string name_of_one_node_asString(long int v) const { return VertexName...
    method are_connected (line 50) | bool are_connected(const EdgeType &e) const {
    method neighbours (line 57) | pair<const VertexIDType *, const VertexIDType *>
    method neighbours (line 64) | pair<VertexIDType *, VertexIDType *> neighbours(VertexIDType i) {
  function H (line 19) | H hash_integer( // This is used in populateHash and key_for_vertexName f...
  type bloomGraph (line 28) | struct bloomGraph {
    method bloomGraph (line 35) | bloomGraph(void) : vertex_count(0), edge_count(0) {}
    method vcount (line 37) | long unsigned int vcount(void) const { return vertex_count; }
    method ecount (line 39) | long unsigned int ecount(void) const {
    method degree (line 42) | inline long unsigned int degree(long int v) const { return degrees.at(...
    method VertexNameType (line 44) | VertexNameType name_of_one_node(long int v) const { return vertex_mapp...
    method string (line 46) | string name_of_one_node_asString(long int v) const { return VertexName...
    method are_connected (line 50) | bool are_connected(const EdgeType &e) const {
    method neighbours (line 57) | pair<const VertexIDType *, const VertexIDType *>
    method neighbours (line 64) | pair<VertexIDType *, VertexIDType *> neighbours(VertexIDType i) {

FILE: Algorithms/2011-GCE/src-refactor/util/range.hpp
  class IteratorRange (line 13) | class IteratorRange {
    method IteratorRange (line 21) | IteratorRange(const Iterator &_begin, const Iterator &_end) : current(...
    method IteratorRange (line 23) | IteratorRange(std::pair<Iterator, Iterator> be) : current(be.first), e...
    method empty (line 25) | bool empty() const { return current == end; }
    method Iterated (line 27) | Iterated &front() const { return *current; }
    method Iterator (line 29) | Iterator frontIterator() const { return current; }
    method popFront (line 31) | void popFront() { ++current; }
  class ContainerProperties (line 35) | class ContainerProperties {
  class ContainerRange (line 43) | class ContainerRange : public IteratorRange<typename ContainerProperties...
    method ContainerRange (line 45) | ContainerRange(Container &c) : IteratorRange<typename ContainerPropert...
  class ContainerRangeReverse (line 50) | class ContainerRangeReverse : public IteratorRange<typename ContainerPro...
    method ContainerRangeReverse (line 52) | ContainerRangeReverse(Container &c) : IteratorRange<typename Container...
  class RangeTypes (line 58) | class RangeTypes {
  class ChainedRange (line 65) | class ChainedRange { // Chain Two together
    method ChainedRange (line 69) | ChainedRange(const Range &_first, const Range &_second) : first(_first...
    method empty (line 71) | bool empty() const { return first.empty() && second.empty(); }
    method firstEmpty (line 73) | bool firstEmpty() const { return first.empty(); }
    method front (line 75) | typename RangeTypes<Range>::ElementType front() const { return first.e...
    method popFront (line 77) | void popFront() { if (first.empty()) second.popFront(); else first.pop...

FILE: Algorithms/2011-MOSES/src-original/Range.cpp
  type amd (line 5) | namespace amd {
    function rangeOverStream (line 7) | std::auto_ptr< Range<std::string> > rangeOverStream(std::istream &_ist...

FILE: Algorithms/2011-MOSES/src-original/Range.hpp
  class IteratorRange (line 23) | class IteratorRange {
    method IteratorRange (line 30) | IteratorRange(const Iterator & _begin, const Iterator & _end) : curren...
    method IteratorRange (line 31) | IteratorRange(std::pair<Iterator,Iterator> be) : current(be.first), en...
    method empty (line 33) | bool empty() const { return current == end; }
    method Iterated (line 34) | Iterated & front() const { return *current; }
    method Iterator (line 35) | Iterator   frontIterator() const { return  current; }
    method popFront (line 36) | void popFront() { ++current; }
  class ContainerProperties (line 40) | class ContainerProperties {
  class ContainerRange (line 47) | class ContainerRange : public IteratorRange< typename ContainerPropertie...
    method ContainerRange (line 49) | ContainerRange(Container &c) : IteratorRange< typename ContainerProper...
  class RangeTypes (line 55) | class RangeTypes {
  class ChainedRange (line 62) | class ChainedRange { // Chain Two together
    method ChainedRange (line 66) | ChainedRange(const Range &_first, const Range &_second) : first(_first...
    method empty (line 67) | bool empty() const { return first.empty() && second.empty(); }
    method firstEmpty (line 68) | bool firstEmpty() const { return first.empty(); }
    method front (line 69) | typename RangeTypes<Range>::ElementType front() const { return first.e...
    method popFront (line 70) | void popFront() { if (first.empty()) second.popFront(); else first.pop...
  type Range (line 74) | struct Range {
  type RangeContainer (line 84) | struct RangeContainer
    method RangeContainer (line 89) | explicit RangeContainer(Iterator first, Iterator last) : _current(firs...
    method empty (line 91) | virtual bool empty() const { return _current == _last; }
    method popFront (line 92) | virtual void popFront() { ++_current; }
    method front (line 93) | virtual typename Iterator::reference front() const { return *_current; }
  type amd (line 99) | namespace amd {
    function mk_range (line 101) | std::auto_ptr< Range< typename C::iterator::reference > > mk_range(C &...
    function mk_range (line 105) | std::auto_ptr< Range< typename C::const_iterator::reference > > mk_ran...
    function mk_range_c (line 109) | std::auto_ptr< Range< typename C::const_iterator::reference > > mk_ran...
    function mk_reverse_range (line 113) | std::auto_ptr< Range< typename C::reverse_iterator::reference > > mk_r...
    function mk_reverse_range (line 117) | std::auto_ptr< Range< typename C::const_reverse_iterator::reference > ...
    class RangeOverStream (line 122) | class RangeOverStream : public Range<std::string> {
    class RangeMapper (line 137) | class RangeMapper : public Range<typename boost::result_of<F(typename ...
      method RangeMapper (line 144) | RangeMapper(const T & mapped_, F f_) : mapped(mapped_), f(f_) {}
      method empty (line 145) | bool empty() const { return mapped.empty(); }
      method popFront (line 146) | void popFront() { mapped.popFront(); }
      method value_type (line 147) | value_type front() const {
    function make_mapper_range (line 152) | RangeMapper<T, F> make_mapper_range(const T& m, F f) {
    function map_range (line 157) | RangeMapper<T, F> map_range(const F &f, const T& m) {
    class RangeFilter (line 162) | class RangeFilter : public Range<typename R::value_type> {
      method RangeFilter (line 167) | RangeFilter(const R& _r, const P& _p) : r(_r), p(_p) {
      method empty (line 172) | virtual bool empty() const { return r.empty(); }
      method popFront (line 173) | virtual void popFront() {
      method value_type (line 178) | virtual value_type front() const {
    function make_filter_range (line 183) | RangeFilter<R,P> make_filter_range(const R& r, const P& p) {
    function filter (line 188) | RangeFilter<R,P> filter(const P& p, const R& r) {
    function range_length (line 192) | int range_length(R r) {
    class RangeEnum (line 202) | class RangeEnum : public Range<I> {
      method RangeEnum (line 205) | RangeEnum(I a_) : a(a_) {}
      method empty (line 206) | virtual bool empty() const { return false; }
      method I (line 207) | virtual I front() const { return a; }
      method popFront (line 208) | virtual void popFront() { ++a; }
    function make_counter_range (line 212) | RangeEnum<I> make_counter_range(I first) {
    class RangeZipper (line 218) | class RangeZipper : public Range< std::pair<
      method RangeZipper (line 229) | RangeZipper(const L &l_, const R &r_) : l(l_), r(r_) {}
      method empty (line 230) | virtual bool empty() const { return l.empty() || r.empty(); }
      method value_type (line 231) | virtual value_type front() const { return make_pair(l.front(), r.fro...
      method popFront (line 232) | virtual void popFront() { l.popFront(); r.popFront(); }
    function zip (line 236) | RangeZipper<L,R> zip(const L &l, const R &r) {
    class RangeChain (line 242) | class RangeChain : public Range< typename L::value_type > {
      method RangeChain (line 247) | RangeChain(const L &l_, const R &r_) : l(l_), r(r_) {}
      method empty (line 248) | virtual bool empty() const { return l.empty() && r.empty(); }
      method value_type (line 249) | virtual value_type front() const {
      method popFront (line 255) | virtual void popFront() {
    function chain (line 263) | RangeChain<L,R> chain(const L &l, const R &r) {
  class auto_ptrWithPairedBool (line 285) | class auto_ptrWithPairedBool : public std::auto_ptr<Type> {
    method auto_ptrWithPairedBool (line 287) | auto_ptrWithPairedBool(Type *p) : std::auto_ptr<Type> (p), interrupted...

FILE: Algorithms/2011-MOSES/src-original/aaron_utils.cpp
  function testForError (line 6) | int testForError(FILE * x) { return x==NULL; }
  function testForError (line 7) | int testForError(int x) { return x==-1; }
  function string (line 9) | string show(int64 x) { ostringstream s; s << x; return s.str(); }
  function string (line 10) | string show(const char * x) { ostringstream s; s << x; return s.str(); }
  function string (line 11) | string show(const string &s) { return s; }
  function string (line 19) | string runningAverage::operator() (void) const {
  function DummyOutputStream (line 25) | DummyOutputStream& DummyOutputStream::operator << (int) { return *this; }
  function DummyOutputStream (line 26) | DummyOutputStream& DummyOutputStream::operator << (const char*) { return...
  function string (line 29) | string thousandsSeparated(uint64 x) {
  function istream (line 40) | istream *amd::zcatThis(const char *gzippedFile) {
  type stat (line 50) | struct stat

FILE: Algorithms/2011-MOSES/src-original/aaron_utils.hpp
  class runningAverage (line 60) | class runningAverage {
  type RefPair (line 71) | struct RefPair {
    method RefPair (line 74) | RefPair(T1 &in1, T2 &in2) : e1(in1), e2(in2) { }
  function make_refpair (line 78) | RefPair<T1, T2> make_refpair(T1 &e1, T2 &e2) {
  type DummyOutputStream (line 83) | struct DummyOutputStream {
  type StopWatch (line 89) | struct StopWatch { // TODO: put the stopWatch in another file?
    type timeval (line 90) | struct timeval
    type timeval (line 91) | struct timeval
    method StopWatch (line 92) | StopWatch() {
    method laptime (line 96) | void laptime(void) { laptime(""); }
    method laptime (line 97) | void laptime(const string &tag) {
  class maxOnlymap (line 111) | class maxOnlymap : public map<K, V> {
    method insert (line 113) | pair<typename map<K,V>::iterator,bool> insert ( const typename map<K,V...
  type Timer (line 125) | struct Timer {
    type timeval (line 126) | struct timeval
    method Timer (line 128) | Timer() {
    method Timer (line 131) | Timer(const string &s): _s(s) {
    method age (line 134) | double age() const {
  type amd (line 146) | namespace amd {
    type DebugCounter (line 151) | struct DebugCounter {
    function Histogram (line 160) | void Histogram(T r) {
    function TwoWayTable (line 178) | void TwoWayTable(T1 r1, T2 r2) {
    function constAt (line 227) | typename C::value_type constAt(const C &c, int i) {

FILE: Algorithms/2011-MOSES/src-original/graph_loading.cpp
  type graph_loading (line 25) | namespace graph_loading {
    type readEdgeInvalidLineInDataException (line 27) | struct readEdgeInvalidLineInDataException : public exception { }
    class RangeOfEdges (line 31) | class RangeOfEdges {
      method read_a_row (line 37) | void read_a_row() { updating_p = readEdge(p, l, r); }
      method RangeOfEdges (line 39) | RangeOfEdges(const char* b, const char* e) : p(b), fileEnd(e) { if(p...
      method front (line 40) | pair<Name, Name> front() { return make_pair(l,r); }
      method empty (line 41) | bool empty() { return p == fileEnd; }
      method popFront (line 42) | void popFront() { p = updating_p ; if(p!=fileEnd) read_a_row(); }
    function loadSimpleStringGraphFromFile (line 56) | void loadSimpleStringGraphFromFile(SimpleStringGraph &g, const char *f...
    function loadSimpleIntGraphFromFile (line 60) | void loadSimpleIntGraphFromFile(SimpleIntGraph &bg, const char *fileNa...
    type DegreeTag (line 65) | struct DegreeTag {}
    type NameTag (line 66) | struct NameTag {}
    function DegreeIncrementer (line 67) | void DegreeIncrementer(pair<N,V> &p) { ++p.second; }
    function DegreeDecrementer (line 68) | void DegreeDecrementer(pair<N,V> &p) { --p.second; }
    type state_flag (line 70) | enum state_flag { LOADING_NONE, LOADING_NODES, LOADING_DEGREEMAP, LOAD...
    type lsdkfj (line 71) | struct lsdkfj {
      type state_flag (line 72) | enum state_flag
    function sigUSR1_handler (line 75) | void sigUSR1_handler(int) {
    function loadBloomGraphMMAP (line 86) | static void loadBloomGraphMMAP(bloomGraph<Name> &bg, const char *fileN...
    function loadBloomGraphMMAPFastButFussy (line 273) | void loadBloomGraphMMAPFastButFussy(SimpleIntGraph &bg, const char *fi...
    function findDistinctVertices (line 321) | void findDistinctVertices(RangeOfEdges<SimpleIntGraph::Name> roe, Simp...
    function countDegrees (line 390) | void countDegrees(RangeOfEdges<SimpleIntGraph::Name> roe, SimpleIntGra...
    function convertDegreesToOffsets (line 401) | void convertDegreesToOffsets(SimpleIntGraph &bg) {
    function populateNameToIDHash (line 422) | static void populateNameToIDHash(SimpleIntGraph &bg) {
    function populateNameToIDHash (line 436) | static void populateNameToIDHash(SimpleStringGraph &bg) {
    function addNeighbour (line 452) | static void addNeighbour(VertexIDType edge_source, VertexIDType edge_t...
    function loadEdges (line 479) | void loadEdges(RangeOfEdges<SimpleIntGraph::Name> roe, SimpleIntGraph ...
    function mmapFile (line 499) | pair<const char *, const char *> mmapFile(const char *fileName) {

FILE: Algorithms/2011-MOSES/src-original/graph_loading.hpp
  type graph_loading (line 5) | namespace graph_loading {

FILE: Algorithms/2011-MOSES/src-original/graph_representation.cpp
  function V (line 7) | V bloomGraph<int>::key_for_vertexName(int v) const {
  function V (line 24) | V bloomGraph<string>::key_for_vertexName(string v) const {
  function string (line 42) | string VertexNameToString (const int &l) {

FILE: Algorithms/2011-MOSES/src-original/graph_representation.hpp
  type bloomGraph (line 16) | struct bloomGraph
    method bloomGraph (line 77) | explicit bloomGraph() : GraphWithoutNames() {}
    method VertexNameType (line 83) | VertexNameType name_of_one_node(V v) const { return vertex_mappings.at...
    method VertexNameType (line 84) | VertexNameType name(V v) const { assert(v>=0); assert(v<vcount()); ass...
    method string (line 85) | string name_of_one_node_asString(V v) const { return VertexNameToStrin...
  function H (line 21) | H hash_integer( // This is used in populateHash and key_for_vertexName f...
  function H (line 28) | H hash_integer( // This is used in populateHash and key_for_vertexName f...
  type GraphWithoutNames (line 40) | struct GraphWithoutNames { // this is useful because it doesn't need the...
    method V (line 41) | V vcount(void) const { return vertex_count ; }
    method V (line 42) | V ecount(void) const { return edge_count / 2; }
    method V (line 43) | inline V degree(V v) const { return degrees.at(v); }
    method neighbours (line 44) | pair<const VertexIDType*,const VertexIDType*> neighbours(VertexIDType ...
    method neighbours (line 50) | pair<VertexIDType*,VertexIDType*> neighbours(VertexIDType i) {
    method are_connected (line 56) | bool are_connected(const V &v, const V &v2) const { return are_connect...
    method are_connected (line 57) | bool are_connected(const EdgeType &e) const {
    method GraphWithoutNames (line 64) | GraphWithoutNames(void) : vertex_count(0), edge_count(0) {}
  type bloomGraph (line 74) | struct bloomGraph : public GraphWithoutNames {
    method bloomGraph (line 77) | explicit bloomGraph() : GraphWithoutNames() {}
    method VertexNameType (line 83) | VertexNameType name_of_one_node(V v) const { return vertex_mappings.at...
    method VertexNameType (line 84) | VertexNameType name(V v) const { assert(v>=0); assert(v<vcount()); ass...
    method string (line 85) | string name_of_one_node_asString(V v) const { return VertexNameToStrin...

FILE: Algorithms/2011-MOSES/src-original/groupStats.cpp
  function main (line 21) | int main(int argc, char **argv) {

FILE: Algorithms/2011-MOSES/src-original/grouping.cpp
  type grouping (line 5) | namespace grouping {
    function Foreach (line 21) | Foreach(V n, ns) {
    function Group (line 46) | Group* Grouping::newG () { return this->newG(false); }
    function Group (line 47) | Group* Grouping::newG(bool randomized_p_in) {
    function ForeachContainer (line 55) | ForeachContainer (Group *grp, grps) {
    function deleteEmptyGroup (line 129) | void deleteEmptyGroup(Grouping *pging, Group *grp) { // TODO: This is ...

FILE: Algorithms/2011-MOSES/src-original/grouping.hpp
  type grouping (line 5) | namespace grouping {
    class Group (line 7) | class Group
    class Grouping (line 8) | class Grouping
      type edgeHash (line 34) | struct edgeHash {
      type EdgeCountTriple (line 44) | struct EdgeCountTriple { // TODO: make this private
        method EdgeCountTriple (line 47) | EdgeCountTriple() : shared_comms(0), other_index(0) {}
    type orderGroup (line 10) | struct orderGroup {
    class Grouping (line 14) | class Grouping {
      type edgeHash (line 34) | struct edgeHash {
      type EdgeCountTriple (line 44) | struct EdgeCountTriple { // TODO: make this private
        method EdgeCountTriple (line 47) | EdgeCountTriple() : shared_comms(0), other_index(0) {}
    class Group (line 58) | class Group {

FILE: Algorithms/2011-MOSES/src-original/iterative.hpp
  type iterative (line 3) | namespace iterative {
    type OneNode (line 11) | struct OneNode {
    type PartitionStats (line 20) | struct PartitionStats {
    type Partition (line 33) | struct Partition : public PartitionStats {

FILE: Algorithms/2011-MOSES/src-original/moses.cpp
  function main (line 21) | int main(int argc, char **argv) {

FILE: Algorithms/2011-MOSES/src-original/overlapping.cpp
  function runMutual (line 66) | static void runMutual(void) {
  type overlapping (line 70) | namespace overlapping {
    function overlapping (line 74) | void overlapping(SimpleIntGraph &g) { overlappingT(g); }
    function overlapping (line 75) | void overlapping(SimpleStringGraph &g) { overlappingT(g); }
    function addSeed (line 82) | void addSeed(Grouping &ging, const set<V> &nodes, bool randomized_p_in) {
    function overlappingT (line 100) | static void overlappingT(bloomGraph<N> &g) {
    function tryAndApplyThisOne (line 237) | static bool tryAndApplyThisOne(Grouping &ging, V e, bool randomized_p_...
    function useOneNodeSeeds (line 252) | static void useOneNodeSeeds(Grouping &ging, bloomGraph<N> &g, bool ran...
    function groupStats (line 285) | static void groupStats(const Grouping &ging, bloomGraph<N> &g) {
    function seedGroupingWithPartition (line 361) | void seedGroupingWithPartition(Grouping &ging, const iterative::Partit...
    function count_intersection (line 378) | static size_t count_intersection(It it1b, It it1e, It it2b, It it2e) {
    function count_intersection (line 384) | static size_t count_intersection(const Container &container1, const Co...
    type DeltaSeed (line 393) | struct DeltaSeed {
      method deltadeltaPairEntropy (line 400) | long double deltadeltaPairEntropy() const {
      method DeltaSeed (line 403) | explicit DeltaSeed(V v, int group_size_smaller, Grouping &ging) : _v...
      method addEdge2 (line 406) | void addEdge2(V n, const V* edgeVN_ptr) { // n is connected to _v
      method addEdge (line 410) | void addEdge(V  , int sharedCommunities) { // n is connected to _v /...
      method redoEdge (line 418) | void redoEdge(V  , int previous_sharedCommunities) { // n is connect...
      method _deltaZentropy (line 424) | long double _deltaZentropy() const {
      method _deltaTotalentropy (line 443) | long double _deltaTotalentropy() const {
    type FrontierNode (line 448) | struct FrontierNode {
      method FrontierNode (line 449) | FrontierNode(long double &score, V v) : _score(score), _v(v) {}
      type Incrementer (line 452) | struct Incrementer {
        method Incrementer (line 454) | Incrementer(long double &x) : _x(x) {}
    type VertexTag (line 460) | struct VertexTag {}
    type Frontier (line 461) | struct Frontier : private multi_index_container < // TODO: Some sort o...
      method calcddEE (line 472) | static long double __attribute__ ((noinline)) calcddEE(const Groupin...
      method addNode (line 479) | void addNode(const Grouping &ging, V to, const V *edgeFT_ptr) {
      method erase_best_node (line 493) | void erase_best_node() {
      method erase_this_node (line 497) | int erase_this_node(V to) {
      method best_node_score (line 500) | long double best_node_score() const {
      method V (line 504) | V best_node_v() const {
      method Empty (line 508) | bool Empty() const {
    function logNchoose (line 513) | static long double logNchoose(int64 N, int64 n_c) {
    function growingSeed (line 543) | pair<long double, set<V> > growingSeed(Grouping &ging, int lookahead
    type ThrowingIterator (line 648) | struct ThrowingIterator {
      type Dereferenced (line 649) | struct Dereferenced {}
      method V (line 650) | V & operator *() { throw Dereferenced(); }
    function emptyIntersection (line 653) | bool emptyIntersection(const pair<const V*, const V*> &l, const pair<c...
    function growThisEdge (line 668) | static pair<long double, set<V> > growThisEdge(Grouping &ging, const V...
    function save (line 730) | static void save(Grouping &ging, bloomGraph<N> &g) {
    type hashGroup (line 745) | struct hashGroup {
    function louvainStyle (line 752) | static void louvainStyle(Grouping &ging, bloomGraph<N> &g) {
    function update_p_out (line 838) | static void update_p_out(Grouping &ging) {
    type PairGroupHash (line 846) | struct PairGroupHash {
    function tryMerges (line 851) | static void tryMerges(Grouping &ging) {
    function tryDeletions (line 991) | static void tryDeletions(Grouping &ging, bool SaveScores /*= true*/) {...
    function P_x_given_z (line 1082) | long double P_x_given_z(const Grouping &ging, long double p_o, long do...
    function MOSES_objective (line 1096) | long double MOSES_objective(const Grouping &ging) {
    function estimate_p_in_and_p_out (line 1141) | static void estimate_p_in_and_p_out(Grouping &ging) {

FILE: Algorithms/2011-MOSES/src-original/overlapping.hpp
  type overlapping (line 3) | namespace overlapping {

FILE: Algorithms/2011-MOSES/src-refactor/algorithm/group_status_exec.cpp
  function main (line 16) | int main(int argc, char **argv) {

FILE: Algorithms/2011-MOSES/src-refactor/algorithm/grouping.cpp
  type grouping (line 7) | namespace grouping {
    function Foreach (line 20) | Foreach(V n, ns) {
    function Group (line 48) | Group *Grouping::newG() { return this->newG(false); }
    function Group (line 50) | Group *Grouping::newG(bool randomized_p_in) {
    function ForeachContainer (line 60) | ForeachContainer (Group *grp, grps) {
    function deleteEmptyGroup (line 134) | void deleteEmptyGroup(Grouping *pging,

FILE: Algorithms/2011-MOSES/src-refactor/algorithm/grouping.hpp
  type grouping (line 7) | namespace grouping {
    class Group (line 9) | class Group
    class Grouping (line 11) | class Grouping
      type edgeHash (line 43) | struct edgeHash {
      type EdgeCountTriple (line 55) | struct EdgeCountTriple { // TODO: make this private
        method EdgeCountTriple (line 59) | EdgeCountTriple() : shared_comms(0), other_index(0) {}
    type orderGroup (line 13) | struct orderGroup {
    class Grouping (line 17) | class Grouping {
      type edgeHash (line 43) | struct edgeHash {
      type EdgeCountTriple (line 55) | struct EdgeCountTriple { // TODO: make this private
        method EdgeCountTriple (line 59) | EdgeCountTriple() : shared_comms(0), other_index(0) {}
    class Group (line 72) | class Group {

FILE: Algorithms/2011-MOSES/src-refactor/algorithm/moses.cpp
  function main (line 18) | int main(int argc, char **argv) {

FILE: Algorithms/2011-MOSES/src-refactor/algorithm/overlapping.cpp
  function runMutual (line 69) | static void runMutual(void) {
  type overlapping (line 73) | namespace overlapping {
    function overlapping (line 80) | void overlapping(SimpleIntGraph &g) { overlappingT(g); }
    function overlapping (line 82) | void overlapping(SimpleStringGraph &g) { overlappingT(g); }
    function addSeed (line 95) | void addSeed(Grouping &ging, const set<V> &nodes, bool randomized_p_in) {
    function overlappingT (line 125) | static void overlappingT(bloomGraph<N> &g) {
    function tryAndApplyThisOne (line 264) | static bool tryAndApplyThisOne(Grouping &ging, V e, bool randomized_p_...
    function useOneNodeSeeds (line 281) | static void useOneNodeSeeds(Grouping &ging, bloomGraph<N> &g, bool ran...
    function groupStats (line 316) | static void groupStats(const Grouping &ging, bloomGraph<N> &g) {
    function seedGroupingWithPartition (line 395) | void seedGroupingWithPartition(Grouping &ging, const iterative::Partit...
    function count_intersection (line 412) | static size_t count_intersection(It it1b, It it1e, It it2b, It it2e) {
    function count_intersection (line 419) | static size_t count_intersection(const Container &container1, const Co...
    type DeltaSeed (line 425) | struct DeltaSeed {
      method deltadeltaPairEntropy (line 433) | long double deltadeltaPairEntropy() const {
      method DeltaSeed (line 438) | explicit DeltaSeed(V v, int group_size_smaller, Grouping &ging) : _v...
      method addEdge2 (line 445) | void addEdge2(V n, const V *edgeVN_ptr) { // n is connected to _v
      method addEdge (line 450) | void addEdge(V, int sharedCommunities) {
      method redoEdge (line 457) | void redoEdge(V,
      method _deltaZentropy (line 468) | long double _deltaZentropy() const {
      method _deltaTotalentropy (line 476) | long double _deltaTotalentropy() const {
    type FrontierNode (line 481) | struct FrontierNode {
      method FrontierNode (line 482) | FrontierNode(long double &score, V v) : _score(score), _v(v) {}
      type Incrementer (line 487) | struct Incrementer {
        method Incrementer (line 490) | Incrementer(long double &x) : _x(x) {}
    type VertexTag (line 497) | struct VertexTag {
    type Frontier (line 500) | struct Frontier : private multi_index_container< // TODO: Some sort of...
      method calcddEE (line 511) | static long double __attribute__ ((noinline)) calcddEE(const Groupin...
      method addNode (line 519) | void addNode(const Grouping &ging, V to, const V *edgeFT_ptr) {
      method erase_best_node (line 534) | void erase_best_node() {
      method erase_this_node (line 539) | int erase_this_node(V to) {
      method best_node_score (line 543) | long double best_node_score() const {
      method V (line 548) | V best_node_v() const {
      method Empty (line 553) | bool Empty() const {
    function logNchoose (line 558) | static long double logNchoose(int64 N, int64 n_c) {
    function growingSeed (line 588) | pair<long double, set<V> >
    type ThrowingIterator (line 684) | struct ThrowingIterator {
      type Dereferenced (line 685) | struct Dereferenced {
      method V (line 688) | V &operator*() { throw Dereferenced(); }
    function emptyIntersection (line 693) | bool emptyIntersection(const pair<const V *, const V *> &l, const pair...
    function growThisEdge (line 704) | static pair<long double, set<V> >
    function save (line 764) | static void save(Grouping &ging, bloomGraph<N> &g) {
    type hashGroup (line 779) | struct hashGroup {
    function louvainStyle (line 788) | static void louvainStyle(Grouping &ging, bloomGraph<N> &g) {
    function update_p_out (line 876) | static void update_p_out(Grouping &ging) {
    type PairGroupHash (line 884) | struct PairGroupHash {
    function tryMerges (line 890) | static void tryMerges(Grouping &ging) {
    function tryDeletions (line 1038) | static void tryDeletions(Grouping &ging,
    function P_x_given_z (line 1128) | long double P_x_given_z(const Grouping &ging, long double p_o, long do...
    function MOSES_objective (line 1143) | long double MOSES_objective(const Grouping &ging) {
    function estimate_p_in_and_p_out (line 1185) | static void estimate_p_in_and_p_out(Grouping &ging) {

FILE: Algorithms/2011-MOSES/src-refactor/algorithm/overlapping.hpp
  type overlapping (line 3) | namespace overlapping {

FILE: Algorithms/2011-MOSES/src-refactor/util/aaron_utils.cpp
  function testForError (line 7) | int testForError(FILE *x) { return x == NULL; }
  function testForError (line 9) | int testForError(int x) { return x == -1; }
  function string (line 11) | string show(int64 x) {
  function string (line 17) | string show(const char *x) {
  function string (line 23) | string show(const string &s) { return s; }
  function string (line 33) | string runningAverage::operator()(void) const {
  function DummyOutputStream (line 39) | DummyOutputStream &DummyOutputStream::operator<<(int) { return *this; }
  function DummyOutputStream (line 41) | DummyOutputStream &DummyOutputStream::operator<<(const char *) { return ...
  function string (line 45) | string thousandsSeparated(uint64 x) {
  function istream (line 56) | istream *amd::zcatThis(const char *gzippedFile) {
  type stat (line 67) | struct stat

FILE: Algorithms/2011-MOSES/src-refactor/util/aaron_utils.hpp
  class runningAverage (line 70) | class runningAverage {
  type RefPair (line 84) | struct RefPair {
    method RefPair (line 88) | RefPair(T1 &in1, T2 &in2) : e1(in1), e2(in2) {}
  function make_refpair (line 97) | RefPair<T1, T2> make_refpair(T1 &e1, T2 &e2) {
  type DummyOutputStream (line 102) | struct DummyOutputStream {
  type StopWatch (line 110) | struct StopWatch { // TODO: put the stopWatch in another file?
    type timeval (line 111) | struct timeval
    type timeval (line 112) | struct timeval
    method StopWatch (line 114) | StopWatch() {
    method laptime (line 119) | void laptime(void) { laptime(""); }
    method laptime (line 121) | void laptime(const string &tag) {
  class maxOnlymap (line 138) | class maxOnlymap : public map<K, V> {
    method insert (line 140) | pair<typename map<K, V>::iterator, bool> insert(const typename map<K, ...
  type Timer (line 152) | struct Timer {
    type timeval (line 153) | struct timeval
    method Timer (line 156) | Timer() {
    method Timer (line 160) | Timer(const string &s) : _s(s) {
    method age (line 164) | double age() const {
  type amd (line 178) | namespace amd {
    type DebugCounter (line 184) | struct DebugCounter {
    function Histogram (line 195) | void Histogram(T r) {
    function TwoWayTable (line 214) | void TwoWayTable(T1 r1, T2 r2) {
    function constAt (line 264) | typename C::value_type constAt(const C &c, int i) {

FILE: Algorithms/2011-MOSES/src-refactor/util/graph/graph_loading.cpp
  type graph_loading (line 25) | namespace graph_loading {
    type readEdgeInvalidLineInDataException (line 27) | struct readEdgeInvalidLineInDataException : public exception {
    class RangeOfEdges (line 34) | class RangeOfEdges {
      method read_a_row (line 41) | void read_a_row() { updating_p = readEdge(p, l, r); }
      method RangeOfEdges (line 44) | RangeOfEdges(const char *b, const char *e) : p(b), fileEnd(e) { if (...
      method front (line 46) | pair<Name, Name> front() { return make_pair(l, r); }
      method empty (line 48) | bool empty() { return p == fileEnd; }
      method popFront (line 50) | void popFront() {
    function loadSimpleStringGraphFromFile (line 79) | void loadSimpleStringGraphFromFile(SimpleStringGraph &g, const char *f...
    function loadSimpleIntGraphFromFile (line 84) | void loadSimpleIntGraphFromFile(SimpleIntGraph &bg, const char *fileNa...
    type DegreeTag (line 89) | struct DegreeTag {
    type NameTag (line 91) | struct NameTag {
    function DegreeIncrementer (line 95) | void DegreeIncrementer(pair<N, V> &p) { ++p.second; }
    function DegreeDecrementer (line 98) | void DegreeDecrementer(pair<N, V> &p) { --p.second; }
    type state_flag (line 100) | enum state_flag {
    type lsdkfj (line 103) | struct lsdkfj {
      type state_flag (line 104) | enum state_flag
    function sigUSR1_handler (line 108) | void sigUSR1_handler(int) {
    function loadBloomGraphMMAP (line 123) | static void loadBloomGraphMMAP(bloomGraph<Name> &bg, const char *fileN...
    function loadBloomGraphMMAPFastButFussy (line 315) | void loadBloomGraphMMAPFastButFussy(SimpleIntGraph &bg, const char *fi...
    function findDistinctVertices (line 363) | void findDistinctVertices(RangeOfEdges<SimpleIntGraph::Name> roe, Simp...
    function countDegrees (line 438) | void countDegrees(RangeOfEdges<SimpleIntGraph::Name> roe, SimpleIntGra...
    function convertDegreesToOffsets (line 449) | void convertDegreesToOffsets(SimpleIntGraph &bg) {
    function populateNameToIDHash (line 471) | static void populateNameToIDHash(SimpleIntGraph &bg) {
    function populateNameToIDHash (line 487) | static void populateNameToIDHash(SimpleStringGraph &bg) {
    function addNeighbour (line 504) | static void
    function loadEdges (line 536) | void loadEdges(RangeOfEdges<SimpleIntGraph::Name> roe, SimpleIntGraph ...
    function mmapFile (line 557) | pair<const char *, const char *> mmapFile(const char *fileName) {

FILE: Algorithms/2011-MOSES/src-refactor/util/graph/graph_loading.hpp
  type graph_loading (line 5) | namespace graph_loading {

FILE: Algorithms/2011-MOSES/src-refactor/util/graph/graph_representation.cpp
  function V (line 9) | V bloomGraph<int>::key_for_vertexName(int v) const {
  function V (line 28) | V bloomGraph<string>::key_for_vertexName(string v) const {
  function string (line 46) | string VertexNameToString(const int &l) {

FILE: Algorithms/2011-MOSES/src-refactor/util/graph/graph_representation.hpp
  type bloomGraph (line 17) | struct bloomGraph
    method bloomGraph (line 84) | explicit bloomGraph() : GraphWithoutNames() {}
    method VertexNameType (line 91) | VertexNameType name_of_one_node(V v) const { return vertex_mappings.at...
    method VertexNameType (line 93) | VertexNameType name(V v) const {
    method string (line 100) | string name_of_one_node_asString(V v) const { return VertexNameToStrin...
  function H (line 22) | H hash_integer( // This is used in populateHash and key_for_vertexName f...
  function H (line 31) | H hash_integer( // This is used in populateHash and key_for_vertexName f...
  type GraphWithoutNames (line 43) | struct GraphWithoutNames { // this is useful because it doesn't need the...
    method V (line 44) | V vcount(void) const { return vertex_count; }
    method V (line 46) | V ecount(void) const { return edge_count / 2; }
    method V (line 47) | inline V degree(V v) const { return degrees.at(v); }
    method neighbours (line 49) | pair<const VertexIDType *, const VertexIDType *>
    method neighbours (line 56) | pair<VertexIDType *, VertexIDType *> neighbours(VertexIDType i) {
    method are_connected (line 62) | bool are_connected(const V &v, const V &v2) const { return are_connect...
    method are_connected (line 64) | bool are_connected(const EdgeType &e) const {
    method GraphWithoutNames (line 71) | GraphWithoutNames(void) : vertex_count(0), edge_count(0) {}
  type bloomGraph (line 81) | struct bloomGraph : public GraphWithoutNames {
    method bloomGraph (line 84) | explicit bloomGraph() : GraphWithoutNames() {}
    method VertexNameType (line 91) | VertexNameType name_of_one_node(V v) const { return vertex_mappings.at...
    method VertexNameType (line 93) | VertexNameType name(V v) const {
    method string (line 100) | string name_of_one_node_asString(V v) const { return VertexNameToStrin...

FILE: Algorithms/2011-MOSES/src-refactor/util/graph/iterative.hpp
  type iterative (line 3) | namespace iterative {
    type OneNode (line 12) | struct OneNode {
    type PartitionStats (line 22) | struct PartitionStats {
    type Partition (line 36) | struct Partition : public PartitionStats {

FILE: Algorithms/2011-MOSES/src-refactor/util/range.cpp
  type amd (line 5) | namespace amd {
    function rangeOverStream (line 7) | std::auto_ptr<range<std::string> > rangeOverStream(std::istream &_istr...

FILE: Algorithms/2011-MOSES/src-refactor/util/range.hpp
  class IteratorRange (line 23) | class IteratorRange {
    method IteratorRange (line 31) | IteratorRange(const Iterator &_begin, const Iterator &_end) : current(...
    method IteratorRange (line 33) | IteratorRange(std::pair<Iterator, Iterator> be) : current(be.first), e...
    method empty (line 35) | bool empty() const { return current == end; }
    method Iterated (line 37) | Iterated &front() const { return *current; }
    method Iterator (line 39) | Iterator frontIterator() const { return current; }
    method popFront (line 41) | void popFront() { ++current; }
  class ContainerProperties (line 45) | class ContainerProperties {
  class ContainerRange (line 53) | class ContainerRange : public IteratorRange<typename ContainerProperties...
    method ContainerRange (line 55) | ContainerRange(Container &c) : IteratorRange<typename ContainerPropert...
  class RangeTypes (line 61) | class RangeTypes {
  class ChainedRange (line 68) | class ChainedRange { // Chain Two together
    method ChainedRange (line 72) | ChainedRange(const Range &_first, const Range &_second) : first(_first...
    method empty (line 74) | bool empty() const { return first.empty() && second.empty(); }
    method firstEmpty (line 76) | bool firstEmpty() const { return first.empty(); }
    method front (line 78) | typename RangeTypes<Range>::ElementType front() const { return first.e...
    method popFront (line 80) | void popFront() { if (first.empty()) second.popFront(); else first.pop...
  type range (line 84) | struct range {
  type RangeContainer (line 98) | struct RangeContainer
    method RangeContainer (line 103) | explicit RangeContainer(Iterator first, Iterator last) : _current(firs...
    method empty (line 106) | virtual bool empty() const { return _current == _last; }
    method popFront (line 108) | virtual void popFront() { ++_current; }
    method front (line 110) | virtual typename Iterator::reference front() const { return *_current; }
  type amd (line 117) | namespace amd {
    function mk_range (line 119) | std::auto_ptr<range<typename C::iterator::reference> > mk_range(C &c) {
    function mk_range (line 125) | std::auto_ptr<range<typename C::const_iterator::reference> > mk_range(...
    function mk_range_c (line 131) | std::auto_ptr<range<typename C::const_iterator::reference> > mk_range_...
    function mk_reverse_range (line 137) | std::auto_ptr<range<typename C::reverse_iterator::reference> > mk_reve...
    function mk_reverse_range (line 143) | std::auto_ptr<range<typename C::const_reverse_iterator::reference> > m...
    class RangeOverStream (line 149) | class RangeOverStream : public range<std::string> {
    class RangeMapper (line 170) | class RangeMapper : public range<typename boost::result_of<F(
      method RangeMapper (line 179) | RangeMapper(const T &mapped_, F f_) : mapped(mapped_), f(f_) {}
      method empty (line 181) | bool empty() const { return mapped.empty(); }
      method popFront (line 183) | void popFront() { mapped.popFront(); }
      method value_type (line 185) | value_type front() const {
    function make_mapper_range (line 191) | RangeMapper<T, F> make_mapper_range(const T &m, F f) {
    function map_range (line 197) | RangeMapper<T, F> map_range(const F &f, const T &m) {
    class RangeFilter (line 202) | class RangeFilter : public range<typename R::value_type> {
      method RangeFilter (line 208) | RangeFilter(const R &_r, const P &_p) : r(_r), p(_p) {
      method empty (line 214) | virtual bool empty() const { return r.empty(); }
      method popFront (line 216) | virtual void popFront() {
      method value_type (line 222) | virtual value_type front() const {
    function make_filter_range (line 228) | RangeFilter<R, P> make_filter_range(const R &r, const P &p) {
    function filter (line 234) | RangeFilter<R, P> filter(const P &p, const R &r) {
    function range_length (line 239) | int range_length(R r) {
    class RangeEnum (line 249) | class RangeEnum : public range<I> {
      method RangeEnum (line 252) | RangeEnum(I a_) : a(a_) {}
      method empty (line 254) | virtual bool empty() const { return false; }
      method I (line 256) | virtual I front() const { return a; }
      method popFront (line 258) | virtual void popFront() { ++a; }
    function make_counter_range (line 262) | RangeEnum<I> make_counter_range(I first) {
    class RangeZipper (line 268) | class RangeZipper : public range<std::pair<
      method RangeZipper (line 278) | RangeZipper(const L &l_, const R &r_) : l(l_), r(r_) {}
      method empty (line 280) | virtual bool empty() const { return l.empty() || r.empty(); }
      method value_type (line 282) | virtual value_type front() const { return std::make_pair(l.front(), ...
      method popFront (line 284) | virtual void popFront() {
    function zip (line 291) | RangeZipper<L, R> zip(const L &l, const R &r) {
    class RangeChain (line 297) | class RangeChain : public range<typename L::value_type> {
      method RangeChain (line 303) | RangeChain(const L &l_, const R &r_) : l(l_), r(r_) {}
      method empty (line 305) | virtual bool empty() const { return l.empty() && r.empty(); }
      method value_type (line 307) | virtual value_type front() const {
      method popFront (line 314) | virtual void popFront() {
    function chain (line 323) | RangeChain<L, R> chain(const L &l, const R &r) {
  class auto_ptrWithPairedBool (line 345) | class auto_ptrWithPairedBool : public std::auto_ptr<Type> {
    method auto_ptrWithPairedBool (line 347) | auto_ptrWithPairedBool(Type *p) : std::auto_ptr<Type>(p), interrupted(...

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/dir_weighted_tabdeg.h
  type multimap (line 5) | typedef multimap<double, pair<int, double> > cup_data_struct;
  function compare_r_variables (line 14) | double compare_r_variables(double a, double b, double c, double d) {
  function right_error_function (line 47) | double right_error_function(double x) {
  function log_together (line 53) | double log_together(double minus_log_total, int number) {
  function fitted_exponent (line 86) | double fitted_exponent(int N) {
  function order_statistics_left_cumulative (line 115) | inline double order_statistics_left_cumulative(int N, int pos, double x) {
  function inverse_order_statistics (line 129) | double inverse_order_statistics(int sample_dim, int pos, const double  &...
  function pron_min_exp (line 171) | inline double pron_min_exp(int N, double xi) {
  function compute_probability_to_stop (line 185) | inline double compute_probability_to_stop(const double & a, const double...
  function equivalent_check (line 229) | bool equivalent_check(int pos_first, int pos_last, double & A_average, d...
  function equivalent_check_gather (line 272) | bool equivalent_check_gather(cup_data_struct & a, int & until, const dou...
  function hyper_table (line 327) | inline double hyper_table(int kin_node, int kout_g, int tm, int degree_n...
  function compute_topologic_and_bootstrap_interval (line 332) | inline double compute_topologic_and_bootstrap_interval(int kin_node_out,...
  function compute_global_fitness (line 362) | double compute_global_fitness(int kin_node_in, int kout_g_in, int kin_no...
  function compute_topologic_step (line 492) | inline double compute_topologic_step(int kin_node_out, int kout_g_in, in...
  function compute_global_fitness_step (line 511) | double compute_global_fitness_step(int kin_node_in, int kout_g_in, int k...
  function compute_global_fitness_ofive (line 605) | inline double compute_global_fitness_ofive(int kin_node_in, int kout_g_i...
  function compute_global_fitness_randomized (line 614) | inline double compute_global_fitness_randomized(int kin_node_in, int kou...
  function compute_global_fitness_randomized_short (line 629) | double compute_global_fitness_randomized_short(int kin_node, int kout_g,...
  function class (line 659) | class facts {
  function class (line 706) | class weighted_tabdeg {
  function clear (line 746) | void weighted_tabdeg::clear() {
  function edinsert (line 756) | void weighted_tabdeg::edinsert(int a, int kpin, int kpout, int ktin, int...
  function erase (line 772) | bool weighted_tabdeg::erase(int a) {		// this function erases element a ...
  function is_internal (line 793) | bool weighted_tabdeg::is_internal(int a) {
  function set_deque (line 808) | void weighted_tabdeg::set_deque(deque<int> & vv) {
  function print_nodes (line 818) | void weighted_tabdeg::print_nodes(ostream & outb) {
  function worst_node (line 832) | int weighted_tabdeg::worst_node(int & lab, double & worst_fitness, int k...
  function best_node (line 900) | int weighted_tabdeg::best_node(int & lab, double & best_fitness, int kou...
  function _set_ (line 951) | void weighted_tabdeg::_set_(weighted_tabdeg & one)  {
  function update_group (line 967) | bool weighted_tabdeg::update_group(int a, int delta_degree_out, int delt...
  function update_neighs (line 1030) | bool weighted_tabdeg::update_neighs(int a, int delta_deg_out, int delta_...
  function set_and_update_group (line 1080) | void weighted_tabdeg::set_and_update_group(int nstar, int nn, int kout_g...
  function set_and_update_neighs (line 1105) | void weighted_tabdeg::set_and_update_neighs(int nstar, int nn, int kout_...

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/directed_network.h
  function class (line 13) | class static_network {
  function clear (line 249) | void static_network::clear() {
  function set_graph (line 272) | void static_network::set_graph(map<int, map<int, pair<int, double> > > &...
  function set_oneM_etc (line 322) | void static_network::set_oneM_etc() {
  function set_graph (line 370) | bool static_network::set_graph(string file_name) {
  function set_graph (line 537) | void static_network::set_graph(deque<deque<int> > & link_per_node, deque...
  function static_network (line 614) | int static_network::kin_m (const deque<int> & seq) {
  function kin_m (line 678) | int static_network::kin_m(const set <int> &s) {
  function draw_consecutive (line 695) | int static_network::draw_consecutive(string file_name1, string file_name...
  function draw (line 743) | int static_network::draw(string file_name) {
  function draw_with_weight_probability (line 791) | int static_network::draw_with_weight_probability(string file_name) {
  function static_network (line 840) | void static_network::get_id_label (map <int, int> &a) {
  function deque_id (line 848) | void static_network::deque_id(deque<int> & a) {
  function print_id (line 856) | void static_network::print_id(const deque<int> & a, ostream & pout) {
  function print_id (line 866) | void static_network::print_id(const set<int> & a, ostream & pout) {
  function print_id (line 877) | void static_network::print_id(const deque<deque<int> > & a, ostream & po...
  function print_id (line 886) | void static_network::print_id(const deque<set<int> > & a, ostream & pout) {
  function translate (line 897) | int static_network::translate(deque<deque<int> > & ten) {
  function translate (line 942) | int static_network::translate(deque<int> & ten) {
  function set_subgraph (line 976) | void static_network::set_subgraph(deque<int> & group, deque<deque<int> >...
  function set_proper_weights (line 1023) | void static_network::set_proper_weights() {
  function set_connected_components (line 1079) | void static_network::set_connected_components(deque<deque<int> > & comps) {
  function same_component (line 1116) | void static_network::same_component(int source, set<int> & already_gone) {
  function propagate_distances (line 1156) | int static_network::propagate_distances(deque<int> & new_shell, set<int>...
  function translate_anyway (line 1225) | int static_network::translate_anyway(deque<deque<int> > & ten) {
  function set_upper_network (line 1265) | int static_network::set_upper_network(map<int, map<int, pair<int, double...
  function print_degree_of_homeless (line 1369) | void static_network::print_degree_of_homeless(DI & homel, ostream & outt) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/directed_oslomnet_evaluate.h
  function log_zero (line 4) | inline double log_zero(double a) {
  function class (line 16) | class oslomnet_evaluate : public oslomnet_louvain {
  function set_changendi_cum (line 86) | void oslomnet_evaluate::set_changendi_cum() {
  function set_maxbord (line 117) | int oslomnet_evaluate::set_maxbord() {
  function erase_cgroup (line 134) | void oslomnet_evaluate::erase_cgroup(int wnode) {
  function erase_the_worst (line 219) | bool oslomnet_evaluate::erase_the_worst(int & wnode) {
  function insert_cgroup (line 255) | void oslomnet_evaluate::insert_cgroup(int wnode) {
  function set_cgroup_and_neighs (line 360) | void oslomnet_evaluate::set_cgroup_and_neighs(const deque<int> & G) {
  function cup_on_list (line 381) | double oslomnet_evaluate::cup_on_list(cup_data_struct & a, deque<int> & ...
  function all_external_test (line 523) | double oslomnet_evaluate::all_external_test(int kout_g_in, int tmin, int...
  function initialize_for_evaluation (line 540) | void oslomnet_evaluate::initialize_for_evaluation(weighted_tabdeg & prev...
  function initialize_for_evaluation (line 565) | void oslomnet_evaluate::initialize_for_evaluation(const deque<int> & _c_...
  function partial_CUP (line 588) | double oslomnet_evaluate::partial_CUP(weighted_tabdeg & previous_tab_c, ...
  function CUP_runs (line 656) | double oslomnet_evaluate::CUP_runs(weighted_tabdeg & previous_tab_c, wei...
  function insert_the_best (line 823) | bool oslomnet_evaluate::insert_the_best() {
  function insertion (line 849) | void oslomnet_evaluate::insertion(int changendi) {
  function get_external_scores (line 953) | void oslomnet_evaluate::get_external_scores(weighted_tabdeg & neighs, cu...
  function try_to_assign_homeless_help (line 1011) | int oslomnet_evaluate::try_to_assign_homeless_help(module_collection & m...

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/egocentric_undir.h
  function class (line 5) | class egocentric_net : public oslomnet_louvain {
  function collect_ego_groups_once (line 25) | int egocentric_net::collect_ego_groups_once(int_matrix & E) {
  function add_this_egomodules (line 44) | int egocentric_net::add_this_egomodules(int node, module_collection & Me...

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/hierarchies.h
  function manipulate_string (line 5) | bool manipulate_string(string s, string netfile, string & outs) {
  function external_program_to_call (line 53) | void external_program_to_call(string network_file, oslom_net_global & ma...
  function translate_covers (line 111) | void translate_covers(string previous_tp, string new_tp, string short_tp...
  function no_singletons (line 172) | void no_singletons(char * directory_char, oslom_net_global & luca, modul...
  function write_tp_of_this_level (line 218) | bool write_tp_of_this_level(int level, oslom_net_global & luca, char * d...
  function oslom_level (line 359) | void oslom_level(oslom_net_global & luca, char * directory_char) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/log_table.h
  function class (line 8) | class log_fact_table {
  function _set_ (line 58) | void log_fact_table::_set_(int size) {
  function cum_hyper_right (line 84) | double log_fact_table::cum_hyper_right(int kin_node, int kout_g, int tm,...
  function cum_hyper_left (line 151) | double log_fact_table::cum_hyper_left(int kin_node, int kout_g, int tm, ...
  function cum_binomial_right (line 222) | double log_fact_table::cum_binomial_right(int x, int N, double prob) {
  function cum_binomial_left (line 281) | double log_fact_table::cum_binomial_left(int x, int N, double prob) {
  function slow_symmetric_eq (line 334) | double log_fact_table::slow_symmetric_eq(int k1, int k2, int H, int x) {
  function fast_right_cum_symmetric_eq (line 373) | inline double log_fact_table::fast_right_cum_symmetric_eq(int k1, int k2...

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/louvain_oslomnet.h
  function class (line 6) | class oslom_module {
  type map (line 26) | typedef map<int, pair<int, double> > mapip;
  type map (line 27) | typedef map<int, oslom_module> map_int_om;
  function prints (line 31) | void prints(map_int_om & M) {
  function class (line 45) | class oslomnet_louvain : public static_network {
  function module_initializing (line 89) | void oslomnet_louvain::module_initializing() {
  function unweighted_favorite_of (line 110) | void oslomnet_louvain::unweighted_favorite_of(const int & node, int & fi...
  function weighted_favorite_of (line 167) | void oslomnet_louvain::weighted_favorite_of(const int & node, int & fi, ...
  function update_modules (line 241) | inline void oslomnet_louvain::update_modules(const int & i, const int & ...
  function single_pass_unweighted (line 275) | void oslomnet_louvain::single_pass_unweighted() {
  function single_pass_weighted (line 291) | void oslomnet_louvain::single_pass_weighted() {
  function set_partition_collected (line 305) | void oslomnet_louvain::set_partition_collected(deque<deque<int> > & ten2) {
  function collect_raw_groups_once (line 361) | int oslomnet_louvain::collect_raw_groups_once(deque<deque<int> > & P) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/louvain_oslomnet_dir.h
  function class (line 6) | class oslom_module {
  function class (line 25) | class internal_links_weights {
  type map (line 45) | typedef map<int, internal_links_weights> mapip;
  type map (line 46) | typedef map<int, oslom_module> map_int_om;
  function int_histogram (line 50) | void int_histogram(const int & c, mapip  & hist, const int & w1, const d...
  function prints (line 75) | void prints(map_int_om & M) {
  function class (line 89) | class oslomnet_louvain : public static_network {
  function module_initializing (line 133) | void oslomnet_louvain::module_initializing() {
  function unweighted_favorite_of (line 153) | void oslomnet_louvain::unweighted_favorite_of(const int & node, int & fi...
  function weighted_favorite_of (line 224) | void oslomnet_louvain::weighted_favorite_of(const int & node, int & fi, ...
  function update_modules (line 294) | inline void oslomnet_louvain::update_modules(const int & i, const int & ...
  function single_pass_unweighted (line 343) | void oslomnet_louvain::single_pass_unweighted() {
  function single_pass_weighted (line 359) | void oslomnet_louvain::single_pass_weighted() {
  function set_partition_collected (line 373) | void oslomnet_louvain::set_partition_collected(deque<deque<int> > & ten2) {
  function collect_raw_groups_once (line 428) | int oslomnet_louvain::collect_raw_groups_once(deque<deque<int> > & P) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/main_body.cpp
  function main (line 9) | int main(int argc, char * argv[]) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/main_directed.cpp
  function program_statement (line 76) | void program_statement(char * b) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/main_undirected.cpp
  function program_statement (line 105) | void program_statement(char * b) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/module_collection.h
  function class (line 7) | class module_collection {
  function _set_ (line 68) | void module_collection::_set_(int dim) {
  function insert (line 82) | bool module_collection::insert(deque<int> & c, double bs) {
  function insert (line 93) | bool module_collection::insert(deque<int> & c, double bs, int & new_name) {
  function erase (line 126) | bool module_collection::erase(int a) {
  function print (line 160) | void module_collection::print(ostream & outt, deque<int> & netlabels, bo...
  function fill_gaps (line 199) | void module_collection::fill_gaps() {
  function put_gaps (line 215) | void module_collection::put_gaps() {
  function homeless (line 238) | void module_collection::homeless(deque<int> & h) {
  function coverage (line 260) | int module_collection::coverage() {
  function effective_groups (line 279) | int module_collection::effective_groups() {
  function set_partition (line 298) | void module_collection::set_partition(deque<deque<int> > & A) {
  function set_partition (line 307) | void module_collection::set_partition(deque<deque<int> > & A, deque<doub...
  function check_already (line 329) | bool module_collection::check_already(const deque<int> & c) {
  function compute_inclusions (line 365) | void module_collection::compute_inclusions() {
  function erase_included (line 375) | void module_collection::erase_included() {
  function erase_first_shell (line 402) | bool module_collection::erase_first_shell(map<int, deque<int> > & erase_...
  function almost_equal (line 459) | bool module_collection::almost_equal(int module_id, deque<int> & smaller) {
  function compact (line 503) | void module_collection::compact() {
  function sort_modules (line 550) | void module_collection::sort_modules(deque<int> & module_order) {
  function egomodules_to_merge (line 572) | bool module_collection::egomodules_to_merge(deque<int> & egom, deque<int...
  function merge (line 609) | void module_collection::merge(DI & c) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/oslom_net_global.h
  function class (line 5) | class oslom_net_global : public oslomnet_evaluate {
  function try_to_merge_discarded (line 83) | int oslom_net_global::try_to_merge_discarded(int_matrix & discarded, int...
  function get_single_trial_partition (line 152) | void oslom_net_global::get_single_trial_partition(int_matrix & good_modu...
  function from_matrix_to_module_collection (line 251) | void oslom_net_global::from_matrix_to_module_collection(int_matrix & goo...
  function get_cover (line 271) | void oslom_net_global::get_cover(module_collection & minimal_modules) {
  function check_minimality_all (line 296) | void oslom_net_global::check_minimality_all(int_matrix & A, DD & bss, mo...
  function check_minimality_matrix (line 344) | void oslom_net_global::check_minimality_matrix(int_matrix & A, DD & bss,...
  function check_minimality (line 372) | bool oslom_net_global::check_minimality(deque<int> & group, double & bs_...
  function print_modules (line 445) | void oslom_net_global::print_modules(bool not_homeless, string tp, modul...
  function print_modules (line 461) | void oslom_net_global::print_modules(bool not_homeless, ostream & out1, ...
  function load (line 484) | void oslom_net_global::load(string filename, module_collection & Mall) {
  function get_covers (line 515) | void oslom_net_global::get_covers(string cover_file, int & soft_partitio...
  function ultimate_cover (line 570) | void oslom_net_global::ultimate_cover(string cover_file, int soft_partit...
  function hint (line 614) | void oslom_net_global::hint(module_collection & minimal_modules, string ...
  function print_statistics (line 661) | void oslom_net_global::print_statistics(ostream & outt, module_collectio...

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/oslom_net_unions.cpp
  function from_int_matrix_and_deque_to_deque (line 3) | void from_int_matrix_and_deque_to_deque(int_matrix & its_submodules, con...

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/set_parameters.h
  function general_program_statement (line 13) | void general_program_statement(char * b) {
  function error_statement (line 67) | void error_statement(char * b) {
  function class (line 81) | class Parameters {
  function print (line 161) | void Parameters::print() {
  function set_flag_and_number (line 207) | bool Parameters::set_flag_and_number(double & number_to_set, int & argct...
  function set_flag_and_number (line 239) | bool Parameters::set_flag_and_number(int & number_to_set, int & argct, i...
  function set_flag_and_number_external_program (line 360) | bool Parameters::set_flag_and_number_external_program(string program_nam...
  function _set_ (line 410) | bool Parameters::_set_(int argc, char * argv[]) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/standard_package/cast.cpp
  function cast_string_to_double (line 142) | double cast_string_to_double(string &b) {
  function cast_int (line 152) | inline int cast_int(double u) {
  function cast_string_to_char (line 159) | int cast_string_to_char(string file_name, char *b) {
  function cast_string_to_doubles (line 171) | bool cast_string_to_doubles(string &b, deque<double> & v) {
  function cast_string_to_doubles (line 218) | bool cast_string_to_doubles(string &b, deque<int> & v) {
  function separate_strings (line 235) | bool separate_strings(string &b, deque<string> & v) {
  function approx (line 281) | double approx(double a, int digits) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/standard_package/combinatorics.cpp
  function average_func (line 8) | double average_func(Seq &sq) {
  function variance_func (line 27) | double variance_func(Seq &sq) {
  function average_pf (line 61) | double average_pf(Seq &sq) {
  function variance_pf (line 83) | double variance_pf(Seq &sq) {
  function log_factorial (line 116) | double log_factorial (int num) {
  function log_combination (line 130) | double log_combination (int n, int k) {
  function binomial (line 153) | double binomial(int n, int x, double p) {		//	returns the binomial distr...
  function binomial_cumulative (line 193) | int binomial_cumulative(int n, double p, deque<double> &cum) {
  function powerlaw (line 217) | int powerlaw (int n, int min, double tau, deque<double> &cumulative) {
  function distribution_from_cumulative (line 240) | int distribution_from_cumulative(const deque<double> &cum, deque<double>...
  function cumulative_from_distribution (line 257) | int cumulative_from_distribution (deque<double> &cum, const deque<double...
  function poisson (line 273) | double poisson (int x, double mu) {
  function shuffle_and_set (line 283) | int shuffle_and_set(int *due, int dim) {		// it sets due as a random seq...
  function shuffle_s (line 304) | int shuffle_s(deque<T> &sq) {
  function shuffle_s (line 332) | int shuffle_s(type_ *a, int b) {
  function compute_r (line 360) | double compute_r(int x, int k, int kout, int m) {
  function add_factors (line 375) | int add_factors (deque<double> & num, deque<double> &den, int  n, int k) {
  function compute_hypergeometric (line 406) | double compute_hypergeometric(int i, int k, int kout, int m) {
  function random_from_set (line 475) | int random_from_set(set<int> & s) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/standard_package/deque_numeric.cpp
  function Euclidean_norm (line 23) | double Euclidean_norm(const deque<double> & a) {
  function Euclidean_normalize (line 38) | int Euclidean_normalize(deque<double> & a) {
  function scalar_product (line 53) | double scalar_product(deque<double> & a, deque<double> & b) {
  function orthogonalize (line 77) | int orthogonalize(deque<double> & a, deque<deque<double> > & M) {
  function matrix_time_vector (line 103) | int matrix_time_vector(deque<deque<double> > & Q, deque<double> & v, deq...
  function set_to_deque (line 126) | void set_to_deque(const set<int> & s, deque<int> & a) {
  function set_to_deque (line 136) | void set_to_deque(const set<double> & s, deque<double> & a) {
  function deque_to_set (line 146) | void deque_to_set(const deque<double> & a, set<double> & s) {
  function deque_to_set (line 156) | void deque_to_set(const deque<int> & a, set<int> & s) {
  function deque_to_set_app (line 168) | void deque_to_set_app(const deque<int> & a, set<int> & s) {
  function norm_one (line 180) | double norm_one(const deque<double> & a) {
  function normalize_one (line 195) | int normalize_one(deque<double> & a) {
  function jaccard (line 210) | double jaccard(set<int> & a1,  set<int> & a2) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/standard_package/histograms.cpp
  function intlog_binning (line 14) | int intlog_binning(deque<int> c, int number_of_bins, deque<double> & Xs,...
  function xybinning (line 139) | int xybinning(deque<type> &c, deque<type> &d, int number_of_bins, deque<...
  function xybinning (line 265) | int xybinning(deque<type> &c, deque<type> &d, int number_of_bins, deque<...
  function compute_quantiles (line 275) | void compute_quantiles(double q, deque<double> & y, deque<double> & qs) {
  function xybinning_quantiles (line 301) | int xybinning_quantiles(deque<type> &c, deque<type> &d, int number_of_bi...
  function log_histogram (line 428) | int log_histogram(deque<type> &c, ostream & out, int number_of_bins) {		...
  function log_histogram (line 525) | int log_histogram(deque<double> &c, deque<double> &c2, ostream & out, in...
  function histogram (line 620) | int histogram (vector <type> &c, ostream & out, int number_of_bins, doub...
  function not_norm_histogram_correlated (line 721) | int not_norm_histogram_correlated (deque<type> &c, deque<type> &d, ostre...
  function histogram (line 824) | int histogram (deque <type> &c, ostream & out, int number_of_bins, doubl...
  function not_norm_histogram (line 925) | int not_norm_histogram (vector<type> &c, ostream & out, int number_of_bi...
  function not_norm_histogram (line 1025) | int not_norm_histogram (deque<type> &c, ostream & out, int number_of_bin...
  function histogram (line 1123) | int histogram (deque<double> &c, deque<double> &c2, ostream & out, int n...
  function not_norm_histogram (line 1225) | int not_norm_histogram (deque<double> &c, deque<double> &c2, ostream & o...
  function int_histogram (line 1326) | void int_histogram (vector <int> &c, ostream & out) {
  function int_histogram (line 1355) | void int_histogram (deque <int> &c, ostream & out) {
  function int_histogram (line 1384) | void int_histogram(int c, map<int, int> & hist) {
  function int_histogram (line 1399) | void int_histogram(int c, map<int, double> & hist, double w) {
  function print_cumulative (line 1414) | int print_cumulative (deque<double> & kws, string file, int number_of_st...
  function print_cumulative (line 1440) | int print_cumulative (deque<int> & kws, string file, int number_of_step) {
  function print_cumulative (line 1466) | int print_cumulative (vector<double> & kws, string file, int number_of_s...
  function print_cumulative (line 1493) | int print_cumulative (vector<int> & kws, string file, int number_of_step) {
  function int_histogram (line 1523) | void int_histogram(string infile, string outfile) {
  function int_histogram (line 1550) | void int_histogram(int c, map<int, int> & hist, int w) {
  function int_histogram (line 1567) | void int_histogram(const int & c, map<int, pair<int, double> >  & hist, ...
  function int_histogram (line 1586) | void int_histogram(int c, map<int, pair<double, double> > & hist, double...
  function int_histogram (line 1604) | void int_histogram(int c, map<int, pair<int, int> > & hist, int w1, int ...

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/standard_package/mutual.cpp
  function mutual (line 40) | double mutual (deque<deque<int> > en, deque<deque<int> > ten) {
  function H (line 189) | double H(double a) {
  function H (line 200) | double H(deque <double> &p) {
  function H_x_given_y (line 212) | double H_x_given_y(deque<deque<int> > &en, deque<deque<int> > &ten, int ...
  function mutual2 (line 322) | double mutual2(deque<deque<int> > en, deque<deque<int> > ten) {
  function H_x_given_y3 (line 413) | double H_x_given_y3(deque<deque<int> > &en, deque<deque<int> > &ten, int...
  function mutual3 (line 541) | double mutual3(deque<deque<int> > en, deque<deque<int> > ten) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/standard_package/pajek.cpp
  function number_together (line 4) | int number_together(deque<int> & a) {
  function get_partition_from_file_list_pajek (line 36) | int get_partition_from_file_list_pajek(string s, deque<deque<int> > & te...
  function set_partition_from_list (line 90) | void set_partition_from_list(deque<int> & mems, deque<deque<int> > & ten) {
  function get_partition_from_file_list_pajek_tree (line 129) | int get_partition_from_file_list_pajek_tree(string s, deque<deque<deque<...
  function pajek_format (line 228) | int pajek_format(string filename, bool directed) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/standard_package/partition.cpp
  function get_partition_from_file_tp_format_with_homeless (line 51) | int get_partition_from_file_tp_format_with_homeless(string S, deque<dequ...
  function get_partition_from_file_tp_format (line 95) | int get_partition_from_file_tp_format(string S, map<int, deque<int> > & ...
  function get_partition_from_file_tp_format (line 137) | int get_partition_from_file_tp_format(string S, deque<deque<int> > & M, ...
  function get_partition_from_file_tp_format (line 198) | int get_partition_from_file_tp_format(string S, deque<deque<int> > & M, ...
  function get_partition_from_file_tp_format (line 236) | int get_partition_from_file_tp_format(string S, deque<deque<int> > & M) {
  function get_partition_from_file (line 242) | int get_partition_from_file(string s, deque<deque<int> > & M, int min) {
  function get_partition_from_file (line 271) | int get_partition_from_file(string s, deque<deque<int> > & M) {
  function get_partition_from_file_list (line 277) | int get_partition_from_file_list(string s, deque<deque<int> > & ten) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/standard_package/print.cpp
  function cherr (line 15) | void cherr(double a) {
  function cherr (line 24) | void cherr(double a, double ee) {
  function prints (line 38) | void prints(pair <uno, due> &sq,  ostream &out) {
  function prints (line 46) | void prints(pair <uno, due> &sq) {
  function prints (line 54) | void prints(map <uno, due> &sq,  ostream &out) {
  function prints (line 67) | void prints(multimap <uno, due> &sq,  ostream &out) {
  function prints (line 82) | void prints(Seq &sq, ostream &out) {
  function prints (line 94) | void prints(type_ *a, int b) {
  function printm (line 105) | void printm(C<T>& c, ostream &out) {
  function prints (line 120) | void prints(map <uno, due> &sq) {
  function prints (line 133) | void prints(multimap <uno, due> &sq) {
  function prints (line 147) | void prints(deque<uno> & a, deque<due> &b) {
  function prints (line 155) | void prints(deque<uno> & a, deque<due> &b, ostream &out) {
  function prints (line 164) | void prints(Seq &sq) {
  function prints (line 177) | void prints(const deque<type> & sq) {
  function prints (line 187) | void prints(const vector<type> & sq) {
  function printm (line 200) | void printm(deque<type> & M) {
  function printm (line 210) | void printm(vector<type> & M) {
  function get_data_from_file (line 223) | void get_data_from_file(string s, deque<type> & a1, int col) {
  function get_data_from_file (line 255) | void get_data_from_file(string s, deque<type> & a1) {
  function get_data_from_file (line 264) | void get_data_from_file(string s, deque<type> & a1, deque<type> & a2, in...
  function get_data_from_file (line 301) | void get_data_from_file(string s, deque<type> & a1, deque<type> & a2) {
  function get_data_from_file_string (line 311) | void get_data_from_file_string(string s, deque<string> & a1, int col) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/standard_package/random.cpp
  function ran2 (line 24) | double ran2(long *idum) {
  function ran4 (line 60) | double ran4(bool t, long s) {
  function ran4 (line 77) | double ran4() {
  function srand4 (line 83) | void srand4(void) {
  function srand5 (line 92) | void srand5(int rank) {
  function irand (line 101) | int irand(int n) {
  function srand_file (line 108) | void srand_file(void) {
  function configuration_model (line 132) | int configuration_model(deque<set<int> > & en, deque<int> & degrees) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/standard_package/tabdeg.cpp
  class tabdeg (line 23) | class tabdeg {
    method tabdeg (line 28) | tabdeg(){}
    method size (line 35) | int size() {return nodes_indeg.size();}
  function main (line 155) | int main() {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/undir_weighted_tabdeg.h
  type multimap (line 6) | typedef multimap<double, pair<int, double> > cup_data_struct;
  function compare_r_variables (line 15) | double compare_r_variables(double a, double b, double c, double d) {
  function right_error_function (line 48) | double right_error_function(double x) {
  function log_together (line 56) | double log_together(double minus_log_total, int number) {
  function fitted_exponent (line 89) | double fitted_exponent(int N) {
  function order_statistics_left_cumulative (line 118) | inline double order_statistics_left_cumulative(int N, int pos, double x) {
  function inverse_order_statistics (line 132) | double inverse_order_statistics(int sample_dim, int pos, const double  &...
  function pron_min_exp (line 174) | inline double pron_min_exp(int N, double xi) {
  function compute_probability_to_stop (line 188) | inline double compute_probability_to_stop(const double & a, const double...
  function equivalent_check (line 206) | bool equivalent_check(int pos_first, int pos_last, double & A_average, d...
  function equivalent_check_gather (line 249) | bool equivalent_check_gather(cup_data_struct & a, int & until, const dou...
  function hyper_table (line 302) | inline double hyper_table(int kin_node, int kout_g, int tm, int degree_n...
  function topological_05 (line 314) | inline double topological_05(int kin_node, int kout_g, int tm, int degre...
  function compute_global_fitness (line 322) | double compute_global_fitness(int kin_node, int kout_g, int tm, int degr...
  function compute_global_fitness_step (line 392) | double compute_global_fitness_step(int kin_node, int kout_g, int tm, int...
  function compute_global_fitness_ofive (line 416) | inline double compute_global_fitness_ofive(int kin_node, int kout_g, int...
  function compute_global_fitness_randomized (line 423) | inline double compute_global_fitness_randomized(int kin_node, int kout_g...
  function compute_global_fitness_randomized_short (line 431) | double compute_global_fitness_randomized_short(int kin_node, int kout_g,...
  function class (line 461) | class facts {
  function class (line 481) | class weighted_tabdeg {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/undirected_network.h
  function class (line 13) | class static_network {
  function kplus_global_and_quick (line 139) | void static_network::vertex::kplus_global_and_quick(deque<int> & a, int ...
  function kplus_m (line 173) | int static_network::vertex::kplus_m(const deque<int> &a) {
  function kplus_w (line 192) | double static_network::vertex::kplus_w(const deque<int> &a) {
  function kplus_m (line 214) | int static_network::vertex::kplus_m(const set<int> &a) {
  function clear (line 242) | void static_network::clear() {
  function set_graph (line 265) | void static_network::set_graph(map<int, map<int, pair<int, double> > > &...
  function set_graph (line 314) | bool static_network::set_graph(string file_name) {
  function set_graph (line 547) | void static_network::set_graph(deque<deque<int> > & link_per_node, deque...
  function static_network (line 631) | int static_network::kin_m (const deque<int> & seq) {
  function static_network (line 654) | int static_network::ktot_m (const deque<int> &seq) {
  function ktot_m (line 664) | int static_network::ktot_m(const set <int> &s) {
  function kin_m (line 677) | int static_network::kin_m(const set <int> &s) {
  function draw (line 693) | int static_network::draw(string file_name) {
  function static_network (line 732) | void static_network::get_id_label (map <int, int> &a) {
  function deque_id (line 740) | void static_network::deque_id(deque<int> & a) {
  function print_id (line 748) | void static_network::print_id(const deque<int> & a, ostream & pout) {
  function print_id (line 758) | void static_network::print_id(const set<int> & a, ostream & pout) {
  function print_id (line 769) | void static_network::print_id(const deque<deque<int> > & a, ostream & po...
  function print_id (line 778) | void static_network::print_id(const deque<set<int> > & a, ostream & pout) {
  function translate_anyway (line 790) | int static_network::translate_anyway(deque<deque<int> > & ten) {
  function translate (line 826) | int static_network::translate(deque<deque<int> > & ten) {
  function set_subgraph (line 870) | void static_network::set_subgraph(deque<int> & group, deque<deque<int> >...
  function set_proper_weights (line 917) | void static_network::set_proper_weights() {
  function set_connected_components (line 963) | void static_network::set_connected_components(deque<deque<int> > & comps) {
  function same_component (line 999) | void static_network::same_component(int source, set<int> & already_gone) {
  function propagate_distances (line 1030) | int static_network::propagate_distances(deque<int> & new_shell, set<int>...
  function draw_consecutive (line 1092) | int static_network::draw_consecutive(string file_name1, string file_name...
  function set_upper_network (line 1132) | int static_network::set_upper_network(map<int, map<int, pair<int, double...
  function draw_with_weight_probability (line 1218) | int static_network::draw_with_weight_probability(string file_name) {
  function print_degree_of_homeless (line 1252) | void static_network::print_degree_of_homeless(DI & homel, ostream & outt) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/undirected_oslomnet_evaluate.h
  function log_zero (line 4) | inline double log_zero(double a) {
  function class (line 16) | class oslomnet_evaluate : public oslomnet_louvain {
  function set_changendi_cum (line 83) | void oslomnet_evaluate::set_changendi_cum() {
  function set_maxbord (line 113) | int oslomnet_evaluate::set_maxbord() {
  function erase_cgroup (line 126) | void oslomnet_evaluate::erase_cgroup(int wnode) {
  function erase_the_worst (line 169) | bool oslomnet_evaluate::erase_the_worst(int & wnode) {
  function insert_cgroup (line 201) | void oslomnet_evaluate::insert_cgroup(int wnode) {
  function set_cgroup_and_neighs (line 264) | void oslomnet_evaluate::set_cgroup_and_neighs(const deque<int> & G) {
  function cup_on_list (line 285) | double oslomnet_evaluate::cup_on_list(cup_data_struct & a, deque<int> & ...
  function all_external_test (line 427) | double oslomnet_evaluate::all_external_test(int kout_g, int tm, int Nsta...
  function initialize_for_evaluation (line 443) | void oslomnet_evaluate::initialize_for_evaluation(weighted_tabdeg & prev...
  function initialize_for_evaluation (line 462) | void oslomnet_evaluate::initialize_for_evaluation(const deque<int> & _c_...
  function partial_CUP (line 481) | double oslomnet_evaluate::partial_CUP(weighted_tabdeg & previous_tab_c, ...
  function CUP_runs (line 522) | double oslomnet_evaluate::CUP_runs(weighted_tabdeg & previous_tab_c, wei...
  function insert_the_best (line 677) | bool oslomnet_evaluate::insert_the_best() {
  function insertion (line 700) | void oslomnet_evaluate::insertion(int changendi) {
  function get_external_scores (line 787) | void oslomnet_evaluate::get_external_scores(weighted_tabdeg& neighs, cup...

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/wsarray.h
  function class (line 17) | class wsarray {
  function find (line 88) | int wsarray::find(int a) {
  function push_back (line 128) | void wsarray::push_back(int a, int bb, double b) {
  function freeze (line 139) | void wsarray::freeze() {
  function prints (line 195) | void prints(wsarray &a) {
  function prints (line 207) | void prints(wsarray &a, ostream & pout) {
  function prints (line 219) | void prints(wsarray *a, ostream & pout) {
  function prints (line
Copy disabled (too large) Download .json
Condensed preview — 2675 files, each showing path, character count, and a content snippet. Download the .json file for the full structured content (51,690K chars).
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  {
    "path": ".gitmodules",
    "chars": 417,
    "preview": "[submodule \"SubModules/igraph\"]\n\tpath = SubModules/igraph\n\turl = git@github.com:igraph/igraph.git\n[submodule \"SubModules"
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    "chars": 842,
    "preview": "# Clique Percolation\n## Description\n\nThe sequential clique percolation algorithm is method for detecting clique percolat"
  },
  {
    "path": "Algorithms/2008-CliquePercolation/algorithm_example.py",
    "chars": 337,
    "preview": "import networkx as nx\n\nfrom conradlee_clique_percolation import *\n\nif __name__ == '__main__':\n    with open('example_edg"
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    "path": "Algorithms/2008-CliquePercolation/conradlee_clique_percolation.py",
    "chars": 1352,
    "preview": "import networkx as nx\nfrom collections import defaultdict\n\n\ndef get_percolated_cliques(G, k):\n    percolation_graph = nx"
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    "path": "Algorithms/2008-CliquePercolation/example_edge_list.txt",
    "chars": 35,
    "preview": "1 2\n1 3\n2 3\n3 4\n4 5\n4 7\n5 7\n5 6\n6 7"
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    "preview": "cmake_minimum_required(VERSION 2.8)\nproject(2008-clique-percolation)\nset(CMAKE_CXX_FLAGS \"${CMAKE_CXX_FLAGS} -std=c++14 "
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    "path": "Algorithms/2008-CliquePercolation/src_cpp/ReadMe.md",
    "chars": 20,
    "preview": "## Issues\n\nall fixed"
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    "path": "Algorithms/2008-CliquePercolation/src_cpp/cliqueHash.cpp",
    "chars": 5756,
    "preview": "/*\nscp, The sequential clique percolation algorithm.\nCopyright (C) 2011  Aalto University\n\nThis program is free software"
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    "preview": "/*\nscp, The sequential clique percolation algorithm.\nCopyright (C) 2011  Aalto University\n\nThis program is free software"
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    "preview": "/*\nscp, The sequential clique percolation algorithm.\nCopyright (C) 2011  Aalto University\n\nThis program is free software"
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    "chars": 18326,
    "preview": "\t\t    GNU GENERAL PUBLIC LICENSE\r\n\t\t       Version 2, June 1991\r\n\r\n Copyright (C) 1989, 1991 Free Software Foundation, I"
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    "preview": "import os\n\nexecutable = \"../k_clique\"\ntempDir = \"../\"\ntestDataDir = \"../testData/\"\n\n\ndef listComp(l1, l2):\n    if len(l1"
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    "preview": "files: IOX.cc IOX.h StringEx.cc StringEx.h files.cc\n\tg++ -fpic -c files.cc -std=c++11\n\tg++ -shared -o libfiles.so files."
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    "path": "Algorithms/2009-Connected-Iterative-Scan/src-orginal/Libraries/Network/TemporalNetwork.cc",
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    "preview": "#include \"TemporalNetwork.h\"\n\n/**\n *@fn TemporalNetwork::AddNetwork ( const string& filename, const string& delimiters )"
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    "path": "Algorithms/2009-Connected-Iterative-Scan/src-orginal/Libraries/Network/TemporalNetwork.h",
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    "preview": "#ifndef RPI_TEMPORAL_NETWORK\n#define RPI_TEMPORAL_NETWORK\n\n#include <set>\n#include <map>\n#include <iostream>\n#include <v"
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    "path": "Algorithms/2009-Connected-Iterative-Scan/src-orginal/Libraries/Network/makefile",
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    "preview": "all: format network\n\nformat: Format.cc\n\tg++ -fpic -c Format.cc -o Format.o -std=c++11\n\tg++ -shared -o libFormat.so Forma"
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    "preview": "#Connected Iterative Scan \nConnected Iterative Scan is also known at times as Locally Optimal Sets.\n\n##Building\nTo make "
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  {
    "path": "Algorithms/2009-Connected-Iterative-Scan/src-orginal/main.cc",
    "chars": 15800,
    "preview": "#include <algorithm>\n#include <limits>\n\n#include \"Libraries/Network/TemporalNetwork.h\"\n#include \"Libraries/Params/Parame"
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  {
    "path": "Algorithms/2009-Connected-Iterative-Scan/src-orginal/makefile",
    "chars": 387,
    "preview": "all:\n\tcd Libraries/Files; make;\n\tcd Libraries/Params; make;\n\tcd Libraries/Network; make;\n\tmake cis\n\ncis: main.cc \n\tg++ m"
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    "path": "Algorithms/2009-Connected-Iterative-Scan/src-refactor/CMakeLists.txt",
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    "path": "Algorithms/2009-Connected-Iterative-Scan/src-refactor/ReadMe.md",
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    "preview": "#Connected Iterative Scan \nConnected Iterative Scan is also known at times as Locally Optimal Sets.\n\n\n##File Organizatio"
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    "path": "Algorithms/2009-Connected-Iterative-Scan/src-refactor/dataset/network.cl",
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    "path": "Algorithms/2009-Connected-Iterative-Scan/src-refactor/dataset/network_seeded.cl",
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    "path": "Algorithms/2009-Connected-Iterative-Scan/src-refactor/graph/network.cc",
    "chars": 4617,
    "preview": "#include \"network.h\"\n\n/**\n *@fn void AddEdge( shared_ptr < string > fr, shared_ptr < string > to, const double& weight, "
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  {
    "path": "Algorithms/2009-Connected-Iterative-Scan/src-refactor/graph/network.h",
    "chars": 1746,
    "preview": "#ifndef RPI_NETWORK\n#define RPI_NETWORK\n\n#include <map>\n#include <set>\n#include <memory>\n#include <fstream>\n\nusing names"
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  {
    "path": "Algorithms/2009-Connected-Iterative-Scan/src-refactor/graph/temporal_network.cc",
    "chars": 2940,
    "preview": "#include \"temporal_network.h\"\n\n/**\n *@fn TemporalNetwork::AddNetwork ( const string& filename, const string& delimiters "
  },
  {
    "path": "Algorithms/2009-Connected-Iterative-Scan/src-refactor/graph/temporal_network.h",
    "chars": 1394,
    "preview": "#ifndef RPI_TEMPORAL_NETWORK\n#define RPI_TEMPORAL_NETWORK\n\n#include <set>\n#include <map>\n#include <iostream>\n#include <v"
  },
  {
    "path": "Algorithms/2009-Connected-Iterative-Scan/src-refactor/main.cc",
    "chars": 17610,
    "preview": "#include <algorithm>\n\n#include \"graph/temporal_network.h\"\n#include \"util/parameters_helper.h\"\n\nusing namespace std;\n\n/**"
  },
  {
    "path": "Algorithms/2009-Connected-Iterative-Scan/src-refactor/useless/RandomNetwork.h",
    "chars": 459,
    "preview": "#ifndef RNET_RPI\n#define RNET_RPI\n\n#include \"../Network/network.h\"\n#include \"../Random/PowerLaw.h\"\n\nvoid RandomNetwork ("
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  {
    "path": "Algorithms/2009-Connected-Iterative-Scan/src-refactor/util/graph_io_helper.cc",
    "chars": 3602,
    "preview": "#include \"graph_io_helper.h\"\n\nusing namespace std;\n\n/**\n *@fn void ChangeDelimiter ( const string& filein, const string&"
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  {
    "path": "Algorithms/2009-Connected-Iterative-Scan/src-refactor/util/graph_io_helper.h",
    "chars": 1062,
    "preview": "#include <vector>\n#include <map>\n\n#include \"io_helper.h\"\n\nusing namespace std;\n\n/**\n *@fn void ChangeDelimiter ( const s"
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  {
    "path": "Algorithms/2009-Connected-Iterative-Scan/src-refactor/util/io_helper.cc",
    "chars": 2658,
    "preview": "#include \"io_helper.h\"\n\n/**\n * @fn bool fline_tr(ifstream* fin, vector <string> fields, string delim)\n\n * Retrieve a lin"
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  {
    "path": "Algorithms/2009-Connected-Iterative-Scan/src-refactor/util/io_helper.h",
    "chars": 417,
    "preview": "#ifndef ICE_IOX\n#define ICE_IOX\n\n#include \"string_helper.h\"\n#include <string>\n#include <iostream>\n#include <vector>\n#inc"
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  {
    "path": "Algorithms/2009-Connected-Iterative-Scan/src-refactor/util/parameters_helper.cc",
    "chars": 3147,
    "preview": "/**\n* Implementation of the parameters class\n*/\n#include \"parameters_helper.h\"\n\n/**\n * @fn void Parameters::Read(int arg"
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  {
    "path": "Algorithms/2009-Connected-Iterative-Scan/src-refactor/util/parameters_helper.h",
    "chars": 2250,
    "preview": "/**\n* Class to help read in multiple command line (flagged) parameters\n*\n*\tTO DO:\n* \t\tError Messages\n*/\n\n#ifndef ICE_PAR"
  },
  {
    "path": "Algorithms/2009-Connected-Iterative-Scan/src-refactor/util/string_helper.cc",
    "chars": 1573,
    "preview": "\n/**\n * @fn const std::string trim (const std::string& pString, const std::string& pWhitespace)\n * Remove beginning and "
  },
  {
    "path": "Algorithms/2009-Connected-Iterative-Scan/src-refactor/util/string_helper.h",
    "chars": 863,
    "preview": "#ifndef ICE_STR\n#define ICE_STR\n\n#include <string>\n#include <cstring>\n#include <sstream>\n\nusing namespace std;\n\nconst st"
  },
  {
    "path": "Algorithms/2009-EAGLE/.gitignore",
    "chars": 22,
    "preview": "bin \nobj \nsrc/*.so\n*~\n"
  },
  {
    "path": "Algorithms/2009-EAGLE/ReadMe.md",
    "chars": 229,
    "preview": "# EAGLE\n## Description\n\ncontent | detail\n--- | ---\n[src](src) | refactored successfully built passed version source code"
  },
  {
    "path": "Algorithms/2009-EAGLE/graphs/eagle.edl",
    "chars": 324,
    "preview": "0\t1\n0\t2\n0\t3\n0\t4\n0\t5\n1\t2\n1\t3\n1\t4\n1\t5\n2\t3\n2\t4\n2\t5\n2\t6\n2\t7\n2\t8\n3\t4\n3\t5\n3\t9\n4\t5\n4\t10\n6\t7\n6\t11\n6\t12\n6\t13\n6\t8\n7\t11\n7\t12\n7\t14\n7"
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  {
    "path": "Algorithms/2009-EAGLE/graphs/eagle.graphml",
    "chars": 7408,
    "preview": "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<graphml xmlns=\"http://graphml.graphdrawing.org/xmlns\"\n         xmlns:xsi=\"http:/"
  },
  {
    "path": "Algorithms/2009-EAGLE/graphs/generate.sh",
    "chars": 169,
    "preview": "#!/bin/bash\n\nfor i in `ls originals`; do\n  echo Elaboro $i\n  python tools/converter.py originals/$i $i.graphml\n  python "
  },
  {
    "path": "Algorithms/2009-EAGLE/graphs/originals/eagle",
    "chars": 333,
    "preview": "1\t2\n1\t3\n1\t4\n1\t5\n1\t6\n2\t3\n2\t4\n2\t5\n2\t6\n3\t4\n3\t5\n3\t6\n3\t7\n3\t8\n3\t13\n4\t5\n4\t6\n4\t23\n5\t6\n5\t22\n7\t8\n7\t9\n7\t10\n7\t12\n7\t13\n8\t9\n8\t10\n8\t11\n"
  },
  {
    "path": "Algorithms/2009-EAGLE/graphs/tools/converter.py",
    "chars": 2753,
    "preview": "import igraph\nimport progressbar\nimport sys\n\nif len(sys.argv) < 3:\n  print \"Synopsis: %s graph.edl output [gz|edl|gml] ["
  },
  {
    "path": "Algorithms/2009-EAGLE/graphs/tools/examples.py",
    "chars": 2827,
    "preview": "import sys\nimport time\n\nfrom progressbar import ProgressBar, Percentage, Bar, ETA, FileTransferSpeed, \\\n     RotatingMar"
  },
  {
    "path": "Algorithms/2009-EAGLE/graphs/tools/progressbar.py",
    "chars": 14017,
    "preview": "#!/usr/bin/python\n# -*- coding: iso-8859-1 -*-\n#\n# progressbar  - Text progressbar library for python.\n# Copyright (c) 2"
  },
  {
    "path": "Algorithms/2009-EAGLE/graphs/tools/utils.pyx",
    "chars": 0,
    "preview": ""
  },
  {
    "path": "Algorithms/2009-EAGLE/relazione/Makefile",
    "chars": 595,
    "preview": "CC=g++\nCFLAGS=-c -Wall -I/usr/local/include/igraph -O3 -pipe  -I./include -ffast-math -ftree-vectorize -fopenmp\nLDFLAGS="
  },
  {
    "path": "Algorithms/2009-EAGLE/relazione/relazione.lyx",
    "chars": 32976,
    "preview": "#LyX 2.0 created this file. For more info see http://www.lyx.org/\n\\lyxformat 413\n\\begin_document\n\\begin_header\n\\textclas"
  },
  {
    "path": "Algorithms/2009-EAGLE/src/CMakeLists.txt",
    "chars": 736,
    "preview": "cmake_minimum_required(VERSION 2.8)\nproject(2009-eagle)\nset(CMAKE_CXX_FLAGS \"${CMAKE_CXX_FLAGS} -std=c++14 -O3 -g\")\n\nfin"
  },
  {
    "path": "Algorithms/2009-EAGLE/src/ReadMe.md",
    "chars": 325,
    "preview": "#Attention\n##Current Status\n\nBuild successfully.\n\nFix interface-changing-bug due to change of igraph library. In [commun"
  },
  {
    "path": "Algorithms/2009-EAGLE/src/communities.cpp",
    "chars": 12418,
    "preview": "\n#include <algorithm>\n#include <fstream>\n#include <sstream>\n#include <iostream>\n\n#include <boost/foreach.hpp>\n#include <"
  },
  {
    "path": "Algorithms/2009-EAGLE/src/communities.h",
    "chars": 19732,
    "preview": "#ifndef __COMMUNITIES_H\n#define __COMMUNITIES_H\n\n#include <omp.h>\n\n#include <string>\n#include <set>\n\n#include <iostream>"
  },
  {
    "path": "Algorithms/2009-EAGLE/src/eagle.cpp",
    "chars": 7016,
    "preview": "\n#include <fstream>\n\n#include <boost/archive/text_oarchive.hpp>\n\n#include \"eagle.h\"\n#include \"max_cache.h\"\n\n\nusing names"
  },
  {
    "path": "Algorithms/2009-EAGLE/src/eagle.h",
    "chars": 495,
    "preview": "#ifndef __EAGLE_H\n#define __EAGLE_H\n\n#include <string>\n\n#include \"communities.h\"\n\nclass MaxCache;\n\nclass EAGLE {\nprivate"
  },
  {
    "path": "Algorithms/2009-EAGLE/src/main.cpp",
    "chars": 1565,
    "preview": "#include <fstream>\n#include \"eagle.h\"\n\nusing namespace std;\n\nint main(int argc, char *argv[]) {\n    int mode;\n    const "
  },
  {
    "path": "Algorithms/2009-EAGLE/src/max_cache.cpp",
    "chars": 2337,
    "preview": "#include <cmath>\n\n#include \"max_cache.h\"\n\nusing namespace std;\n\nbool MaxCache::isEmpty() {\n    int s = cache.size();\n\n  "
  },
  {
    "path": "Algorithms/2009-EAGLE/src/max_cache.h",
    "chars": 2705,
    "preview": "#ifndef __MAXCACHE_H\n#define __MAXCACHE_H\n\n#include <list>\n#include <set>\n\n/** Elemento della cache\n Un massimo è identi"
  },
  {
    "path": "Algorithms/2009-LineGraph/altix/axlgc.sh",
    "chars": 892,
    "preview": "#!/bin/bash\n#PBS -l walltime=24:00:00 \n#PBS -l mem=60Gb \n#PBS -l ncpus=4 \n#PBS -m abe\n# Script to run linegraphcreator ("
  },
  {
    "path": "Algorithms/2009-LineGraph/altix/axmakelgc.sh",
    "chars": 103,
    "preview": "module load intel-suite\r\nicpc -xP -mcmodel=large -i-dynamic -o linegraphcreator TseGraph.cpp main.cpp\r\n"
  },
  {
    "path": "Algorithms/2009-LineGraph/deprecated/LineGraphCreator.html",
    "chars": 9284,
    "preview": "<html>\r\n    <head>\r\n        <title>LineGraphCreator</title>\r\n        <meta http-equiv=\"Content-Type\" content=\"text/html;"
  },
  {
    "path": "Algorithms/2009-LineGraph/deprecated/lgc.bat",
    "chars": 76,
    "preview": "dist\\Release\\MinGW-Windows\\linegraphcreator.exe %1 %2 %3 %4 %5 %6 %7 %8 %9\r\n"
  },
  {
    "path": "Algorithms/2009-LineGraph/deprecated/makefileClever",
    "chars": 311,
    "preview": "# taken from http://mrbook.org/tutorials/make/\r\nCC=g++\r\nCFLAGS=-c -Wall\r\nLDFLAGS=-O2\r\nSOURCES=main.cpp TseGraph.cpp\r\nOBJ"
  },
  {
    "path": "Algorithms/2009-LineGraph/deprecated/makefileTSE",
    "chars": 352,
    "preview": "# taken from http://mrbook.org/tutorials/make/ CC=g++ CFLAGS=-c\r\n-Wall LDFLAGS=-O2\r\n\r\nall: linegraphcreator\r\n\r\nlinegraph"
  },
  {
    "path": "Algorithms/2009-LineGraph/deprecated/makelgc.bat",
    "chars": 569,
    "preview": "@echo off\r\nif defined PRGDIR goto :runtg\r\ncall c:\\bin\\setenv\r\n:runtg\r\n@echo --- Compiling LineGraphCreator in C++ from m"
  },
  {
    "path": "Algorithms/2009-LineGraph/readme.txt",
    "chars": 777,
    "preview": "readme.txt file for LineGraphCreator Version 091222\r\n\r\nLook at the LineGraphCreator.html file for more information.\r\n\r\nT"
  },
  {
    "path": "Algorithms/2009-LineGraph/src/TseGraph.cpp",
    "chars": 6835,
    "preview": "/*\r\n * File:   TseGraph.cpp\r\n * Author: T.S.Evans, Physics Dept., Imperial College London\r\n * TseGraph is for weighted o"
  },
  {
    "path": "Algorithms/2009-LineGraph/src/TseGraph.h",
    "chars": 3241,
    "preview": "#include <stdlib.h>\r\n#include <stdio.h>\r\n#include <iostream>\r\n#include <iomanip>\r\n#include <fstream>\r\n#include <vector>\r"
  },
  {
    "path": "Algorithms/2009-LineGraph/src/main.cpp",
    "chars": 11637,
    "preview": "/* \n * File:   main.cpp\n * Author: T.S.Evans, Physics Dept., Imperial College London\n * These line graphs are defined in"
  },
  {
    "path": "Algorithms/2010-CONGA/ReadMe.md",
    "chars": 291,
    "preview": "# 2010-CONGA\n## Three Available Jar Files\n\ncontent | detail\n--- | ---\n[copra](conga_src/src/main/resources/copra.jar) | "
  },
  {
    "path": "Algorithms/2010-CONGA/conga_src/ReadMe.md",
    "chars": 1262,
    "preview": "#Info\n##Author \n\nhttp://gregory.org/research/networks/\n\n\n##Usage of CM (clique_modularity), 2009\n\n> This page provides t"
  },
  {
    "path": "Algorithms/2010-CONGA/conga_src/dataset/dolphins_edges.txt",
    "chars": 903,
    "preview": "29\t43\n29\t52\n29\t35\n29\t51\n29\t45\n0\t10\n0\t42\n0\t15\n0\t40\n0\t47\n0\t14\n39\t57\n24\t29\n24\t51\n24\t45\n50\t51\n23\t51\n23\t36\n23\t45\n34\t37\n34\t44\n"
  },
  {
    "path": "Algorithms/2010-CONGA/conga_src/dataset/karate.txt",
    "chars": 967,
    "preview": "28\n-- 3\n-- 24\n-- 25\n-- 34\n3\n-- 28\n-- 10\n-- 29\n-- 2\n-- 33\n-- 9\n-- 4\n-- 14\n-- 8\n-- 1\n29\n-- 32\n-- 3\n-- 34\n27\n-- 30\n-- 34\n14"
  },
  {
    "path": "Algorithms/2010-CONGA/conga_src/pom.xml",
    "chars": 1758,
    "preview": "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<project xmlns=\"http://maven.apache.org/POM/4.0.0\"\n         xmlns:xsi=\"http://www"
  },
  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/CM.java",
    "chars": 8531,
    "preview": "package clique_modularity;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower deco"
  },
  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/algorithm/BK/BK.java",
    "chars": 4283,
    "preview": "package clique_modularity.algorithm.BK;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fe"
  },
  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/algorithm/BK/BronKerboschCFFast.java",
    "chars": 4809,
    "preview": "package clique_modularity.algorithm.BK;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fe"
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    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/algorithm/KJ/KJ.java",
    "chars": 5111,
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    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/algorithm/MaxClique.java",
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    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/input_output/ReadEdges.java",
    "chars": 1603,
    "preview": "package clique_modularity.input_output;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fe"
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/input_output/WriteCliques.java",
    "chars": 1082,
    "preview": "package clique_modularity.input_output;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fe"
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/ARRAY2.java",
    "chars": 222,
    "preview": "package clique_modularity.util;\n\nimport clique_modularity.util.graph.ELEMENT;\n\n/**\n * Created by cheyulin on 2/27/17.\n *"
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/ARRAY_FIX.java",
    "chars": 222,
    "preview": "package clique_modularity.util;\n\n/**\n * Created by cheyulin on 2/27/17.\n */\n\n\npublic class ARRAY_FIX {\n    public int[] "
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/Pair.java",
    "chars": 392,
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    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/Tree.java",
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    "preview": "package clique_modularity.util;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower"
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    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/benchmark/GG.java",
    "chars": 56090,
    "preview": "package clique_modularity.util.benchmark;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by "
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/benchmark/GGResult.java",
    "chars": 538,
    "preview": "package clique_modularity.util.benchmark;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by "
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/community/CPP.java",
    "chars": 10087,
    "preview": "package clique_modularity.util.community;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by "
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/community/CommPair.java",
    "chars": 387,
    "preview": "package clique_modularity.util.community;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by "
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/community/CommPairSet.java",
    "chars": 1907,
    "preview": "package clique_modularity.util.community;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by "
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/community/CompleteCliques.java",
    "chars": 3153,
    "preview": "package clique_modularity.util.community;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by "
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/community/CompleteCliques1.java",
    "chars": 2089,
    "preview": "package clique_modularity.util.community;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by "
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/community/RebuildCommunities.java",
    "chars": 11891,
    "preview": "package clique_modularity.util.community;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by "
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/community/RemoveCliques.java",
    "chars": 3073,
    "preview": "package clique_modularity.util.community;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by "
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/graph/ELEMENT.java",
    "chars": 348,
    "preview": "package clique_modularity.util.graph;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fern"
  },
  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/metric/Modularity.java",
    "chars": 4324,
    "preview": "package clique_modularity.util.metric;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fer"
  },
  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/metric/Omega.java",
    "chars": 5210,
    "preview": "package clique_modularity.util.metric;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fer"
  },
  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/conga/CONGA.java",
    "chars": 84824,
    "preview": "package conga;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower decompiler)\n//\n\n"
  },
  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/conga/algorithm/Between.java",
    "chars": 15006,
    "preview": "package conga.algorithm;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower decomp"
  },
  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/conga/algorithm/CPP.java",
    "chars": 30436,
    "preview": "package conga.algorithm;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower decomp"
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/conga/algorithm/PB.java",
    "chars": 3059,
    "preview": "package conga.algorithm;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower decomp"
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/Pair.java",
    "chars": 380,
    "preview": "package conga.util;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower decompiler)"
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/StrPair.java",
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    "preview": "package conga.util;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower decompiler)"
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    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/Tree.java",
    "chars": 542,
    "preview": "package conga.util;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower decompiler)"
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/benchmark/GResult.java",
    "chars": 427,
    "preview": "package conga.util.benchmark;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower d"
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/community/BP.java",
    "chars": 300,
    "preview": "package conga.util.community;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower d"
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/community/ClusterInfo.java",
    "chars": 424,
    "preview": "package conga.util.community;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower d"
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/community/Stats.java",
    "chars": 2590,
    "preview": "package conga.util.community;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower d"
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/graph/Edge.java",
    "chars": 628,
    "preview": "package conga.util.graph;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower decom"
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/graph/LabelledEdge.java",
    "chars": 379,
    "preview": "package conga.util.graph;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower decom"
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/graph/Split.java",
    "chars": 381,
    "preview": "package conga.util.graph;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower decom"
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/graph/Vertex.java",
    "chars": 809,
    "preview": "package conga.util.graph;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower decom"
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/metric/ModOverlap.java",
    "chars": 11148,
    "preview": "package conga.util.metric;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower deco"
  },
  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/copra/Project.java",
    "chars": 5680,
    "preview": "package copra;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower decompiler)\n//\n\n"
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/copra/algorithm/COPRA.java",
    "chars": 46129,
    "preview": "package copra.algorithm;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower decomp"
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/copra/util/LabelPair.java",
    "chars": 382,
    "preview": "package copra.util;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower decompiler)"
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  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/copra/util/SetPair.java",
    "chars": 556,
    "preview": "package copra.util;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower decompiler)"
  },
  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/copra/util/VecPair.java",
    "chars": 364,
    "preview": "package copra.util;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower decompiler)"
  },
  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/copra/util/Vert.java",
    "chars": 495,
    "preview": "package copra.util;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower decompiler)"
  },
  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/copra/util/community/ClusterLabel.java",
    "chars": 6322,
    "preview": "package copra.util.community;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower d"
  },
  {
    "path": "Algorithms/2010-CONGA/conga_src/src/main/java/copra/util/metric/ModOverlap.java",
    "chars": 11090,
    "preview": "package copra.util.metric;//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower deco"
  },
  {
    "path": "Algorithms/2010-LinkCommunity/README.markdown",
    "chars": 850,
    "preview": "About\n=====\n\nHere is the code for finding link communities [1] in complex networks.\nCurrently, we have two implementatio"
  },
  {
    "path": "Algorithms/2010-LinkCommunity/cpp/COPYING",
    "chars": 35146,
    "preview": "                    GNU GENERAL PUBLIC LICENSE\n                       Version 3, 29 June 2007\n\n Copyright (C) 2007 Free "
  },
  {
    "path": "Algorithms/2010-LinkCommunity/cpp/README",
    "chars": 2759,
    "preview": "Link Communities C++\n\nThis directory contains C++ code and helper files to perform link clustering for very\nlarge networ"
  },
  {
    "path": "Algorithms/2010-LinkCommunity/cpp/calcAndWrite_Jaccards.cpp",
    "chars": 5497,
    "preview": "// calcAndWrite_Jaccards.cpp\n// Jim Bagrow\n// Last Modified: 2008-12-30\n\n/*\nCopyright 2008,2009,2010 James Bagrow\n\n\nThis"
  },
  {
    "path": "Algorithms/2010-LinkCommunity/cpp/clusterJaccsFile.cpp",
    "chars": 6711,
    "preview": "// clusterJaccsFile.cpp\n// Jim Bagrow\n// Last Modified: 2009-03-10\n\n/*\nCopyright 2008,2009,2010 James Bagrow\n\n\nThis prog"
  },
  {
    "path": "Algorithms/2010-LinkCommunity/cpp/edgelist2pairs.py",
    "chars": 5446,
    "preview": "#!/usr/bin/env python\n# encoding: utf-8\n\n# edgelist2pairs.py\n# Jim Bagrow\n# Last Modified: 2008-12-29\n\n\"\"\"\nCopyright 200"
  },
  {
    "path": "Algorithms/2010-LinkCommunity/cpp/karate.pairs",
    "chars": 404,
    "preview": "0 1\n0 2\n0 3\n0 4\n0 5\n0 6\n0 7\n0 8\n0 9\n0 10\n0 11\n0 12\n0 13\n0 14\n0 15\n0 16\n1 2\n1 3\n1 7\n12 1\n13 1\n1 14\n1 15\n1 17\n2 3\n2 7\n2 8\n"
  },
  {
    "path": "Algorithms/2010-LinkCommunity/cpp/lesmis.pairs",
    "chars": 1507,
    "preview": "0 1\n2 0\n3 0\n4 0\n5 0\n6 0\n7 0\n8 0\n0 9\n0 10\n2 3\n2 10\n3 10\n11 10\n12 10\n13 10\n14 10\n15 10\n16 10\n17 10\n18 10\n19 10\n20 10\n10 21"
  },
  {
    "path": "Algorithms/2010-LinkCommunity/cpp/link_clustering.sh",
    "chars": 3125,
    "preview": "#!/usr/bin/env bash\n\n# link_clustering.sh\n# Jim Bagrow\n# Last Modified: 2010-02-16\n\n# Copyright 2009,2010 James Bagrow\n#"
  },
  {
    "path": "Algorithms/2010-LinkCommunity/cpp/loop_thresholds.sh",
    "chars": 1119,
    "preview": "#!/usr/bin/env bash\n\n# loop_thresholds.sh\n# Jim Bagrow\n# Last Modified: 2009-03-10\n\n\n# Copyright 2009,2010 James Bagrow\n"
  },
  {
    "path": "Algorithms/2010-LinkCommunity/cpp/partition_density.py",
    "chars": 2377,
    "preview": "#!/usr/bin/env python\n# encoding: utf-8\n\n# partition_density.py\n# Jim Bagrow\n# Last Modified: 2010-02-16\n\n# Copyright 20"
  },
  {
    "path": "Algorithms/2010-LinkCommunity/python/karate.pairs",
    "chars": 404,
    "preview": "0 1\n0 2\n0 3\n0 4\n0 5\n0 6\n0 7\n0 8\n0 9\n0 10\n0 11\n0 12\n0 13\n0 14\n0 15\n0 16\n1 2\n1 3\n1 7\n12 1\n13 1\n1 14\n1 15\n1 17\n2 3\n2 7\n2 8\n"
  },
  {
    "path": "Algorithms/2010-LinkCommunity/python/link_clustering.py",
    "chars": 15668,
    "preview": "#!/usr/bin/env python\n# encoding: utf-8\n\n# link_clustering.py\n# Jim Bagrow, Yong-Yeol Ahn\n# Last Modified: 2010-08-27\n\n#"
  },
  {
    "path": "Algorithms/2010-LinkCommunity/python_yche_refactor/ReadMe.md",
    "chars": 1417,
    "preview": "#LinkComm\n##Current Status\nOnly support undirected graph(weighted or unweighted are all supported), which could be found"
  },
  {
    "path": "Algorithms/2010-LinkCommunity/python_yche_refactor/example_edge_list.txt",
    "chars": 53,
    "preview": "1   2\n1   3\n2   3\n3   4\n4   5\n4   7\n5   7\n5   6\n6   7"
  },
  {
    "path": "Algorithms/2010-LinkCommunity/python_yche_refactor/graph_io_helper.py",
    "chars": 2944,
    "preview": "#!/usr/bin/env python\n# encoding: utf-8\n\n\nfrom operator import itemgetter\nfrom collections import defaultdict\n\n\ndef get_"
  },
  {
    "path": "Algorithms/2010-LinkCommunity/python_yche_refactor/link_clustering.py",
    "chars": 2436,
    "preview": "#!/usr/bin/env python\n# encoding: utf-8\n\nimport os\nfrom optparse import OptionParser\nfrom graph_io_helper import *\nfrom "
  },
  {
    "path": "Algorithms/2010-LinkCommunity/python_yche_refactor/link_clustering_algo.py",
    "chars": 6940,
    "preview": "#!/usr/bin/env python\n# encoding: utf-8\n\nfrom copy import copy\nfrom heapq import heappush, heappop\nfrom itertools import"
  },
  {
    "path": "Algorithms/2010-LinkCommunity/python_yche_refactor/play_ground.py",
    "chars": 67,
    "preview": "import itertools\n\nprint list(itertools.combinations([1, 2, 3], 2))\n"
  },
  {
    "path": "Algorithms/2010-LinkCommunity/python_yche_refactor/results_sample/example_edge_list_maxS0.166667_maxD0.703704.comm2edges.txt",
    "chars": 42,
    "preview": "1\t4,7\t5,6\t4,5\t6,7\t5,7\n2\t2,3\t1,3\t1,2\n3\t3,4\n"
  },
  {
    "path": "Algorithms/2010-LinkCommunity/python_yche_refactor/results_sample/example_edge_list_maxS0.166667_maxD0.703704.comm2nodes.txt",
    "chars": 24,
    "preview": "1\t5\t4\t7\t6\n2\t1\t3\t2\n3\t3\t4\n"
  },
  {
    "path": "Algorithms/2010-LinkCommunity/python_yche_refactor/results_sample/example_edge_list_maxS0.166667_maxD0.703704.edge2comm.txt",
    "chars": 54,
    "preview": "5\t6\t1\n4\t5\t1\n5\t7\t1\n4\t7\t1\n6\t7\t1\n2\t3\t2\n1\t3\t2\n1\t2\t2\n3\t4\t3\n"
  },
  {
    "path": "Algorithms/2010-LinkCommunity/python_yche_refactor/results_sample/example_edge_list_thr_D.txt",
    "chars": 131,
    "preview": "1.0 0.0\n1.0 0.0\n0.75 0.0\n0.6 0.666666666667\n0.4 0.703703703704\n0.166666666667 0.703703703704\n0.142857142857 0.5185185185"
  },
  {
    "path": "Algorithms/2010-TopGC/ReadMe.md",
    "chars": 128,
    "preview": "# TopGC\n## Links\n- [related github repo](https://github.com/akhiljain93/rampaging-elephant/tree/master/private/clusterin"
  },
  {
    "path": "Algorithms/2010-TopGC/src_original/Graphs/graph.sample.clusters_directed",
    "chars": 2137,
    "preview": "112\t113\t1140\t1493\t196\t198\t248\t422\t478\t483\t484\t500\t501\t669\t740\t762\t932\t\n1027\t1098\t1196\t1286\t1462\t1663\t1728\t1792\t1883\t1982"
  },
  {
    "path": "Algorithms/2010-TopGC/src_original/Graphs/original/graph.raw",
    "chars": 5399638,
    "preview": "0\t1\t4.30086159319852\n0\t40\t3.5028596081151\n0\t41\t0.940829346722639\n0\t56\t1.99662652712411\n0\t78\t1.05279766076136\n0\t93\t3.5163"
  },
  {
    "path": "Algorithms/2010-TopGC/src_original/Graphs/original/graph1.raw",
    "chars": 192063,
    "preview": "0\t1\t430086159319852\n0\t40\t35028596081151\n0\t41\t0940829346722639\n0\t56\t199662652712411\n0\t78\t105279766076136\n0\t93\t35163543304"
  },
  {
    "path": "Algorithms/2010-TopGC/src_original/Graphs/original/graph_temp.raw",
    "chars": 21,
    "preview": "0\t1\t34\n0\t2\t20\n3\t1\t20\n"
  },
  {
    "path": "Algorithms/2010-TopGC/src_original/Graphs/original/graph_temp2.raw",
    "chars": 14,
    "preview": "0\t1\t34\n0\t2\t20\n"
  },
  {
    "path": "Algorithms/2010-TopGC/src_original/Graphs/original/mkidx.c",
    "chars": 2227,
    "preview": "#include <stdio.h>\n#include <stdlib.h>\n#include <getopt.h>\n\n#define NDATA 10000\n\nstruct list {\n\tstruct list *next;\n\tint "
  },
  {
    "path": "Algorithms/2010-TopGC/src_original/README",
    "chars": 3481,
    "preview": "\nTopGC\n-----\nTopGC is a Graph Clustering program that probabilistically finds the top\nclusterings of nodes within large "
  },
  {
    "path": "Algorithms/2010-TopGC/src_original/edgew.txt",
    "chars": 684764,
    "preview": "0 7\r\n0 15\r\n0 74\r\n0 75\r\n0 85\r\n0 98\r\n0 100\r\n0 101\r\n0 112\r\n0 117\r\n0 140\r\n0 143\r\n0 145\r\n0 159\r\n0 2019\r\n0 2380\r\n1 1\r\n1 5\r\n1 1"
  },
  {
    "path": "Algorithms/2010-TopGC/src_original/mkidx.c",
    "chars": 2685,
    "preview": "#include <stdio.h>\n#include <stdlib.h>\n#include <getopt.h>\n\n#define NDATA 10000\n\nstruct list\n{\n  struct list *next;\n  in"
  },
  {
    "path": "Algorithms/2010-TopGC/src_refactor/pom.xml",
    "chars": 1163,
    "preview": "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<project xmlns=\"http://maven.apache.org/POM/4.0.0\"\n         xmlns:xsi=\"http://www"
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    "path": "Algorithms/2010-TopGC/src_refactor/src/main/java/FindMostProm.java",
    "chars": 22827,
    "preview": "//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower decompiler)\n//\n\nimport java.ut"
  },
  {
    "path": "Algorithms/2010-TopGC/src_refactor/src/main/java/HoldBucket.java",
    "chars": 1286,
    "preview": "//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower decompiler)\n//\n\nimport java.ut"
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  {
    "path": "Algorithms/2010-TopGC/src_refactor/src/main/java/HoldInt.java",
    "chars": 201,
    "preview": "//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower decompiler)\n//\n\npublic class H"
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  {
    "path": "Algorithms/2010-TopGC/src_refactor/src/main/java/IntAndDouble.java",
    "chars": 519,
    "preview": "//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower decompiler)\n//\n\npublic class I"
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  {
    "path": "Algorithms/2010-TopGC/src_refactor/src/main/java/LSH.java",
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    "preview": "//\n// Source code recreated from a .class file by IntelliJ IDEA\n// (powered by Fernflower decompiler)\n//\n\nimport java.ut"
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]

// ... and 2475 more files (download for full content)

About this extraction

This page contains the full source code of the RapidsAtHKUST/CommunityDetectionCodes GitHub repository, extracted and formatted as plain text for AI agents and large language models (LLMs). The extraction includes 2675 files (87.2 MB), approximately 11.7M tokens, and a symbol index with 9797 extracted functions, classes, methods, constants, and types. Use this with OpenClaw, Claude, ChatGPT, Cursor, Windsurf, or any other AI tool that accepts text input. You can copy the full output to your clipboard or download it as a .txt file.

Extracted by GitExtract — free GitHub repo to text converter for AI. Built by Nikandr Surkov.

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