SYMBOL INDEX (101 symbols across 16 files)

FILE: java/ActiveSubnetworkSearchAlgorithms/ActiveSubnetworkSearch.java
  class ActiveSubnetworkSearch (line 24) | public class ActiveSubnetworkSearch {
    method activeSubnetworkSearch (line 33) | public static void activeSubnetworkSearch(){

FILE: java/ActiveSubnetworkSearchAlgorithms/GAIndividual.java
  class GAIndividual (line 16) | public class GAIndividual implements Comparable<Object>{
    method GAIndividual (line 23) | public GAIndividual(HashSet<Node> nodesOnSet){
    method GAIndividual (line 38) | public GAIndividual(ArrayList<Boolean> representationBoolean){
    method compareTo (line 58) | @Override
    method getRepresentationBoolean (line 92) | public ArrayList<Boolean> getRepresentationBoolean() {
    method getNetworkNodeList (line 96) | public ArrayList<Node> getNetworkNodeList() {
    method getNodesOnSet (line 100) | public HashSet<Node> getNodesOnSet() {
    method getSubnetworkList (line 104) | public ArrayList<Subnetwork> getSubnetworkList() {
    method getHighestScoringSubnetwork (line 108) | public Subnetwork getHighestScoringSubnetwork(){
    method getScore (line 116) | public double getScore(){
    method toString (line 124) | public String toString(){

FILE: java/ActiveSubnetworkSearchAlgorithms/GeneticAlgorithm.java
  type SelectionType (line 20) | enum SelectionType {RANKSELECTION, ROULETTEWHEEL}
  type CrossoverType (line 21) | enum CrossoverType {SINGLEPOINT, MULTIPOINT, UNIFORM}
  class GeneticAlgorithm (line 23) | public class GeneticAlgorithm {
    method geneticAlgorithm (line 32) | public ArrayList<Subnetwork> geneticAlgorithm(){
    method printSituation (line 118) | private void printSituation(ArrayList<GAIndividual> population){
    method initializePopulation (line 125) | private void initializePopulation(ArrayList<GAIndividual> population, ...
    method createRandomGAIndividual (line 146) | private GAIndividual createRandomGAIndividual(){
    method createNewPopulation (line 154) | private ArrayList<GAIndividual> createNewPopulation(ArrayList<GAIndivi...
  class NewPopulationFactory (line 185) | class NewPopulationFactory implements Runnable{
    method NewPopulationFactory (line 192) | public NewPopulationFactory(ArrayList<GAIndividual> population, ArrayL...
    method run (line 199) | @Override
    method selection (line 215) | private GAIndividual[] selection(ArrayList<GAIndividual> population) {
    method crossoverAndMutation (line 250) | private GAIndividual[] crossoverAndMutation(GAIndividual parent1, GAIn...

FILE: java/ActiveSubnetworkSearchAlgorithms/GreedySearch.java
  class GreedySearch (line 18) | public class GreedySearch {
    method greedySearch (line 52) | public ArrayList<Subnetwork> greedySearch() {
    method filterSubnetworkList (line 146) | private ArrayList<Subnetwork> filterSubnetworkList(ArrayList<Subnetwor...
    method initializeMaxDepth (line 195) | private void initializeMaxDepth(Node current, int depth) {
    method runGreedySearchRecursive (line 222) | private boolean runGreedySearchRecursive(int depth, Subnetwork component,
    method runGreedyRemovalSearch (line 269) | private void runGreedyRemovalSearch(Subnetwork component, HashSet remo...

FILE: java/ActiveSubnetworkSearchAlgorithms/SimulatedAnnealing.java
  class SimulatedAnnealing (line 29) | public class SimulatedAnnealing {
    method simulatedAnnealing (line 36) | public ArrayList<Subnetwork> simulatedAnnealing() {
    method toggleNodeState (line 149) | public void toggleNodeState(HashSet<Node> nodesOnSet, HashSet<Node> no...
    method printSituation (line 159) | public void printSituation(ArrayList<Subnetwork> subnetworkList){

FILE: java/ActiveSubnetworkSearchMisc/Gaussian.java
  class Gaussian (line 25) | public class Gaussian {
    method pdf (line 28) | public static double pdf(double x) {
    method pdf (line 33) | public static double pdf(double x, double mu, double sigma) {
    method cdf (line 38) | public static double cdf(double z) {
    method cdf (line 50) | public static double cdf(double z, double mu, double sigma) {
    method inverseCDF (line 55) | public static double inverseCDF(double y) {
    method inverseCDF (line 60) | private static double inverseCDF(double y, double delta, double lo, do...

FILE: java/ActiveSubnetworkSearchMisc/ScoreCalculations.java
  class ScoreCalculations (line 25) | public class ScoreCalculations {
    method ScoreCalculations (line 38) | public ScoreCalculations(ArrayList<SimpleEntry<String, Double>> namePV...
    method fillNodeToPValueMap (line 44) | private void fillNodeToPValueMap(ArrayList<SimpleEntry<String, Double>...
    method process (line 77) | public void process() {
    method getPValue (line 85) | public Double getPValue(Node node) {
    method getZScore (line 89) | public Double getZScore(Node node) {
    method calculateZScores (line 93) | private void calculateZScores() {
    method calculateMeanAndStdForMonteCarlo (line 102) | private void calculateMeanAndStdForMonteCarlo() {
    method calculateScoreOfSubnetwork (line 192) | public double calculateScoreOfSubnetwork(Subnetwork subnetwork, boolea...
    method calculateScoreOfSubnetwork (line 202) | public double calculateScoreOfSubnetwork(ArrayList<Node> nodeList, boo...
    method calculateScoreOfSubnetwork (line 219) | public double calculateScoreOfSubnetwork(int numberOfNodes, double zSu...
    method normalizeScore (line 233) | private double normalizeScore(double score, int numberOfNodes){
    method penaltyForSize (line 237) | private double penaltyForSize(double score, int numberOfNodes){

FILE: java/ActiveSubnetworkSearchMisc/Subnetwork.java
  class Subnetwork (line 13) | public class Subnetwork implements Comparable<Object> {
    method Subnetwork (line 23) | public Subnetwork(ArrayList<Node> nodeList){
    method getNodeList (line 38) | public ArrayList<Node> getNodeList(){
    method getNeighborSet (line 42) | public HashSet<Node> getNeighborSet(){
    method getNeighborList (line 48) | public ArrayList<Node> getNeighborList(){
    method numberOfNodes (line 56) | public int numberOfNodes(){
    method getScore (line 60) | public double getScore(){
    method compareTo (line 64) | @Override
    method contains (line 69) | public boolean contains(Node node){
    method addNode (line 73) | public void addNode(Node node){
    method removeNode (line 83) | public void removeNode(Node node){
    method extractNeighborSet (line 95) | private void extractNeighborSet(){

FILE: java/ActiveSubnetworkSearchMisc/ZStatistics.java
  class ZStatistics (line 8) | public class ZStatistics {
    method oneMinusNormalCDFInverse (line 10) | public static double oneMinusNormalCDFInverse(double p) {
    method oneMinusNormalCDFInversePLT5 (line 26) | private static double oneMinusNormalCDFInversePLT5(double p) {

FILE: java/Application/AppActiveSubnetworkSearch.java
  class AppActiveSubnetworkSearch (line 11) | public class AppActiveSubnetworkSearch {
    method main (line 16) | public static void main(String[] args) {
    method processArguments (line 28) | public static void processArguments(String[] args) throws Exception {

FILE: java/Application/Parameters.java
  class Parameters (line 8) | public class Parameters {
    type SearchMethod (line 13) | public enum SearchMethod{GR, SA, GA}

FILE: java/File/ExperimentFileReader.java
  class ExperimentFileReader (line 16) | public class ExperimentFileReader {
    method readExperimentFile (line 18) | public static ArrayList<SimpleEntry<String, Double>> readExperimentFil...

FILE: java/File/SIFReader.java
  class SIFReader (line 15) | public class SIFReader {
    method readSIF (line 17) | public static Network readSIF(String path){

FILE: java/Network/Network.java
  class Network (line 13) | public class Network {
    method Network (line 18) | public Network() {
    method addInteraction (line 22) | public void addInteraction(String strNode1, String strNode2){
    method addInteraction (line 28) | public void addInteraction(Node node1, Node node2){
    method getNeighborSet (line 47) | public HashSet<Node> getNeighborSet(Node node){
    method getNodeList (line 51) | public ArrayList<Node> getNodeList(){
    method areAdjacent (line 55) | public boolean areAdjacent(Node node1, Node node2){
    method getNumberOfNodes (line 59) | public int getNumberOfNodes(){
    method getNumberOfInteractions (line 63) | public int getNumberOfInteractions(){

FILE: java/Network/Node.java
  class Node (line 9) | public class Node {
    method Node (line 12) | public Node(String name){
    method getName (line 16) | public String getName(){
    method toString (line 20) | @Override
    method hashCode (line 25) | @Override
    method equals (line 30) | @Override

FILE: java/Network/SubnetworkFinder.java
  class SubnetworkFinder (line 14) | public class SubnetworkFinder {
    method SubnetworkFinder (line 19) | public SubnetworkFinder(){
    method findSubnetworksDFS (line 31) | public ArrayList<Subnetwork> findSubnetworksDFS(HashSet<Node> nodesOnS...
    method search (line 45) | private void search(Node node, ArrayList<Node> subnetworkNodeList){
    method findSubnetworksDFSNonRecursive (line 57) | public ArrayList<Subnetwork> findSubnetworksDFSNonRecursive(HashSet<No...
    method findSubnetworksBFS (line 87) | public ArrayList<Subnetwork> findSubnetworksBFS(HashSet<Node> nodesOnS...