SYMBOL INDEX (1906 symbols across 163 files)

FILE: code/Classifier/CLPL.py
  class CLPL (line 8) | class CLPL:
    method __init__ (line 10) | def __init__(self, feature_size, label_size, type_hierarchy, lambda_re...
    method fit (line 18) | def fit(self, train_x, train_y):
    method predict (line 60) | def predict(self, x):
  class Pegasos (line 102) | class Pegasos:
    method __init__ (line 104) | def __init__(self, feature_size, lambda_reg=0.1, max_iter=500, batch_s...
    method fit (line 111) | def fit(self, train_x, val_x, train_y):
    method predict (line 138) | def predict(self, x, val):
    method L2_regularize (line 145) | def L2_regularize(self, eta_t):
    method predict_prob (line 152) | def predict_prob(self, x, val):

FILE: code/Classifier/Classifier.py
  function classify (line 15) | def classify(classifier, feature_size, label_size, train_x, train_y, lea...
  function predict_em (line 41) | def predict_em(model, test_x, type_hierarchy, _threshold):
  function predict (line 65) | def predict(model, test_x, type_hierarchy, _threshold):
  function casestudy (line 84) | def casestudy(filename, output, mention_mapping, label_mapping, clean_me...
  function putback (line 93) | def putback(sent_json, mention_mapping, label_mapping, clean_mentions):
  function compare (line 124) | def compare(item1, item2):

FILE: code/Classifier/Classifier_em.py
  function classify (line 15) | def classify(classifier, feature_size, label_size, train_x, train_y, lea...
  function predict_em (line 37) | def predict_em(model, test_x, type_hierarchy, _threshold):

FILE: code/Classifier/DataIO.py
  function load_as_list (line 4) | def load_as_list(filename):
  function save_from_tuples (line 31) | def save_from_tuples(filename, indexes, data):
  function save_from_list (line 47) | def save_from_list(filename, indexes, data):
  function load_as_dict (line 62) | def load_as_dict(filename):
  function load_map (line 86) | def load_map(filename, mode):
  function load_mention_type (line 97) | def load_mention_type(filename):
  function file_len (line 105) | def file_len(filename):

FILE: code/Classifier/HierarchySVM.py
  class HierarchySVM (line 6) | class HierarchySVM:
    method __init__ (line 8) | def __init__(self, feature_size, type_hierarchy, current_types, level=...
    method fit_em (line 32) | def fit_em(self, train_x, train_y):
    method predict_em (line 72) | def predict_em(self, x):

FILE: code/Classifier/Logistic.py
  class Logistic (line 6) | class Logistic:
    method __init__ (line 7) | def __init__(self, feature_size, label_size, threshold):
    method fit (line 15) | def fit(self, train_x, train_y):
    method fit_em (line 36) | def fit_em(self, train_x, train_y):
    method predict (line 40) | def predict(self, train_x):
    method predict_em (line 53) | def predict_em(self, train_x):

FILE: code/Classifier/MulticlassSVM.py
  class MulticlassSVM (line 6) | class MulticlassSVM:
    method __init__ (line 8) | def __init__(self, feature_size, label_size, lambda_reg=0.1, max_iter=...
    method fit (line 28) | def fit(self, train_x, train_y):
    method predict (line 62) | def predict(self, x):

FILE: code/Classifier/PLSVM.py
  class PLSVM (line 9) | class PLSVM:
    method __init__ (line 11) | def __init__(self, feature_size, label_size, type_hierarchy, lambda_re...
    method fit (line 24) | def fit(self, train_x, train_y):
    method predict (line 52) | def predict(self, x):
    method find_max (line 91) | def find_max(self, Y, x):
    method update_weight (line 102) | def update_weight(self, dW, eta_t, m):
    method inner_prod (line 115) | def inner_prod(weight, x):
    method kernel (line 122) | def kernel(x1, x2):

FILE: code/Classifier/Perceptron.py
  class MultilabelPerceptron (line 6) | class MultilabelPerceptron:
    method __init__ (line 8) | def __init__(self, feature_size, label_size, weights=None, learning_ra...
    method fit (line 20) | def fit(self, train_x, train_y):
    method fit_em (line 42) | def fit_em(self, train_x, train_y):
    method predict (line 61) | def predict(self, x):
    method predict_em (line 76) | def predict_em(self, x):

FILE: code/Classifier/SVM.py
  class SVM (line 9) | class SVM:
    method __init__ (line 13) | def __init__(self, feature_size, lambda_reg=0.1, max_iter=50):
    method fit (line 20) | def fit(self, train_x, train_y):
    method predict (line 49) | def predict(self, x):
    method L2_regularize (line 56) | def L2_regularize(self, eta_t):
    method predict_prob (line 63) | def predict_prob(self, x):
    method kernel (line 71) | def kernel(x1, x2):

FILE: code/Classifier/TypeHierarchy.py
  class TypeSet (line 5) | class TypeSet:
    method __init__ (line 6) | def __init__(self, file_name, number_of_types):
    method get_type_path (line 20) | def get_type_path(self, label):
    method get_subtypes (line 31) | def get_subtypes(self, label):
  class TypeHierarchy (line 37) | class TypeHierarchy:
    method __init__ (line 38) | def __init__(self, file_name, number_of_types):
    method get_type_path (line 50) | def get_type_path(self, label):
    method get_subtypes (line 61) | def get_subtypes(self, label):

FILE: code/Classifier/liblinear.py
  function print_null (line 42) | def print_null(s):
  function genFields (line 45) | def genFields(names, types):
  function fillprototype (line 48) | def fillprototype(f, restype, argtypes):
  class feature_node (line 52) | class feature_node(Structure):
    method __str__ (line 57) | def __str__(self):
  function gen_feature_nodearray (line 60) | def gen_feature_nodearray(xi, feature_max=None, issparse=True):
  class problem (line 87) | class problem(Structure):
    method __init__ (line 92) | def __init__(self, y, x, bias = -1):
    method set_bias (line 114) | def set_bias(self, bias):
  class parameter (line 129) | class parameter(Structure):
    method __init__ (line 134) | def __init__(self, options = None):
    method __str__ (line 139) | def __str__(self):
    method set_to_default_values (line 149) | def set_to_default_values(self):
    method parse_options (line 168) | def parse_options(self, options):
  class model (line 258) | class model(Structure):
    method __init__ (line 263) | def __init__(self):
    method __del__ (line 266) | def __del__(self):
    method get_nr_feature (line 271) | def get_nr_feature(self):
    method get_nr_class (line 274) | def get_nr_class(self):
    method get_labels (line 277) | def get_labels(self):
    method get_decfun_coef (line 283) | def get_decfun_coef(self, feat_idx, label_idx=0):
    method get_decfun_bias (line 286) | def get_decfun_bias(self, label_idx=0):
    method get_decfun (line 289) | def get_decfun(self, label_idx=0):
    method is_probability_model (line 294) | def is_probability_model(self):
    method is_regression_model (line 297) | def is_regression_model(self):
  function toPyModel (line 300) | def toPyModel(model_ptr):

FILE: code/Classifier/liblinearutil.py
  function svm_read_problem (line 13) | def svm_read_problem(data_file_name):
  function load_model (line 35) | def load_model(model_file_name):
  function save_model (line 48) | def save_model(model_file_name, model):
  function evaluations (line 56) | def evaluations(ty, pv):
  function train (line 85) | def train(arg1, arg2=None, arg3=None):
  function predict (line 186) | def predict(y, x, m, options=""):

FILE: code/DataProcessor/Feature/abstract_feature.py
  class AbstractFeature (line 4) | class AbstractFeature(object):
    method apply (line 5) | def apply(self, sentence, mention, features):

FILE: code/DataProcessor/Feature/brown_feature.py
  class BrownFeature (line 7) | class BrownFeature(AbstractFeature):
    method __init__ (line 9) | def __init__(self, brown_file):
    method apply (line 17) | def apply(self, sentence, mention, features):

FILE: code/DataProcessor/Feature/dependency_feature.py
  class DependencyFeature (line 7) | class DependencyFeature(AbstractFeature):
    method apply (line 13) | def apply(self, sentence, mention, features):
    method accept_pos (line 46) | def accept_pos(self, pos):
    method accept_dep (line 49) | def accept_dep(self, dep):

FILE: code/DataProcessor/Feature/em_brown_feature.py
  class EMBrownFeature (line 7) | class EMBrownFeature(AbstractFeature):
    method __init__ (line 9) | def __init__(self, brown_file):
    method apply (line 17) | def apply(self, sentence, mention, features):

FILE: code/DataProcessor/Feature/em_dependency_feature.py
  class EMDependencyFeature (line 7) | class EMDependencyFeature(AbstractFeature):
    method apply (line 13) | def apply(self, sentence, mention, features):
    method accept_pos (line 46) | def accept_pos(self, pos):
    method accept_dep (line 49) | def accept_dep(self, dep):

FILE: code/DataProcessor/Feature/em_other_feature.py
  class EMPosFeature (line 7) | class EMPosFeature(AbstractFeature):
    method apply (line 9) | def apply(self, sentence, mention, features):
  class EMLengthFeature (line 14) | class EMLengthFeature(AbstractFeature):
    method apply (line 16) | def apply(self, sentence, mention, features):
  class EMWordShapeFeature (line 24) | class EMWordShapeFeature(AbstractFeature):
    method get_word_shape (line 25) | def get_word_shape(self, token):
    method apply (line 32) | def apply(self, sentence, mention, features):
  class EMCharacterFeature (line 37) | class EMCharacterFeature(AbstractFeature):
    method apply (line 38) | def apply(self, sentence, mention, features):

FILE: code/DataProcessor/Feature/em_token_feature.py
  function get_lemma (line 12) | def get_lemma(word, pos):
  class EMHeadFeature (line 28) | class EMHeadFeature(AbstractFeature):
    method get_head (line 31) | def get_head(sentence, mention):
    method apply (line 41) | def apply(self, sentence, mention, features):
  class EMTokenFeature (line 48) | class EMTokenFeature(AbstractFeature):
    method apply (line 50) | def apply(self, sentence, mention, features):
  class EMContextFeature (line 55) | class EMContextFeature(AbstractFeature):
    method __init__ (line 57) | def __init__(self, window_size=1):
    method apply (line 60) | def apply(self, sentence, mention, features):
  class EMContextGramFeature (line 69) | class EMContextGramFeature(AbstractFeature):
    method __init__ (line 71) | def __init__(self, window_size=1):
    method apply (line 74) | def apply(self, sentence, mention, features):

FILE: code/DataProcessor/Feature/other_feature.py
  class PosFeature (line 7) | class PosFeature(AbstractFeature):
    method apply (line 9) | def apply(self, sentence, mention, features):
  class DistanceFeature (line 19) | class DistanceFeature(AbstractFeature):
    method apply (line 21) | def apply(self, sentence, mention, features):
  class EntityMentionOrderFeature (line 27) | class EntityMentionOrderFeature(AbstractFeature):
    method apply (line 29) | def apply(self, sentence, mention, features):
  class NumOfEMBetweenFeature (line 35) | class NumOfEMBetweenFeature(AbstractFeature):
    method apply (line 37) | def apply(self, sentence, mention, features):
  class EMTypeFeature (line 41) | class EMTypeFeature(AbstractFeature):
    method apply (line 42) | def apply(self, sentence, mention, features):
  class SpecialPatternFeature (line 51) | class SpecialPatternFeature(AbstractFeature):
    method apply (line 53) | def apply(self, sentence, mention, features):

FILE: code/DataProcessor/Feature/token_feature.py
  function get_lemma (line 12) | def get_lemma(word, pos):
  class HeadFeature (line 28) | class HeadFeature(AbstractFeature):
    method get_head (line 32) | def get_head(sentence, start, end):
    method apply (line 42) | def apply(self, sentence, mention, features):
  class EntityMentionTokenFeature (line 54) | class EntityMentionTokenFeature(AbstractFeature):
    method apply (line 56) | def apply(self, sentence, mention, features):
  class BetweenEntityMentionTokenFeature (line 62) | class BetweenEntityMentionTokenFeature(AbstractFeature):
    method apply (line 64) | def apply(self, sentence, mention, features):
  class ContextFeature (line 77) | class ContextFeature(AbstractFeature):
    method __init__ (line 79) | def __init__(self, window_size=1):
    method apply (line 82) | def apply(self, sentence, mention, features):
  class ContextGramFeature (line 98) | class ContextGramFeature(AbstractFeature):
    method __init__ (line 100) | def __init__(self, window_size=1):
    method apply (line 103) | def apply(self, sentence, mention, features):

FILE: code/DataProcessor/feature_generation.py
  function get_number (line 12) | def get_number(filename):

FILE: code/DataProcessor/liblinear_processor.py
  function load_as_list (line 6) | def load_as_list(filename):
  function write_train_as_liblinear (line 33) | def write_train_as_liblinear(train_x, train_y, filename):
  function write_test_as_liblinear (line 43) | def write_test_as_liblinear(test_x, filename):

FILE: code/DataProcessor/mention.py
  class RelationMention (line 4) | class RelationMention(object):
    method __init__ (line 20) | def __init__(self, em1Start, em1End, em2Start, em2End, numOfEMBetween,...
    method __str__ (line 28) | def __str__(self):
  class EntityMention (line 34) | class EntityMention(object):
    method __init__ (line 50) | def __init__(self, start, end, labels):
    method __str__ (line 55) | def __str__(self):
  class Sentence (line 62) | class Sentence(object):
    method __init__ (line 74) | def __init__(self, articleId, sentId, tokens):
    method __str__ (line 82) | def __str__(self):
    method add_relationMention (line 91) | def add_relationMention(self, relationMention):
    method add_entityMention (line 95) | def add_entityMention(self, entityMention):
    method size (line 99) | def size(self):

FILE: code/DataProcessor/mention_reader.py
  class MentionReader (line 7) | class MentionReader:
    method __init__ (line 19) | def __init__(self, mention_file):
    method close (line 24) | def close(self):
    method has_next (line 27) | def has_next(self):
    method next (line 34) | def next(self):
    method _decode (line 43) | def _decode(mention_json):

FILE: code/DataProcessor/ner_feature.py
  class NERFeature (line 9) | class NERFeature(object):
    method __init__ (line 11) | def __init__(self, is_train, brown_file, requireEmType, isEntityMentio...
    method extract (line 64) | def extract(self, sentence, mention):
  function pipeline (line 96) | def pipeline(json_file, brown_file, outdir, requireEmType, isEntityMenti...
  function pipeline_test (line 153) | def pipeline_test(json_file, brown_file, featurefile, labelfile, outdir,...
  function load_map (line 198) | def load_map(input):
  function write_map (line 208) | def write_map(mapping, output):
  function filter (line 214) | def filter(featurefile, trainfile, featureout,trainout):
  function write_map2 (line 250) | def write_map2(mapping, output):

FILE: code/DataProcessor/nlp_parse.py
  class NLPParser (line 14) | class NLPParser(object):
    method __init__ (line 22) | def __init__(self):
    method parse (line 26) | def parse(self, sent):
  function parse (line 38) | def parse(sentences, g, lock, procNum, isTrain, parsePOSBeforehand=False):
  function process (line 62) | def process(buffered, parser, g, lock, isTrain, rmCount, discardRmCount,...
  function find_index (line 162) | def find_index(sen_split, word_split):
  function createPosAndTokensMap (line 180) | def createPosAndTokensMap(sentences, parser):

FILE: code/DataProcessor/pruning_heuristics.py
  class PruneStrategy (line 10) | class PruneStrategy:
    method __init__ (line 11) | def __init__(self, strategy):
    method no_prune (line 15) | def no_prune(self, fileid, is_ground, labels):
  function prune (line 19) | def prune(indir, outdir, strategy, feature_number, type_number, neg_labe...

FILE: code/DataProcessor/statistic.py
  function distribution (line 10) | def distribution(indir):
  function supertype (line 30) | def supertype(indir):

FILE: code/Evaluation/emb_prediction.py
  function sim_func (line 16) | def sim_func(v1, v2, _MODE):
  class Embedding (line 29) | class Embedding:
    method __init__ (line 30) | def __init__(self, file_name):
    method get_embedding (line 50) | def get_embedding(self, index):
  class Network (line 53) | class Network:
    method __init__ (line 54) | def __init__(self, file_name):
    method get_neighbors (line 66) | def get_neighbors(self, idx):
  class Predicter_useFeatureEmb (line 71) | class Predicter_useFeatureEmb:
    method __init__ (line 72) | def __init__(self, embs_feature, embs_type, network_mention_feature, t...
    method get_mention_embedding (line 80) | def get_mention_embedding(self, mention_id):
    method predict_types_for_rm_maximum (line 92) | def predict_types_for_rm_maximum(self, mention_id, candidate):
  function predict (line 108) | def predict(indir, outdir, _method, _sim_func, _threshold, output, none_...
  function min_max_normalization (line 152) | def min_max_normalization(scores):
  function load_mentionids (line 166) | def load_mentionids(filename):
  function load_candidates (line 178) | def load_candidates(filename, indexes):
  function load_all_candidates (line 192) | def load_all_candidates(filename, indexes):

FILE: code/Evaluation/evaluation.py
  function find_none_index (line 5) | def find_none_index(file_name):
  function load_labels (line 14) | def load_labels(file_name):
  function load_raw_labels (line 27) | def load_raw_labels(file_name, ground_truth):
  function load_label_score (line 37) | def load_label_score(file_name):
  function evaluate_rm (line 56) | def evaluate_rm(prediction, ground_truth):
  function evaluate_rm_neg (line 82) | def evaluate_rm_neg(prediction, ground_truth, none_label_index):

FILE: code/Evaluation/tune_threshold.py
  function min_max_nomalization (line 8) | def min_max_nomalization(prediction):
  function evaluate_threshold (line 22) | def evaluate_threshold(_threshold, ground_truth):
  function evaluate_threshold_neg (line 32) | def evaluate_threshold_neg(_threshold, ground_truth, none_label_index):
  function tune_threshold (line 42) | def tune_threshold(_threshold_list, ground_truth, none_label_index):

FILE: code/Model/FCM/code/BaseComponentModel.h
  type std (line 22) | typedef std::tr1::unordered_map<string, int> feat2int;
  type std (line 23) | typedef std::tr1::unordered_map<string, string> word2clus;
  function class (line 25) | class BaseComponentModel

FILE: code/Model/FCM/code/Commons.h
  type word_info (line 21) | struct word_info {

FILE: code/Model/FCM/code/EmbeddingModel.cpp
  function pairCompare (line 25) | bool pairCompare(pair<int, string> a, pair<int, string> b) {

FILE: code/Model/FCM/code/EmbeddingModel.h
  type std (line 31) | typedef std::tr1::unordered_map<string, int> word2int;
  type real (line 32) | typedef float real;
  function class (line 78) | class EmbeddingModel

FILE: code/Model/FCM/code/FctCoarseModel.h
  function class (line 14) | class FctCoarseModel: public BaseComponentModel

FILE: code/Model/FCM/code/FctConvolutionModel.h
  function class (line 14) | class FctConvolutionModel: public BaseComponentModel

FILE: code/Model/FCM/code/FctDeepModel.h
  function class (line 14) | class FctDeepModel: public BaseComponentModel

FILE: code/Model/FCM/code/FeatureModel.h
  function class (line 21) | class FeatureModel

FILE: code/Model/FCM/code/FullFctModel.cpp
  function string (line 1325) | string FullFctModel::ProcSenseTag(string input_type) {
  function string (line 1331) | string FullFctModel::ProcNeTag(string input_type) {
  function string (line 1342) | string FullFctModel::ToLower(string& s) {

FILE: code/Model/FCM/code/FullFctModel.h
  function class (line 18) | class FeaParams {
  function class (line 58) | class FullFctModel

FILE: code/Model/FCM/code/Instances.h
  function class (line 22) | class BaseInstance{
  function class (line 78) | class CoarseFctInstance {
  function class (line 128) | class RealFctPathInstance {
  function class (line 164) | class FctConvolutionInstance {
  function class (line 186) | class FeatureInstance {

FILE: code/Model/FCM/code/RE_FCT.cpp
  function ArgPos (line 33) | int ArgPos(char *str, int argc, char **argv) {
  function main (line 45) | int main(int argc, char **argv) {

FILE: code/Model/FCM/code/RE_FCT_fixed.cpp
  function ArgPos (line 33) | int ArgPos(char *str, int argc, char **argv) {
  function main (line 45) | int main(int argc, char **argv) {

FILE: code/Model/FCM/word2vec.cpp
  type vocab_word (line 31) | struct vocab_word {
  type vocab_word (line 39) | struct vocab_word
  function InitUnigramTable (line 52) | void InitUnigramTable() {
  function ReadWord (line 71) | void ReadWord(char *word, FILE *fin) {
  function GetWordHash (line 95) | int GetWordHash(char *word) {
  function SearchVocab (line 103) | int SearchVocab(char *word) {
  function ReadWordIndex (line 114) | int ReadWordIndex(FILE *fin) {
  function AddWordToVocab (line 122) | int AddWordToVocab(char *word) {
  function VocabCompare (line 141) | int VocabCompare(const void *a, const void *b) {
  function SortVocab (line 146) | void SortVocab() {
  function ReduceVocab (line 177) | void ReduceVocab() {
  function CreateBinaryTree (line 200) | void CreateBinaryTree() {
  function LearnVocabFromTrainFile (line 269) | void LearnVocabFromTrainFile() {
  function SaveVocab (line 306) | void SaveVocab() {
  function ReadVocab (line 313) | void ReadVocab() {
  function InitNet (line 346) | void InitNet() {
  function TrainModel (line 589) | void TrainModel() {
  function ArgPos (line 669) | int ArgPos(char *str, int argc, char **argv) {
  function main (line 681) | int main(int argc, char **argv) {

FILE: code/Model/baselines/hypenet/evaluation.py
  function find_none_index (line 5) | def find_none_index(file_name):
  function load_labels (line 15) | def load_labels(file_name):
  function load_raw_labels (line 29) | def load_raw_labels(file_name, ground_truth):
  function load_label_score (line 40) | def load_label_score(file_name):
  function evaluate_em (line 59) | def evaluate_em(prediction, ground_truth):
  function evaluate_rm (line 100) | def evaluate_rm(prediction, ground_truth):
  function evaluate_rm_gold (line 126) | def evaluate_rm_gold(prediction, ground_truth):
  function evaluate_rm_neg (line 152) | def evaluate_rm_neg(prediction, ground_truth, none_label_index):
  function min_max_nomalization (line 184) | def min_max_nomalization(prediction):
  function evaluate_threshold (line 199) | def evaluate_threshold(_threshold, ground_truth, prediction):
  function evaluate_threshold_neg (line 210) | def evaluate_threshold_neg(_threshold, ground_truth, none_label_index, p...
  function tune_threshold (line 221) | def tune_threshold(_threshold_list, ground_truth, none_label_index, pred...

FILE: code/Model/baselines/hypenet/helper.py
  function lst_2_dic (line 94) | def lst_2_dic(lst):
  function sequence_from_dic (line 121) | def sequence_from_dic(lst, dic):
  function train_val_test_split (line 130) | def train_val_test_split(X, id_file=None):
  function train_val_test_split_auto (line 142) | def train_val_test_split_auto(X, y):
  function get_none_id (line 148) | def get_none_id(type_filename):
  function get_class_num (line 156) | def get_class_num(type_filename):
  function evaluate_rm_neg (line 166) | def evaluate_rm_neg(prediction, ground_truth, none_label_index):

FILE: code/Model/baselines/hypenet/lemmatize.py
  function get_stanford_annotations (line 10) | def get_stanford_annotations(text, port=9000,

FILE: code/Model/baselines/hypenet/preprocess.py
  function is_overlap (line 4) | def is_overlap(a, b):
  function process_file (line 11) | def process_file(in_file, out_file, rel_types, training=True):
  function process (line 39) | def process(fin1, fin2, fout):

FILE: code/Model/baselines/hypenet/sentence_normalize.py
  function get_stanford_annotations (line 10) | def get_stanford_annotations(text, port=9000,

FILE: code/Model/baselines/hypenet/sentence_tokens.py
  function get_stanford_annotations (line 8) | def get_stanford_annotations(text, port=9000,

FILE: code/Model/baselines/hypenet/shortest_dep.py
  function get_vocab_dic_split (line 11) | def get_vocab_dic_split(filename):
  function get_vocab_dic (line 21) | def get_vocab_dic(filename):
  function get_stanford_annotations (line 30) | def get_stanford_annotations(text, port=9000,

FILE: code/Model/baselines/hypenet/test_corenlp.py
  function get_stanford_annotations (line 8) | def get_stanford_annotations(text, annotators='tokenize,ssplit,pos,lemma...

FILE: code/Model/baselines/sdp-lstm/dependency-kbp/analyze.py
  function get_unk_count_in_dataset (line 18) | def get_unk_count_in_dataset(loader):
  function analyze_unk (line 34) | def analyze_unk():
  function main (line 54) | def main():

FILE: code/Model/baselines/sdp-lstm/dependency-kbp/data_utils.py
  function load_datasets (line 167) | def load_datasets(fname, labelfname, maxlen=MAX_SEQ_LEN, lowercase=True):
  function build_vocab (line 204) | def build_vocab(datasets, use_count):
  function build_vocab_for_field (line 222) | def build_vocab_for_field(datasets, fieldname):
  function convert_words_to_ids (line 239) | def convert_words_to_ids(datasets, word2id):
  function convert_fields_to_ids (line 250) | def convert_fields_to_ids(datasets, field2map):
  function preprocess (line 267) | def preprocess():
  function dump_to_file (line 318) | def dump_to_file(filename, obj):
  function load_from_dump (line 324) | def load_from_dump(filename):
  class DataLoader (line 330) | class DataLoader():
    method __init__ (line 331) | def __init__(self, dump_name, batch_size, pad_len, shuffle=True, subsa...
    method next_batch (line 346) | def next_batch(self):
    method get_residual (line 366) | def get_residual(self):
    method reset_pointer (line 380) | def reset_pointer(self):
    method corrupt_sentence (line 383) | def corrupt_sentence(self, tokens):
    method write_keys (line 392) | def write_keys(self, key_file, id2label=None, include_residual=False):
  function main (line 407) | def main():

FILE: code/Model/baselines/sdp-lstm/dependency-kbp/emb_utils.py
  function _load_glove_vec (line 13) | def _load_glove_vec(fname, vocab, dim):
  function _load_bin_vec (line 28) | def _load_bin_vec(fname, vocab):
  function _add_random_vec (line 52) | def _add_random_vec(word_vecs, vocab, dim=300, scale=1.0):
  function prepare_pretrained_embedding (line 61) | def prepare_pretrained_embedding(fname, word2id, dim):
  function main (line 74) | def main():

FILE: code/Model/baselines/sdp-lstm/dependency-kbp/eval.py
  function evaluate (line 36) | def evaluate():
  function _write_prediction_file (line 107) | def _write_prediction_file(preds, confs, all_probs, id2label, pred_file,...
  function _get_model (line 120) | def _get_model(is_train):
  function main (line 128) | def main(_):

FILE: code/Model/baselines/sdp-lstm/dependency-kbp/scorer.py
  function score (line 6) | def score(key_file, pred_files, f_measure=1, verbose=False):

FILE: code/Model/baselines/sdp-lstm/dependency-kbp/sprnn_model.py
  function _variable_on_cpu (line 34) | def _variable_on_cpu(name, shape, initializer):
  function _get_lstm_graph_info (line 39) | def _get_lstm_graph_info():
  function _create_embedding_layer (line 54) | def _create_embedding_layer(name, vocab_size, dim, inputs, is_train):
  function _get_rnn_cell (line 61) | def _get_rnn_cell(hidden_size, num_layers, is_train, dropout):
  function max_over_time (line 71) | def max_over_time(inputs, index, seq_lens):
  function attention_over_time (line 84) | def attention_over_time(inputs, hidden, params, index, seq_lens):
  function _create_attention_layer (line 106) | def _create_attention_layer(rnn_outputs, rnn_final_hidden, seq_lens, dim...
  function _create_rnn_along_subpath (line 121) | def _create_rnn_along_subpath(subpath_sent_batch, seq_lens, dim, batch_s...
  class SPRNNModel (line 155) | class SPRNNModel(object):
    method __init__ (line 161) | def __init__(self, vocab_size, is_train=True):
    method build_graph (line 166) | def build_graph(self):
    method assign_lr (line 247) | def assign_lr(self, session, lr_value):
    method assign_embedding (line 250) | def assign_embedding(self, session, pretrained):

FILE: code/Model/baselines/sdp-lstm/dependency-kbp/train-cv.py
  function train (line 51) | def train():
  function _get_training_info (line 259) | def _get_training_info():
  function _get_model (line 272) | def _get_model(is_train, vocab_size):
  function _summary_for_scalar (line 281) | def _summary_for_scalar(name, value):
  function _write_prediction_file (line 285) | def _write_prediction_file(preds, confs, id2label, pred_file):
  function main (line 293) | def main(argv=None):

FILE: code/Model/baselines/sdp-lstm/dependency-kbp/utils.py
  function _get_feed_dict_for_others (line 3) | def _get_feed_dict_for_others(model, x_batch, y_batch, x_lens, use_pos=T...
  function _get_feed_dict_for_sprnn (line 13) | def _get_feed_dict_for_sprnn(model, x_batch, y_batch, x_lens, use_pos=Tr...

FILE: code/Model/baselines/sdp-lstm/dependency/analyze.py
  function get_unk_count_in_dataset (line 18) | def get_unk_count_in_dataset(loader):
  function analyze_unk (line 34) | def analyze_unk():
  function main (line 54) | def main():

FILE: code/Model/baselines/sdp-lstm/dependency/data_utils.py
  function load_datasets (line 165) | def load_datasets(fnames, lowercase=True):
  function convert_to_dependency_path (line 177) | def convert_to_dependency_path(dataset):
  function add_dep_path_to_dataset (line 207) | def add_dep_path_to_dataset(node_indices, ancestor_index, original_row, ...
  function build_vocab (line 220) | def build_vocab(datasets, use_count):
  function build_vocab_for_field (line 238) | def build_vocab_for_field(datasets, fieldname):
  function filter_seqlen (line 256) | def filter_seqlen(fnames, maxlen):
  function convert_words_to_ids (line 271) | def convert_words_to_ids(datasets, word2id):
  function convert_fields_to_ids (line 282) | def convert_fields_to_ids(datasets, field2map):
  function create_dependency_path_datasets (line 299) | def create_dependency_path_datasets():
  function preprocess (line 312) | def preprocess():
  function dump_to_file (line 367) | def dump_to_file(filename, obj):
  function load_from_dump (line 373) | def load_from_dump(filename):
  class DataLoader (line 379) | class DataLoader():
    method __init__ (line 380) | def __init__(self, dump_name, batch_size, pad_len, shuffle=True, subsa...
    method next_batch (line 395) | def next_batch(self):
    method get_residual (line 415) | def get_residual(self):
    method reset_pointer (line 429) | def reset_pointer(self):
    method corrupt_sentence (line 432) | def corrupt_sentence(self, tokens):
    method write_keys (line 441) | def write_keys(self, key_file, id2label=None, include_residual=False):
  function main (line 456) | def main():

FILE: code/Model/baselines/sdp-lstm/dependency/emb_utils.py
  function _load_glove_vec (line 15) | def _load_glove_vec(fname, vocab, dim):
  function _load_bin_vec (line 30) | def _load_bin_vec(fname, vocab):
  function _add_random_vec (line 54) | def _add_random_vec(word_vecs, vocab, dim=300, scale=1.0):
  function prepare_pretrained_embedding (line 63) | def prepare_pretrained_embedding(fname, word2id, dim):
  function main (line 76) | def main():

FILE: code/Model/baselines/sdp-lstm/dependency/eval.py
  function evaluate (line 36) | def evaluate():
  function _write_prediction_file (line 107) | def _write_prediction_file(preds, confs, all_probs, id2label, pred_file,...
  function _get_model (line 120) | def _get_model(is_train):
  function main (line 128) | def main(_):

FILE: code/Model/baselines/sdp-lstm/dependency/scorer.py
  function score (line 6) | def score(key_file, pred_files, f_measure=1, verbose=False):

FILE: code/Model/baselines/sdp-lstm/dependency/sprnn_model.py
  function _variable_on_cpu (line 34) | def _variable_on_cpu(name, shape, initializer):
  function _get_lstm_graph_info (line 39) | def _get_lstm_graph_info():
  function _create_embedding_layer (line 54) | def _create_embedding_layer(name, vocab_size, dim, inputs, is_train):
  function _get_rnn_cell (line 61) | def _get_rnn_cell(hidden_size, num_layers, is_train, dropout):
  function max_over_time (line 71) | def max_over_time(inputs, index, seq_lens):
  function attention_over_time (line 84) | def attention_over_time(inputs, hidden, params, index, seq_lens):
  function _create_attention_layer (line 106) | def _create_attention_layer(rnn_outputs, rnn_final_hidden, seq_lens, dim...
  function _create_rnn_along_subpath (line 121) | def _create_rnn_along_subpath(subpath_sent_batch, seq_lens, dim, batch_s...
  class SPRNNModel (line 155) | class SPRNNModel(object):
    method __init__ (line 161) | def __init__(self, is_train=True):
    method build_graph (line 165) | def build_graph(self):
    method assign_lr (line 246) | def assign_lr(self, session, lr_value):
    method assign_embedding (line 249) | def assign_embedding(self, session, pretrained):

FILE: code/Model/baselines/sdp-lstm/dependency/train.py
  function train (line 54) | def train():
  function _get_training_info (line 293) | def _get_training_info():
  function _get_model (line 306) | def _get_model(is_train):
  function _summary_for_scalar (line 315) | def _summary_for_scalar(name, value):
  function _write_prediction_file (line 319) | def _write_prediction_file(preds, confs, id2label, pred_file):
  function main (line 327) | def main(argv=None):

FILE: code/Model/baselines/sdp-lstm/dependency/tree.py
  class Node (line 18) | class Node:  # a node in the tree
    method __init__ (line 19) | def __init__(self, idx):
  class Tree (line 27) | class Tree:
    method __init__ (line 28) | def __init__(self, conll_data):
    method parse_from_conll (line 53) | def parse_from_conll(self, conll_fields):
    method get_shortest_path_through_root (line 75) | def get_shortest_path_through_root(self):
    method get_shortest_path_through_ancestor (line 88) | def get_shortest_path_through_ancestor(self):
    method copy_fields_at_index (line 110) | def copy_fields_at_index(self, idx, target_fields):
    method __repr__ (line 117) | def __repr__(self):
  function assign_node_levels (line 126) | def assign_node_levels(node, level):
  function get_entity_head (line 132) | def get_entity_head(entity_idx_seq, idx2node):
  function get_path_to_root (line 153) | def get_path_to_root(node):
  function get_path_to_node (line 163) | def get_path_to_node(current_node, target_node_idx):
  function get_common_ancestor (line 178) | def get_common_ancestor(root_to_node1, root_to_node2):

FILE: code/Model/baselines/sdp-lstm/dependency/utils.py
  function _get_feed_dict_for_others (line 3) | def _get_feed_dict_for_others(model, x_batch, y_batch, x_lens, use_pos=T...
  function _get_feed_dict_for_sprnn (line 13) | def _get_feed_dict_for_sprnn(model, x_batch, y_batch, x_lens, use_pos=Tr...

FILE: code/Model/baselines/sentence-level-models/cotype2json.py
  class NLPParser (line 18) | class NLPParser(object):
    method __init__ (line 26) | def __init__(self):
    method get_ner (line 29) | def get_ner(self, tokens):
  function find_index (line 37) | def find_index(sen_split, word_split):
  function read (line 56) | def read(data, in_dir, out_dir):

FILE: code/Model/baselines/sentence-level-models/model.py
  class Model (line 17) | class Model(object):
    method __init__ (line 18) | def __init__(self, args, device, rel2id, word_emb=None):
    method update (line 44) | def update(self, batch):
    method predict (line 56) | def predict(self, batch):
    method eval (line 66) | def eval(self, dset, vocab=None, output_false_file=None):
    method save (line 109) | def save(self, filename, epoch):
    method load (line 122) | def load(self, filename):

FILE: code/Model/baselines/sentence-level-models/models/bgru.py
  class BGRU (line 10) | class BGRU(nn.Module):
    method __init__ (line 11) | def __init__(self, args, rel2id, word_emb=None):
    method forward (line 62) | def forward(self, inputs):

FILE: code/Model/baselines/sentence-level-models/models/cnn.py
  class CNN (line 10) | class CNN(nn.Module):
    method __init__ (line 11) | def __init__(self, args, rel2id, word_emb=None):
    method forward (line 58) | def forward(self, inputs):

FILE: code/Model/baselines/sentence-level-models/models/lstm.py
  class LSTM (line 10) | class LSTM(nn.Module):
    method __init__ (line 11) | def __init__(self, args, rel2id, word_emb=None):
    method forward (line 63) | def forward(self, inputs):

FILE: code/Model/baselines/sentence-level-models/models/pcnn.py
  class PCNN (line 10) | class PCNN(nn.Module):
    method __init__ (line 11) | def __init__(self, args, rel2id, word_emb=None):
    method masked_conv (line 57) | def masked_conv(self, input, mask):
    method forward (line 74) | def forward(self, inputs):

FILE: code/Model/baselines/sentence-level-models/models/position_aware_lstm.py
  class PositionAwareLSTM (line 10) | class PositionAwareLSTM(nn.Module):
    method __init__ (line 11) | def __init__(self, args, rel2id, word_emb=None):
    method forward (line 61) | def forward(self, inputs):

FILE: code/Model/baselines/sentence-level-models/tacred2json.py
  function read (line 12) | def read(data, in_dir, out_dir, need_dependency = False):

FILE: code/Model/baselines/sentence-level-models/utils.py
  function ensure_dir (line 33) | def ensure_dir(d, verbose=True):
  class Dataset (line 39) | class Dataset(object):
    method __init__ (line 40) | def __init__(self, filename, args, word2id, device, rel2id=None, shuff...
    method get_id_maps (line 109) | def get_id_maps(self, instances):
  function get_padded_tensor (line 121) | def get_padded_tensor(tokens_list, batch_size):
  class CVDataset (line 131) | class CVDataset(object):
    method __init__ (line 132) | def __init__(self, instances, args, word2id, device, rel2id, shuffle=F...
  function get_cv_dataset (line 201) | def get_cv_dataset(filename, args, word2id, device, rel2id, dev_ratio=0.1):
  function map_to_ids (line 220) | def map_to_ids(tokens, vocab):
  function get_positions (line 224) | def get_positions(start_idx, end_idx, length):
  function sort_all (line 229) | def sort_all(batch, lens):
  function eval (line 236) | def eval(pred, labels):

FILE: code/Model/baselines/sentence-level-models/vocab.py
  function build_embedding (line 12) | def build_embedding(wv_file, vocab, wv_dim):
  function load_glove_vocab (line 26) | def load_glove_vocab(file, wv_dim):
  function normalize_glove (line 38) | def normalize_glove(token):
  class Vocab (line 49) | class Vocab(object):
    method __init__ (line 50) | def __init__(self, filename, load=False, word_counter=None, threshold=0):
    method load (line 72) | def load(self, filename):
    method save (line 78) | def save(self, filename):
    method map (line 87) | def map(self, token_list):
    method unmap (line 93) | def unmap(self, idx_list):
    method get_embeddings (line 99) | def get_embeddings(self, word_vectors=None, dim=100):
  function parse_args (line 110) | def parse_args():
  function main (line 123) | def main():
  function load_tokens (line 173) | def load_tokens(filename):
  function build_vocab (line 182) | def build_vocab(tokens, glove_vocab, min_freq):
  function count_oov (line 195) | def count_oov(tokens, vocab):
  function entity_masks (line 201) | def entity_masks():

FILE: code/Model/dw/deepwalk-bipa.cpp
  type vocab_word (line 20) | struct vocab_word {
  type vocab_word (line 28) | struct vocab_word
  function InitUnigramTable (line 49) | void InitUnigramTable() {
  function GetWordHash (line 68) | int GetWordHash(char *word) {
  function SearchVocab (line 76) | int SearchVocab(char *word) {
  function LearnVocabFromTrainFile (line 86) | void LearnVocabFromTrainFile() {
  function InitNet (line 171) | void InitNet() {
  function ReadNet (line 189) | void ReadNet()
  function TrainModel (line 314) | void TrainModel() {
  function ArgPos (line 394) | int ArgPos(char *str, int argc, char **argv) {
  function main (line 406) | int main(int argc, char **argv) {

FILE: code/Model/dw/deepwalk-hete-em.cpp
  type vocab_word (line 20) | struct vocab_word {
  type vocab_word (line 28) | struct vocab_word
  function InitUnigramTable (line 49) | void InitUnigramTable() {
  function GetWordHash (line 68) | int GetWordHash(char *word) {
  function SearchVocab (line 76) | int SearchVocab(char *word) {
  function LearnVocabFromTrainFile (line 86) | void LearnVocabFromTrainFile() {
  function InitNet (line 207) | void InitNet() {
  function ReadNet (line 225) | void ReadNet()
  function TrainModel (line 379) | void TrainModel() {
  function ArgPos (line 483) | int ArgPos(char *str, int argc, char **argv) {
  function main (line 495) | int main(int argc, char **argv) {

FILE: code/Model/dw/deepwalk-hete.cpp
  type vocab_word (line 20) | struct vocab_word {
  type vocab_word (line 28) | struct vocab_word
  function InitUnigramTable (line 49) | void InitUnigramTable() {
  function GetWordHash (line 68) | int GetWordHash(char *word) {
  function SearchVocab (line 76) | int SearchVocab(char *word) {
  function LearnVocabFromTrainFile (line 86) | void LearnVocabFromTrainFile() {
  function InitNet (line 207) | void InitNet() {
  function ReadNet (line 225) | void ReadNet()
  function TrainModel (line 379) | void TrainModel() {
  function ArgPos (line 483) | int ArgPos(char *str, int argc, char **argv) {
  function main (line 495) | int main(int argc, char **argv) {

FILE: code/Model/multir/src/cc/factorie/protobuf/DocumentProtos.java
  class DocumentProtos (line 6) | public final class DocumentProtos {
    method DocumentProtos (line 7) | private DocumentProtos() {}
    method registerAllExtensions (line 8) | public static void registerAllExtensions(
    class Document (line 11) | public static final class Document extends
      method Document (line 14) | private Document() {
      method Document (line 17) | private Document(boolean noInit) {}
      method getDefaultInstance (line 20) | public static Document getDefaultInstance() {
      method getDefaultInstanceForType (line 24) | public Document getDefaultInstanceForType() {
      method getDescriptor (line 28) | public static final com.google.protobuf.Descriptors.Descriptor
      method internalGetFieldAccessorTable (line 33) | protected com.google.protobuf.GeneratedMessage.FieldAccessorTable
      class Sentence (line 38) | public static final class Sentence extends
        method Sentence (line 41) | private Sentence() {
        method Sentence (line 44) | private Sentence(boolean noInit) {}
        method getDefaultInstance (line 47) | public static Sentence getDefaultInstance() {
        method getDefaultInstanceForType (line 51) | public Sentence getDefaultInstanceForType() {
        method getDescriptor (line 55) | public static final com.google.protobuf.Descriptors.Descriptor
        method internalGetFieldAccessorTable (line 60) | protected com.google.protobuf.GeneratedMessage.FieldAccessorTable
        method getTokensList (line 69) | public java.util.List<cc.factorie.protobuf.DocumentProtos.Document...
        method getTokensCount (line 72) | public int getTokensCount() { return tokens_.size(); }
        method getTokens (line 73) | public cc.factorie.protobuf.DocumentProtos.Document.Token getToken...
        method getMentionsList (line 81) | public java.util.List<cc.factorie.protobuf.DocumentProtos.Document...
        method getMentionsCount (line 84) | public int getMentionsCount() { return mentions_.size(); }
        method getMentions (line 85) | public cc.factorie.protobuf.DocumentProtos.Document.Mention getMen...
        method hasDepTree (line 93) | public boolean hasDepTree() { return hasDepTree; }
        method getDepTree (line 94) | public cc.factorie.protobuf.DocumentProtos.Document.DepTree getDep...
        method initFields (line 96) | private void initFields() {
        method isInitialized (line 99) | public final boolean isInitialized() {
        method writeTo (line 112) | public void writeTo(com.google.protobuf.CodedOutputStream output)
        method getSerializedSize (line 128) | public int getSerializedSize() {
        method parseFrom (line 150) | public static cc.factorie.protobuf.DocumentProtos.Document.Sentenc...
        method parseFrom (line 155) | public static cc.factorie.protobuf.DocumentProtos.Document.Sentenc...
        method parseFrom (line 162) | public static cc.factorie.protobuf.DocumentProtos.Document.Sentenc...
        method parseFrom (line 166) | public static cc.factorie.protobuf.DocumentProtos.Document.Sentenc...
        method parseFrom (line 173) | public static cc.factorie.protobuf.DocumentProtos.Document.Sentenc...
        method parseFrom (line 177) | public static cc.factorie.protobuf.DocumentProtos.Document.Sentenc...
        method parseDelimitedFrom (line 184) | public static cc.factorie.protobuf.DocumentProtos.Document.Sentenc...
        method parseDelimitedFrom (line 193) | public static cc.factorie.protobuf.DocumentProtos.Document.Sentenc...
        method parseFrom (line 204) | public static cc.factorie.protobuf.DocumentProtos.Document.Sentenc...
        method parseFrom (line 209) | public static cc.factorie.protobuf.DocumentProtos.Document.Sentenc...
        method newBuilder (line 217) | public static Builder newBuilder() { return Builder.create(); }
        method newBuilderForType (line 218) | public Builder newBuilderForType() { return newBuilder(); }
        method newBuilder (line 219) | public static Builder newBuilder(cc.factorie.protobuf.DocumentProt...
        method toBuilder (line 222) | public Builder toBuilder() { return newBuilder(this); }
        class Builder (line 224) | public static final class Builder extends
          method Builder (line 229) | private Builder() {}
          method create (line 231) | private static Builder create() {
          method internalGetResult (line 237) | protected cc.factorie.protobuf.DocumentProtos.Document.Sentence ...
          method clear (line 241) | public Builder clear() {
          method clone (line 250) | public Builder clone() {
          method getDescriptorForType (line 254) | public com.google.protobuf.Descriptors.Descriptor
          method getDefaultInstanceForType (line 259) | public cc.factorie.protobuf.DocumentProtos.Document.Sentence get...
          method isInitialized (line 263) | public boolean isInitialized() {
          method build (line 266) | public cc.factorie.protobuf.DocumentProtos.Document.Sentence bui...
          method buildParsed (line 273) | private cc.factorie.protobuf.DocumentProtos.Document.Sentence bu...
          method buildPartial (line 282) | public cc.factorie.protobuf.DocumentProtos.Document.Sentence bui...
          method mergeFrom (line 300) | public Builder mergeFrom(com.google.protobuf.Message other) {
          method mergeFrom (line 309) | public Builder mergeFrom(cc.factorie.protobuf.DocumentProtos.Doc...
          method mergeFrom (line 330) | public Builder mergeFrom(
          method getTokensList (line 378) | public java.util.List<cc.factorie.protobuf.DocumentProtos.Docume...
          method getTokensCount (line 381) | public int getTokensCount() {
          method getTokens (line 384) | public cc.factorie.protobuf.DocumentProtos.Document.Token getTok...
          method setTokens (line 387) | public Builder setTokens(int index, cc.factorie.protobuf.Documen...
          method setTokens (line 394) | public Builder setTokens(int index, cc.factorie.protobuf.Documen...
          method addTokens (line 398) | public Builder addTokens(cc.factorie.protobuf.DocumentProtos.Doc...
          method addTokens (line 408) | public Builder addTokens(cc.factorie.protobuf.DocumentProtos.Doc...
          method addAllTokens (line 415) | public Builder addAllTokens(
          method clearTokens (line 423) | public Builder clearTokens() {
          method getMentionsList (line 429) | public java.util.List<cc.factorie.protobuf.DocumentProtos.Docume...
          method getMentionsCount (line 432) | public int getMentionsCount() {
          method getMentions (line 435) | public cc.factorie.protobuf.DocumentProtos.Document.Mention getM...
          method setMentions (line 438) | public Builder setMentions(int index, cc.factorie.protobuf.Docum...
          method setMentions (line 445) | public Builder setMentions(int index, cc.factorie.protobuf.Docum...
          method addMentions (line 449) | public Builder addMentions(cc.factorie.protobuf.DocumentProtos.D...
          method addMentions (line 459) | public Builder addMentions(cc.factorie.protobuf.DocumentProtos.D...
          method addAllMentions (line 466) | public Builder addAllMentions(
          method clearMentions (line 474) | public Builder clearMentions() {
          method hasDepTree (line 480) | public boolean hasDepTree() {
          method getDepTree (line 483) | public cc.factorie.protobuf.DocumentProtos.Document.DepTree getD...
          method setDepTree (line 486) | public Builder setDepTree(cc.factorie.protobuf.DocumentProtos.Do...
          method setDepTree (line 494) | public Builder setDepTree(cc.factorie.protobuf.DocumentProtos.Do...
          method mergeDepTree (line 499) | public Builder mergeDepTree(cc.factorie.protobuf.DocumentProtos....
          method clearDepTree (line 510) | public Builder clearDepTree() {
      class Token (line 528) | public static final class Token extends
        method Token (line 531) | private Token() {
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          method clear (line 1115) | public Builder clear() {
          method clone (line 1124) | public Builder clone() {
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          method getDefaultInstanceForType (line 1133) | public cc.factorie.protobuf.DocumentProtos.Document.Mention getD...
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          method buildParsed (line 1147) | private cc.factorie.protobuf.DocumentProtos.Document.Mention bui...
          method buildPartial (line 1156) | public cc.factorie.protobuf.DocumentProtos.Document.Mention buil...
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        method writeTo (line 1415) | public void writeTo(com.google.protobuf.CodedOutputStream output)
        method getSerializedSize (line 1431) | public int getSerializedSize() {
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        method parseFrom (line 1468) | public static cc.factorie.protobuf.DocumentProtos.Document.DepTree...
        method parseFrom (line 1475) | public static cc.factorie.protobuf.DocumentProtos.Document.DepTree...
        method parseFrom (line 1479) | public static cc.factorie.protobuf.DocumentProtos.Document.DepTree...
        method parseFrom (line 1486) | public static cc.factorie.protobuf.DocumentProtos.Document.DepTree...
        method parseFrom (line 1490) | public static cc.factorie.protobuf.DocumentProtos.Document.DepTree...
        method parseDelimitedFrom (line 1497) | public static cc.factorie.protobuf.DocumentProtos.Document.DepTree...
        method parseDelimitedFrom (line 1506) | public static cc.factorie.protobuf.DocumentProtos.Document.DepTree...
        method parseFrom (line 1517) | public static cc.factorie.protobuf.DocumentProtos.Document.DepTree...
        method parseFrom (line 1522) | public static cc.factorie.protobuf.DocumentProtos.Document.DepTree...
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        method newBuilderForType (line 1531) | public Builder newBuilderForType() { return newBuilder(); }
        method newBuilder (line 1532) | public static Builder newBuilder(cc.factorie.protobuf.DocumentProt...
        method toBuilder (line 1535) | public Builder toBuilder() { return newBuilder(this); }
        class Builder (line 1537) | public static final class Builder extends
          method Builder (line 1542) | private Builder() {}
          method create (line 1544) | private static Builder create() {
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          method clear (line 1554) | public Builder clear() {
          method clone (line 1563) | public Builder clone() {
          method getDescriptorForType (line 1567) | public com.google.protobuf.Descriptors.Descriptor
          method getDefaultInstanceForType (line 1572) | public cc.factorie.protobuf.DocumentProtos.Document.DepTree getD...
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          method buildParsed (line 1586) | private cc.factorie.protobuf.DocumentProtos.Document.DepTree bui...
          method buildPartial (line 1595) | public cc.factorie.protobuf.DocumentProtos.Document.DepTree buil...
          method mergeFrom (line 1613) | public Builder mergeFrom(com.google.protobuf.Message other) {
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        method writeTo (line 1859) | public void writeTo(com.google.protobuf.CodedOutputStream output)
        method getSerializedSize (line 1878) | public int getSerializedSize() {
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        method parseFrom (line 1909) | public static cc.factorie.protobuf.DocumentProtos.Document.Relatio...
        method parseFrom (line 1916) | public static cc.factorie.protobuf.DocumentProtos.Document.Relatio...
        method parseFrom (line 1920) | public static cc.factorie.protobuf.DocumentProtos.Document.Relatio...
        method parseFrom (line 1927) | public static cc.factorie.protobuf.DocumentProtos.Document.Relatio...
        method parseFrom (line 1931) | public static cc.factorie.protobuf.DocumentProtos.Document.Relatio...
        method parseDelimitedFrom (line 1938) | public static cc.factorie.protobuf.DocumentProtos.Document.Relatio...
        method parseDelimitedFrom (line 1947) | public static cc.factorie.protobuf.DocumentProtos.Document.Relatio...
        method parseFrom (line 1958) | public static cc.factorie.protobuf.DocumentProtos.Document.Relatio...
        method parseFrom (line 1963) | public static cc.factorie.protobuf.DocumentProtos.Document.Relatio...
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        method newBuilderForType (line 1972) | public Builder newBuilderForType() { return newBuilder(); }
        method newBuilder (line 1973) | public static Builder newBuilder(cc.factorie.protobuf.DocumentProt...
        method toBuilder (line 1976) | public Builder toBuilder() { return newBuilder(this); }
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          method create (line 1985) | private static Builder create() {
          method internalGetResult (line 1991) | protected cc.factorie.protobuf.DocumentProtos.Document.RelationM...
          method clear (line 1995) | public Builder clear() {
          method clone (line 2004) | public Builder clone() {
          method getDescriptorForType (line 2008) | public com.google.protobuf.Descriptors.Descriptor
          method getDefaultInstanceForType (line 2013) | public cc.factorie.protobuf.DocumentProtos.Document.RelationMent...
          method isInitialized (line 2017) | public boolean isInitialized() {
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          method buildParsed (line 2027) | private cc.factorie.protobuf.DocumentProtos.Document.RelationMen...
          method buildPartial (line 2036) | public cc.factorie.protobuf.DocumentProtos.Document.RelationMent...
          method mergeFrom (line 2046) | public Builder mergeFrom(com.google.protobuf.Message other) {
          method mergeFrom (line 2055) | public Builder mergeFrom(cc.factorie.protobuf.DocumentProtos.Doc...
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      method getSentences (line 2217) | public cc.factorie.protobuf.DocumentProtos.Document.Sentence getSent...
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      method getSerializedSize (line 2244) | public int getSerializedSize() {
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      method parseFrom (line 2267) | public static cc.factorie.protobuf.DocumentProtos.Document parseFrom(
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      method parseFrom (line 2278) | public static cc.factorie.protobuf.DocumentProtos.Document parseFrom(
      method parseFrom (line 2285) | public static cc.factorie.protobuf.DocumentProtos.Document parseFrom...
      method parseFrom (line 2289) | public static cc.factorie.protobuf.DocumentProtos.Document parseFrom(
      method parseDelimitedFrom (line 2296) | public static cc.factorie.protobuf.DocumentProtos.Document parseDeli...
      method parseDelimitedFrom (line 2305) | public static cc.factorie.protobuf.DocumentProtos.Document parseDeli...
      method parseFrom (line 2316) | public static cc.factorie.protobuf.DocumentProtos.Document parseFrom(
      method parseFrom (line 2321) | public static cc.factorie.protobuf.DocumentProtos.Document parseFrom(
      method newBuilder (line 2329) | public static Builder newBuilder() { return Builder.create(); }
      method newBuilderForType (line 2330) | public Builder newBuilderForType() { return newBuilder(); }
      method newBuilder (line 2331) | public static Builder newBuilder(cc.factorie.protobuf.DocumentProtos...
      method toBuilder (line 2334) | public Builder toBuilder() { return newBuilder(this); }
      class Builder (line 2336) | public static final class Builder extends
        method Builder (line 2341) | private Builder() {}
        method create (line 2343) | private static Builder create() {
        method internalGetResult (line 2349) | protected cc.factorie.protobuf.DocumentProtos.Document internalGet...
        method clear (line 2353) | public Builder clear() {
        method clone (line 2362) | public Builder clone() {
        method getDescriptorForType (line 2366) | public com.google.protobuf.Descriptors.Descriptor
        method getDefaultInstanceForType (line 2371) | public cc.factorie.protobuf.DocumentProtos.Document getDefaultInst...
        method isInitialized (line 2375) | public boolean isInitialized() {
        method build (line 2378) | public cc.factorie.protobuf.DocumentProtos.Document build() {
        method buildParsed (line 2385) | private cc.factorie.protobuf.DocumentProtos.Document buildParsed()
        method buildPartial (line 2394) | public cc.factorie.protobuf.DocumentProtos.Document buildPartial() {
        method mergeFrom (line 2408) | public Builder mergeFrom(com.google.protobuf.Message other) {
        method mergeFrom (line 2417) | public Builder mergeFrom(cc.factorie.protobuf.DocumentProtos.Docum...
        method mergeFrom (line 2432) | public Builder mergeFrom(
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        method setFilename (line 2475) | public Builder setFilename(java.lang.String value) {
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        method setSentences (line 2499) | public Builder setSentences(int index, cc.factorie.protobuf.Docume...
        method setSentences (line 2506) | public Builder setSentences(int index, cc.factorie.protobuf.Docume...
        method addSentences (line 2510) | public Builder addSentences(cc.factorie.protobuf.DocumentProtos.Do...
        method addSentences (line 2520) | public Builder addSentences(cc.factorie.protobuf.DocumentProtos.Do...
        method addAllSentences (line 2527) | public Builder addAllSentences(
        method clearSentences (line 2535) | public Builder clearSentences() {
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        method internalGetFieldAccessorTable (line 2601) | protected com.google.protobuf.GeneratedMessage.FieldAccessorTable
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        method getSourceId (line 2618) | public int getSourceId() { return sourceId_; }
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        method getSentence (line 2644) | public java.lang.String getSentence() { return sentence_; }
        method initFields (line 2646) | private void initFields() {
        method isInitialized (line 2648) | public final boolean isInitialized() {
        method writeTo (line 2655) | public void writeTo(com.google.protobuf.CodedOutputStream output)
        method getSerializedSize (line 2677) | public int getSerializedSize() {
        method parseFrom (line 2712) | public static cc.factorie.protobuf.DocumentProtos.Relation.Relatio...
        method parseFrom (line 2717) | public static cc.factorie.protobuf.DocumentProtos.Relation.Relatio...
        method parseFrom (line 2724) | public static cc.factorie.protobuf.DocumentProtos.Relation.Relatio...
        method parseFrom (line 2728) | public static cc.factorie.protobuf.DocumentProtos.Relation.Relatio...
        method parseFrom (line 2735) | public static cc.factorie.protobuf.DocumentProtos.Relation.Relatio...
        method parseFrom (line 2739) | public static cc.factorie.protobuf.DocumentProtos.Relation.Relatio...
        method parseDelimitedFrom (line 2746) | public static cc.factorie.protobuf.DocumentProtos.Relation.Relatio...
        method parseDelimitedFrom (line 2755) | public static cc.factorie.protobuf.DocumentProtos.Relation.Relatio...
        method parseFrom (line 2766) | public static cc.factorie.protobuf.DocumentProtos.Relation.Relatio...
        method parseFrom (line 2771) | public static cc.factorie.protobuf.DocumentProtos.Relation.Relatio...
        method newBuilder (line 2779) | public static Builder newBuilder() { return Builder.create(); }
        method newBuilderForType (line 2780) | public Builder newBuilderForType() { return newBuilder(); }
        method newBuilder (line 2781) | public static Builder newBuilder(cc.factorie.protobuf.DocumentProt...
        method toBuilder (line 2784) | public Builder toBuilder() { return newBuilder(this); }
        class Builder (line 2786) | public static final class Builder extends
          method Builder (line 2791) | private Builder() {}
          method create (line 2793) | private static Builder create() {
          method internalGetResult (line 2799) | protected cc.factorie.protobuf.DocumentProtos.Relation.RelationM...
          method clear (line 2803) | public Builder clear() {
          method clone (line 2812) | public Builder clone() {
          method getDescriptorForType (line 2816) | public com.google.protobuf.Descriptors.Descriptor
          method getDefaultInstanceForType (line 2821) | public cc.factorie.protobuf.DocumentProtos.Relation.RelationMent...
          method isInitialized (line 2825) | public boolean isInitialized() {
          method build (line 2828) | public cc.factorie.protobuf.DocumentProtos.Relation.RelationMent...
          method buildParsed (line 2835) | private cc.factorie.protobuf.DocumentProtos.Relation.RelationMen...
          method buildPartial (line 2844) | public cc.factorie.protobuf.DocumentProtos.Relation.RelationMent...
          method mergeFrom (line 2858) | public Builder mergeFrom(com.google.protobuf.Message other) {
          method mergeFrom (line 2867) | public Builder mergeFrom(cc.factorie.protobuf.DocumentProtos.Rel...
          method mergeFrom (line 2891) | public Builder mergeFrom(
          method hasFilename (line 2938) | public boolean hasFilename() {
          method getFilename (line 2941) | public java.lang.String getFilename() {
          method setFilename (line 2944) | public Builder setFilename(java.lang.String value) {
          method clearFilename (line 2952) | public Builder clearFilename() {
          method hasSourceId (line 2959) | public boolean hasSourceId() {
          method getSourceId (line 2962) | public int getSourceId() {
          method setSourceId (line 2965) | public Builder setSourceId(int value) {
          method clearSourceId (line 2970) | public Builder clearSourceId() {
          method hasDestId (line 2977) | public boolean hasDestId() {
          method getDestId (line 2980) | public int getDestId() {
          method setDestId (line 2983) | public Builder setDestId(int value) {
          method clearDestId (line 2988) | public Builder clearDestId() {
          method getFeatureList (line 2995) | public java.util.List<java.lang.String> getFeatureList() {
          method getFeatureCount (line 2998) | public int getFeatureCount() {
          method getFeature (line 3001) | public java.lang.String getFeature(int index) {
          method setFeature (line 3004) | public Builder setFeature(int index, java.lang.String value) {
          method addFeature (line 3011) | public Builder addFeature(java.lang.String value) {
          method addAllFeature (line 3021) | public Builder addAllFeature(
          method clearFeature (line 3029) | public Builder clearFeature() {
          method hasSentence (line 3035) | public boolean hasSentence() {
          method getSentence (line 3038) | public java.lang.String getSentence() {
          method setSentence (line 3041) | public Builder setSentence(java.lang.String value) {
          method clearSentence (line 3049) | public Builder clearSentence() {
      method hasSourceGuid (line 3071) | public boolean hasSourceGuid() { return hasSourceGuid; }
      method getSourceGuid (line 3072) | public java.lang.String getSourceGuid() { return sourceGuid_; }
      method hasDestGuid (line 3078) | public boolean hasDestGuid() { return hasDestGuid; }
      method getDestGuid (line 3079) | public java.lang.String getDestGuid() { return destGuid_; }
      method hasRelType (line 3085) | public boolean hasRelType() { return hasRelType; }
      method getRelType (line 3086) | public java.lang.String getRelType() { return relType_; }
      method getMentionList (line 3092) | public java.util.List<cc.factorie.protobuf.DocumentProtos.Relation.R...
      method getMentionCount (line 3095) | public int getMentionCount() { return mention_.size(); }
      method getMention (line 3096) | public cc.factorie.protobuf.DocumentProtos.Relation.RelationMentionR...
      method initFields (line 3100) | private void initFields() {
      method isInitialized (line 3102) | public final boolean isInitialized() {
      method writeTo (line 3112) | public void writeTo(com.google.protobuf.CodedOutputStream output)
      method getSerializedSize (line 3131) | public int getSerializedSize() {
      method parseFrom (line 3157) | public static cc.factorie.protobuf.DocumentProtos.Relation parseFrom(
      method parseFrom (line 3162) | public static cc.factorie.protobuf.DocumentProtos.Relation parseFrom(
      method parseFrom (line 3169) | public static cc.factorie.protobuf.DocumentProtos.Relation parseFrom...
      method parseFrom (line 3173) | public static cc.factorie.protobuf.DocumentProtos.Relation parseFrom(
      method parseFrom (line 3180) | public static cc.factorie.protobuf.DocumentProtos.Relation parseFrom...
      method parseFrom (line 3184) | public static cc.factorie.protobuf.DocumentProtos.Relation parseFrom(
      method parseDelimitedFrom (line 3191) | public static cc.factorie.protobuf.DocumentProtos.Relation parseDeli...
      method parseDelimitedFrom (line 3200) | public static cc.factorie.protobuf.DocumentProtos.Relation parseDeli...
      method parseFrom (line 3211) | public static cc.factorie.protobuf.DocumentProtos.Relation parseFrom(
      method parseFrom (line 3216) | public static cc.factorie.protobuf.DocumentProtos.Relation parseFrom(
      method newBuilder (line 3224) | public static Builder newBuilder() { return Builder.create(); }
      method newBuilderForType (line 3225) | public Builder newBuilderForType() { return newBuilder(); }
      method newBuilder (line 3226) | public static Builder newBuilder(cc.factorie.protobuf.DocumentProtos...
      method toBuilder (line 3229) | public Builder toBuilder() { return newBuilder(this); }
      class Builder (line 3231) | public static final class Builder extends
        method Builder (line 3236) | private Builder() {}
        method create (line 3238) | private static Builder create() {
        method internalGetResult (line 3244) | protected cc.factorie.protobuf.DocumentProtos.Relation internalGet...
        method clear (line 3248) | public Builder clear() {
        method clone (line 3257) | public Builder clone() {
        method getDescriptorForType (line 3261) | public com.google.protobuf.Descriptors.Descriptor
        method getDefaultInstanceForType (line 3266) | public cc.factorie.protobuf.DocumentProtos.Relation getDefaultInst...
        method isInitialized (line 3270) | public boolean isInitialized() {
        method build (line 3273) | public cc.factorie.protobuf.DocumentProtos.Relation build() {
        method buildParsed (line 3280) | private cc.factorie.protobuf.DocumentProtos.Relation buildParsed()
        method buildPartial (line 3289) | public cc.factorie.protobuf.DocumentProtos.Relation buildPartial() {
        method mergeFrom (line 3303) | public Builder mergeFrom(com.google.protobuf.Message other) {
        method mergeFrom (line 3312) | public Builder mergeFrom(cc.factorie.protobuf.DocumentProtos.Relat...
        method mergeFrom (line 3333) | public Builder mergeFrom(
        method hasSourceGuid (line 3378) | public boolean hasSourceGuid() {
        method getSourceGuid (line 3381) | public java.lang.String getSourceGuid() {
        method setSourceGuid (line 3384) | public Builder setSourceGuid(java.lang.String value) {
        method clearSourceGuid (line 3392) | public Builder clearSourceGuid() {
        method hasDestGuid (line 3399) | public boolean hasDestGuid() {
        method getDestGuid (line 3402) | public java.lang.String getDestGuid() {
        method setDestGuid (line 3405) | public Builder setDestGuid(java.lang.String value) {
        method clearDestGuid (line 3413) | public Builder clearDestGuid() {
        method hasRelType (line 3420) | public boolean hasRelType() {
        method getRelType (line 3423) | public java.lang.String getRelType() {
        method setRelType (line 3426) | public Builder setRelType(java.lang.String value) {
        method clearRelType (line 3434) | public Builder clearRelType() {
        method getMentionList (line 3441) | public java.util.List<cc.factorie.protobuf.DocumentProtos.Relation...
        method getMentionCount (line 3444) | public int getMentionCount() {
        method getMention (line 3447) | public cc.factorie.protobuf.DocumentProtos.Relation.RelationMentio...
        method setMention (line 3450) | public Builder setMention(int index, cc.factorie.protobuf.Document...
        method setMention (line 3457) | public Builder setMention(int index, cc.factorie.protobuf.Document...
        method addMention (line 3461) | public Builder addMention(cc.factorie.protobuf.DocumentProtos.Rela...
        method addMention (line 3471) | public Builder addMention(cc.factorie.protobuf.DocumentProtos.Rela...
        method addAllMention (line 3478) | public Builder addAllMention(
        method clearMention (line 3486) | public Builder clearMention() {
    class Entity (line 3503) | public static final class Entity extends
      method Entity (line 3506) | private Entity() {
      method Entity (line 3509) | private Entity(boolean noInit) {}
      method getDefaultInstance (line 3512) | public static Entity getDefaultInstance() {
      method getDefaultInstanceForType (line 3516) | public Entity getDefaultInstanceForType() {
      method getDescriptor (line 3520) | public static final com.google.protobuf.Descriptors.Descriptor
      method internalGetFieldAccessorTable (line 3525) | protected com.google.protobuf.GeneratedMessage.FieldAccessorTable
      class EntityMentionRef (line 3530) | public static final class EntityMentionRef extends
        method EntityMentionRef (line 3533) | private EntityMentionRef() {
        method EntityMentionRef (line 3536) | private EntityMentionRef(boolean noInit) {}
        method getDefaultInstance (line 3539) | public static EntityMentionRef getDefaultInstance() {
        method getDefaultInstanceForType (line 3543) | public EntityMentionRef getDefaultInstanceForType() {
        method getDescriptor (line 3547) | public static final com.google.protobuf.Descriptors.Descriptor
        method internalGetFieldAccessorTable (line 3552) | protected com.google.protobuf.GeneratedMessage.FieldAccessorTable
        method hasFilename (line 3561) | public boolean hasFilename() { return hasFilename; }
        method getFilename (line 3562) | public java.lang.String getFilename() { return filename_; }
        method hasId (line 3568) | public boolean hasId() { return hasId; }
        method getId (line 3569) | public int getId() { return id_; }
        method getFeatureList (line 3575) | public java.util.List<java.lang.String> getFeatureList() {
        method getFeatureCount (line 3578) | public int getFeatureCount() { return feature_.size(); }
        method getFeature (line 3579) | public java.lang.String getFeature(int index) {
        method initFields (line 3583) | private void initFields() {
        method isInitialized (line 3585) | public final boolean isInitialized() {
        method writeTo (line 3591) | public void writeTo(com.google.protobuf.CodedOutputStream output)
        method getSerializedSize (line 3607) | public int getSerializedSize() {
        method parseFrom (line 3634) | public static cc.factorie.protobuf.DocumentProtos.Entity.EntityMen...
        method parseFrom (line 3639) | public static cc.factorie.protobuf.DocumentProtos.Entity.EntityMen...
        method parseFrom (line 3646) | public static cc.factorie.protobuf.DocumentProtos.Entity.EntityMen...
        method parseFrom (line 3650) | public static cc.factorie.protobuf.DocumentProtos.Entity.EntityMen...
        method parseFrom (line 3657) | public static cc.factorie.protobuf.DocumentProtos.Entity.EntityMen...
        method parseFrom (line 3661) | public static cc.factorie.protobuf.DocumentProtos.Entity.EntityMen...
        method parseDelimitedFrom (line 3668) | public static cc.factorie.protobuf.DocumentProtos.Entity.EntityMen...
        method parseDelimitedFrom (line 3677) | public static cc.factorie.protobuf.DocumentProtos.Entity.EntityMen...
        method parseFrom (line 3688) | public static cc.factorie.protobuf.DocumentProtos.Entity.EntityMen...
        method parseFrom (line 3693) | public static cc.factorie.protobuf.DocumentProtos.Entity.EntityMen...
        method newBuilder (line 3701) | public static Builder newBuilder() { return Builder.create(); }
        method newBuilderForType (line 3702) | public Builder newBuilderForType() { return newBuilder(); }
        method newBuilder (line 3703) | public static Builder newBuilder(cc.factorie.protobuf.DocumentProt...
        method toBuilder (line 3706) | public Builder toBuilder() { return newBuilder(this); }
        class Builder (line 3708) | public static final class Builder extends
          method Builder (line 3713) | private Builder() {}
          method create (line 3715) | private static Builder create() {
          method internalGetResult (line 3721) | protected cc.factorie.protobuf.DocumentProtos.Entity.EntityMenti...
          method clear (line 3725) | public Builder clear() {
          method clone (line 3734) | public Builder clone() {
          method getDescriptorForType (line 3738) | public com.google.protobuf.Descriptors.Descriptor
          method getDefaultInstanceForType (line 3743) | public cc.factorie.protobuf.DocumentProtos.Entity.EntityMentionR...
          method isInitialized (line 3747) | public boolean isInitialized() {
          method build (line 3750) | public cc.factorie.protobuf.DocumentProtos.Entity.EntityMentionR...
          method buildParsed (line 3757) | private cc.factorie.protobuf.DocumentProtos.Entity.EntityMention...
          method buildPartial (line 3766) | public cc.factorie.protobuf.DocumentProtos.Entity.EntityMentionR...
          method mergeFrom (line 3780) | public Builder mergeFrom(com.google.protobuf.Message other) {
          method mergeFrom (line 3789) | public Builder mergeFrom(cc.factorie.protobuf.DocumentProtos.Ent...
          method mergeFrom (line 3807) | public Builder mergeFrom(
          method hasFilename (line 3846) | public boolean hasFilename() {
          method getFilename (line 3849) | public java.lang.String getFilename() {
          method setFilename (line 3852) | public Builder setFilename(java.lang.String value) {
          method clearFilename (line 3860) | public Builder clearFilename() {
          method hasId (line 3867) | public boolean hasId() {
          method getId (line 3870) | public int getId() {
          method setId (line 3873) | public Builder setId(int value) {
          method clearId (line 3878) | public Builder clearId() {
          method getFeatureList (line 3885) | public java.util.List<java.lang.String> getFeatureList() {
          method getFeatureCount (line 3888) | public int getFeatureCount() {
          method getFeature (line 3891) | public java.lang.String getFeature(int index) {
          method setFeature (line 3894) | public Builder setFeature(int index, java.lang.String value) {
          method addFeature (line 3901) | public Builder addFeature(java.lang.String value) {
          method addAllFeature (line 3911) | public Builder addAllFeature(
          method clearFeature (line 3919) | public Builder clearFeature() {
      method hasGuid (line 3940) | public boolean hasGuid() { return hasGuid; }
      method getGuid (line 3941) | public java.lang.String getGuid() { return guid_; }
      method hasName (line 3947) | public boolean hasName() { return hasName; }
      method getName (line 3948) | public java.lang.String getName() { return name_; }
      method hasType (line 3954) | public boolean hasType() { return hasType; }
      method getType (line 3955) | public java.lang.String getType() { return type_; }
      method hasPred (line 3961) | public boolean hasPred() { return hasPred; }
      method getPred (line 3962) | public java.lang.String getPred() { return pred_; }
      method getMentionList (line 3968) | public java.util.List<cc.factorie.protobuf.DocumentProtos.Entity.Ent...
      method getMentionCount (line 3971) | public int getMentionCount() { return mention_.size(); }
      method getMention (line 3972) | public cc.factorie.protobuf.DocumentProtos.Entity.EntityMentionRef g...
      method initFields (line 3976) | private void initFields() {
      method isInitialized (line 3978) | public final boolean isInitialized() {
      method writeTo (line 3986) | public void writeTo(com.google.protobuf.CodedOutputStream output)
      method getSerializedSize (line 4008) | public int getSerializedSize() {
      method parseFrom (line 4038) | public static cc.factorie.protobuf.DocumentProtos.Entity parseFrom(
      method parseFrom (line 4043) | public static cc.factorie.protobuf.DocumentProtos.Entity parseFrom(
      method parseFrom (line 4050) | public static cc.factorie.protobuf.DocumentProtos.Entity parseFrom(b...
      method parseFrom (line 4054) | public static cc.factorie.protobuf.DocumentProtos.Entity parseFrom(
      method parseFrom (line 4061) | public static cc.factorie.protobuf.DocumentProtos.Entity parseFrom(j...
      method parseFrom (line 4065) | public static cc.factorie.protobuf.DocumentProtos.Entity parseFrom(
      method parseDelimitedFrom (line 4072) | public static cc.factorie.protobuf.DocumentProtos.Entity parseDelimi...
      method parseDelimitedFrom (line 4081) | public static cc.factorie.protobuf.DocumentProtos.Entity parseDelimi...
      method parseFrom (line 4092) | public static cc.factorie.protobuf.DocumentProtos.Entity parseFrom(
      method parseFrom (line 4097) | public static cc.factorie.protobuf.DocumentProtos.Entity parseFrom(
      method newBuilder (line 4105) | public static Builder newBuilder() { return Builder.create(); }
      method newBuilderForType (line 4106) | public Builder newBuilderForType() { return newBuilder(); }
      method newBuilder (line 4107) | public static Builder newBuilder(cc.factorie.protobuf.DocumentProtos...
      method toBuilder (line 4110) | public Builder toBuilder() { return newBuilder(this); }
      class Builder (line 4112) | public static final class Builder extends
        method Builder (line 4117) | private Builder() {}
        method create (line 4119) | private static Builder create() {
        method internalGetResult (line 4125) | protected cc.factorie.protobuf.DocumentProtos.Entity internalGetRe...
        method clear (line 4129) | public Builder clear() {
        method clone (line 4138) | public Builder clone() {
        method getDescriptorForType (line 4142) | public com.google.protobuf.Descriptors.Descriptor
        method getDefaultInstanceForType (line 4147) | public cc.factorie.protobuf.DocumentProtos.Entity getDefaultInstan...
        method isInitialized (line 4151) | public boolean isInitialized() {
        method build (line 4154) | public cc.factorie.protobuf.DocumentProtos.Entity build() {
        method buildParsed (line 4161) | private cc.factorie.protobuf.DocumentProtos.Entity buildParsed()
        method buildPartial (line 4170) | public cc.factorie.protobuf.DocumentProtos.Entity buildPartial() {
        method mergeFrom (line 4184) | public Builder mergeFrom(com.google.protobuf.Message other) {
        method mergeFrom (line 4193) | public Builder mergeFrom(cc.factorie.protobuf.DocumentProtos.Entit...
        method mergeFrom (line 4217) | public Builder mergeFrom(
        method hasGuid (line 4266) | public boolean hasGuid() {
        method getGuid (line 4269) | public java.lang.String getGuid() {
        method setGuid (line 4272) | public Builder setGuid(java.lang.String value) {
        method clearGuid (line 4280) | public Builder clearGuid() {
        method hasName (line 4287) | public boolean hasName() {
        method getName (line 4290) | public java.lang.String getName() {
        method setName (line 4293) | public Builder setName(java.lang.String value) {
        method clearName (line 4301) | public Builder clearName() {
        method hasType (line 4308) | public boolean hasType() {
        method getType (line 4311) | public java.lang.String getType() {
        method setType (line 4314) | public Builder setType(java.lang.String value) {
        method clearType (line 4322) | public Builder clearType() {
        method hasPred (line 4329) | public boolean hasPred() {
        method getPred (line 4332) | public java.lang.String getPred() {
        method setPred (line 4335) | public Builder setPred(java.lang.String value) {
        method clearPred (line 4343) | public Builder clearPred() {
        method getMentionList (line 4350) | public java.util.List<cc.factorie.protobuf.DocumentProtos.Entity.E...
        method getMentionCount (line 4353) | public int getMentionCount() {
        method getMention (line 4356) | public cc.factorie.protobuf.DocumentProtos.Entity.EntityMentionRef...
        method setMention (line 4359) | public Builder setMention(int index, cc.factorie.protobuf.Document...
        method setMention (line 4366) | public Builder setMention(int index, cc.factorie.protobuf.Document...
        method addMention (line 4370) | public Builder addMention(cc.factorie.protobuf.DocumentProtos.Enti...
        method addMention (line 4380) | public Builder addMention(cc.factorie.protobuf.DocumentProtos.Enti...
        method addAllMention (line 4387) | public Builder addAllMention(
        method clearMention (line 4395) | public Builder clearMention() {
    method getDescriptor (line 4463) | public static com.google.protobuf.Descriptors.FileDescriptor
    method assignDescriptors (line 4500) | public com.google.protobuf.ExtensionRegistry assignDescriptors(
    method internalForceInit (line 4592) | public static void internalForceInit() {}

FILE: code/Model/multir/src/edu/uw/cs/multir/learning/algorithm/AveragedPerceptron.java
  class AveragedPerceptron (line 10) | public class AveragedPerceptron {
    method AveragedPerceptron (line 21) | public AveragedPerceptron(Model model, Random random) {
    method train (line 36) | public Parameters train(Dataset trainingData) {
    method trainingIteration (line 64) | public void trainingIteration(int iteration, Dataset trainingData) {
    method YsAgree (line 94) | private boolean YsAgree(int[] y1, int[] y2) {
    method update (line 104) | public void update(Parse pred, Parse tru) {
    method updateRel (line 124) | private void updateRel(int toState, SparseBinaryVector features,
    method finalizeRel (line 145) | private void finalizeRel() {

FILE: code/Model/multir/src/edu/uw/cs/multir/learning/algorithm/ConditionalInference.java
  class ConditionalInference (line 8) | public class ConditionalInference {
    method infer (line 10) | public static Parse infer(MILDocument doc,
    class Edge (line 132) | static class Edge {
      method Edge (line 136) | Edge(int m, int y, double score) {

FILE: code/Model/multir/src/edu/uw/cs/multir/learning/algorithm/FullInference.java
  class FullInference (line 6) | public class FullInference {
    method infer (line 8) | public static Parse infer(MILDocument doc,

FILE: code/Model/multir/src/edu/uw/cs/multir/learning/algorithm/Model.java
  class Model (line 11) | public class Model {
    method numFeatures (line 16) | public int numFeatures(int rel) {
    method read (line 22) | public void read(String file) throws IOException {
    method write (line 33) | public void write(String file) throws IOException {

FILE: code/Model/multir/src/edu/uw/cs/multir/learning/algorithm/Parameters.java
  class Parameters (line 13) | public class Parameters {
    method sum (line 19) | private DenseVector sum(DenseVector v1, DenseVector v2, float factor) {
    method sum (line 30) | public void sum(Parameters p, float factor) {
    method init (line 35) | public void init() {
    method reset (line 47) | public void reset() {
    method serialize (line 53) | public void serialize(OutputStream os)
    method deserialize (line 60) | public void deserialize(InputStream is)
    method serialize (line 68) | public void serialize(String file)
    method deserialize (line 75) | public void deserialize(String file)

FILE: code/Model/multir/src/edu/uw/cs/multir/learning/algorithm/Parse.java
  class Parse (line 5) | public class Parse {
    method Parse (line 14) | public Parse() {}

FILE: code/Model/multir/src/edu/uw/cs/multir/learning/algorithm/Scorer.java
  class Scorer (line 7) | public class Scorer {
    method Scorer (line 10) | public Scorer() {}
    method scoreMentionRelation (line 13) | public double scoreMentionRelation(MILDocument doc, int m, int rel) {
    method getMentionRelationFeatures (line 21) | public SparseBinaryVector getMentionRelationFeatures(MILDocument doc, ...
    method setParameters (line 25) | public void setParameters(Parameters params) {

FILE: code/Model/multir/src/edu/uw/cs/multir/learning/algorithm/Viterbi.java
  class Viterbi (line 5) | public class Viterbi {
    method Viterbi (line 10) | public Viterbi(Model model, Scorer parseScorer) {
    method parse (line 15) | public Parse parse(MILDocument doc, int mention) {
    class Parse (line 36) | public static class Parse {
      method Parse (line 44) | Parse(int state, double score) {

FILE: code/Model/multir/src/edu/uw/cs/multir/learning/data/Dataset.java
  type Dataset (line 5) | public interface Dataset {
    method numDocs (line 7) | public int numDocs();
    method shuffle (line 9) | public void shuffle(Random random);
    method next (line 11) | public MILDocument next();
    method next (line 13) | public boolean next(MILDocument doc);
    method reset (line 15) | public void reset();

FILE: code/Model/multir/src/edu/uw/cs/multir/learning/data/MILDocument.java
  class MILDocument (line 16) | public class MILDocument {
    method MILDocument (line 32) | public MILDocument() {
    method clear (line 38) | public void clear() {
    method setCapacity (line 42) | public void setCapacity(int targetSize) {
    method read (line 57) | public boolean read(DataInputStream dis) throws IOException {
    method write (line 82) | public void write(DataOutputStream dos) throws IOException {

FILE: code/Model/multir/src/edu/uw/cs/multir/learning/data/MemoryDataset.java
  class MemoryDataset (line 11) | public class MemoryDataset implements Dataset {
    method MemoryDataset (line 16) | public MemoryDataset() {  }
    method MemoryDataset (line 18) | public MemoryDataset(String file)
    method numDocs (line 32) | public int numDocs() { return docs.length; }
    method shuffle (line 34) | public void shuffle(Random random) {
    method next (line 44) | public MILDocument next() {
    method next (line 50) | public boolean next(MILDocument doc) {
    method reset (line 65) | public void reset() {

FILE: code/Model/multir/src/edu/uw/cs/multir/main/AggregatePrecisionRecallCurve.java
  class AggregatePrecisionRecallCurve (line 20) | public class AggregatePrecisionRecallCurve {
    method run (line 22) | public static void run(String dir)
    method eval (line 37) | public static void eval(Dataset test, Parameters params,
    class Prediction (line 98) | static class Prediction {
      method Prediction (line 105) | Prediction(int rel, boolean trueRel, boolean predRel, double score,
    class PrecisionRecallTester (line 117) | static class PrecisionRecallTester {
      method handle (line 120) | public void handle(String[] tokens, boolean[] predictedLabels,
      method handle (line 136) | public void handle(int rel, boolean p, boolean t, double score) {
      method reset (line 146) | public void reset() { numCorrect = numPredictions = numRelations = 0; }
      method precision (line 147) | public double precision() {
      method recall (line 151) | public double recall() {

FILE: code/Model/multir/src/edu/uw/cs/multir/main/Main.java
  class Main (line 5) | public class Main {
    method main (line 7) | public static void main(String[] args) throws IOException {
    method printUsage (line 100) | private static void printUsage() {
    method printUsagePreprocess (line 107) | private static void printUsagePreprocess() {
    method printUsageTrain (line 112) | private static void printUsageTrain() {
    method printUsageTest (line 117) | private static void printUsageTest() {
    method printUsageResults (line 122) | private static void printUsageResults() {
    method printUsageAggPR (line 127) | private static void printUsageAggPR() {
    method printUsageSenPR (line 132) | private static void printUsageSenPR() {
    method printUsageSenRel (line 137) | private static void printUsageSenRel() {

FILE: code/Model/multir/src/edu/uw/cs/multir/main/Preprocess.java
  class Preprocess (line 10) | public class Preprocess {
    method preprocess (line 12) | public static void preprocess(String trainFile, String testFile, Strin...

FILE: code/Model/multir/src/edu/uw/cs/multir/main/ResultWriter.java
  class ResultWriter (line 19) | public class ResultWriter {
    method write (line 24) | public static void write(String dir) throws IOException {
    method eval (line 40) | public static void eval(String mappingFile, Dataset test, Parameters p...

FILE: code/Model/multir/src/edu/uw/cs/multir/main/SententialPrecisionRecallByRelation.java
  class SententialPrecisionRecallByRelation (line 14) | public class SententialPrecisionRecallByRelation {
    method run (line 19) | public static void run(String labelsFile, String resultsFile) throws I...

FILE: code/Model/multir/src/edu/uw/cs/multir/main/SententialPrecisionRecallCurve.java
  class SententialPrecisionRecallCurve (line 14) | public class SententialPrecisionRecallCurve {
    method run (line 21) | public static void run(String labelsFile, String resultsFile) throws I...
    class Example (line 140) | static class Example {
    class Label (line 149) | static class Label {

FILE: code/Model/multir/src/edu/uw/cs/multir/main/Test.java
  class Test (line 14) | public class Test {
    method test (line 16) | public static void test(String dir) throws IOException {

FILE: code/Model/multir/src/edu/uw/cs/multir/main/Train.java
  class Train (line 13) | public class Train {
    method train (line 15) | public static void train(String dir) throws IOException {

FILE: code/Model/multir/src/edu/uw/cs/multir/preprocess/ConvertProtobufToMILDocument.java
  class ConvertProtobufToMILDocument (line 19) | public class ConvertProtobufToMILDocument {
    method main (line 21) | public static void main(String[] args) throws IOException {
    method convert (line 32) | public static void convert(String input, String output, String mapping...

FILE: code/Model/multir/src/edu/uw/cs/multir/preprocess/Mappings.java
  class Mappings (line 17) | public class Mappings {
    method getRelationID (line 22) | public int getRelationID(String relation, boolean addNew) {
    method getRel2RelID (line 32) | public Map<String,Integer> getRel2RelID() {
    method getFeatureID (line 36) | public int getFeatureID(String feature, boolean addNew) {
    method numRelations (line 46) | public int numRelations() {
    method numFeatures (line 50) | public int numFeatures() {
    method write (line 54) | public void write(String file) throws IOException {
    method read (line 62) | public void read(String file) throws IOException {
    method writeMap (line 70) | private void writeMap(Map<String,Integer> m, BufferedWriter w)
    method readMap (line 82) | private void readMap(Map<String,Integer> m, BufferedReader r)

FILE: code/Model/multir/src/edu/uw/cs/multir/util/DenseVector.java
  class DenseVector (line 9) | public class DenseVector {
    method DenseVector (line 13) | public DenseVector(int length) {
    method dotProduct (line 17) | public double dotProduct(SparseBinaryVector v) {
    method reset (line 21) | public void reset() {
    method dotProduct (line 25) | public static double dotProduct(DenseVector v1, SparseBinaryVector v2) {
    method copy (line 33) | public DenseVector copy() {
    method scale (line 39) | public void scale(float factor) {
    method addSparse (line 44) | public void addSparse(SparseBinaryVector v, double factor) {
    method sum (line 49) | public static DenseVector sum(DenseVector v1, DenseVector v2, double f...
    method scale (line 56) | public static DenseVector scale(DenseVector v, float factor) {
    method serialize (line 62) | public void serialize(OutputStream os)
    method deserialize (line 71) | public void deserialize(InputStream is)
    method sum (line 81) | public DenseVector sum(DenseVector v, float factor) {

FILE: code/Model/multir/src/edu/uw/cs/multir/util/SparseBinaryVector.java
  class SparseBinaryVector (line 9) | public class SparseBinaryVector {
    method SparseBinaryVector (line 13) | public SparseBinaryVector() {
    method SparseBinaryVector (line 18) | public SparseBinaryVector(int[] ids, int num) {
    method reset (line 23) | public void reset() {
    method copy (line 27) | public SparseBinaryVector copy() {
    method dotProduct (line 33) | public double dotProduct(SparseBinaryVector v) {
    method serialize (line 50) | public void serialize(OutputStream os)
    method deserialize (line 59) | public void deserialize(InputStream is)
    method toString (line 69) | public String toString() {

FILE: code/Model/pte/line.cpp
  function TrainModel (line 53) | void TrainModel() {
  function ArgPos (line 86) | int ArgPos(char *str, int argc, char **argv) {
  function main (line 98) | int main(int argc, char **argv) {

FILE: code/Model/pte/linelib.cpp
  function real (line 32) | real *line_node::get_vector()
  type struct_node (line 37) | struct struct_node
  type struct_node (line 70) | struct struct_node
  type struct_node (line 70) | struct struct_node

FILE: code/Model/pte/linelib.h
  type real (line 14) | typedef float real;
  type Eigen (line 16) | typedef Eigen::Matrix< real, Eigen::Dynamic,
  type Eigen (line 20) | typedef Eigen::Matrix< real, 1, Eigen::Dynamic,
  type struct_node (line 24) | struct struct_node {
  function class (line 31) | class line_node
  function class (line 54) | class line_link

FILE: code/Model/pte/pte-hete.cpp
  function TrainModel (line 57) | void TrainModel() {
  function ArgPos (line 105) | int ArgPos(char *str, int argc, char **argv) {
  function main (line 117) | int main(int argc, char **argv) {

FILE: code/Model/pte/ransampl.c
  function ransampl_ws (line 23) | ransampl_ws* ransampl_alloc( integer n )
  function ransampl_set (line 39) | void ransampl_set( ransampl_ws *ws, double* p )
  function integer (line 107) | integer ransampl_draw( ransampl_ws *ws, double ran1, double ran2 )
  function ransampl_free (line 114) | void ransampl_free( ransampl_ws *ws )

FILE: code/Model/pte/ransampl.h
  type ransampl_ws (line 30) | typedef struct {

FILE: code/Model/retype/hplelib.cpp
  function real (line 3) | real sigmoid(real x)
  function real (line 40) | real *line_node::get_vector()
  type struct_node (line 45) | struct struct_node
  type struct_node (line 78) | struct struct_node
  type struct_node (line 78) | struct struct_node

FILE: code/Model/retype/hplelib.h
  type real (line 16) | typedef float real;
  type Eigen (line 18) | typedef Eigen::Matrix< real, Eigen::Dynamic,
  type Eigen (line 22) | typedef Eigen::Matrix< real, 1, Eigen::Dynamic,
  type struct_node (line 26) | struct struct_node {
  type struct_neighbor (line 31) | struct struct_neighbor {
  type triple (line 36) | struct triple
  function class (line 53) | class line_node
  function class (line 81) | class line_link
  function class (line 111) | class line_triple

FILE: code/Model/retype/ransampl.c
  function ransampl_ws (line 23) | ransampl_ws* ransampl_alloc( integer n )
  function ransampl_set (line 39) | void ransampl_set( ransampl_ws *ws, double* p )
  function integer (line 107) | integer ransampl_draw( ransampl_ws *ws, double ran1, double ran2 )
  function ransampl_free (line 114) | void ransampl_free( ransampl_ws *ws )

FILE: code/Model/retype/ransampl.h
  type ransampl_ws (line 30) | typedef struct {

FILE: code/Model/retype/retype-rm.cpp
  function func_rand_num (line 27) | double func_rand_num()
  function TrainModel (line 119) | void TrainModel() {
  function ArgPos (line 205) | int ArgPos(char *str, int argc, char **argv) {
  function main (line 217) | int main(int argc, char **argv) {

FILE: code/Model/retype/retype.cpp
  function func_rand_num (line 34) | double func_rand_num()
  function TrainModel (line 175) | void TrainModel() {
  function ArgPos (line 307) | int ArgPos(char *str, int argc, char **argv) {
  function main (line 319) | int main(int argc, char **argv) {

FILE: code/Model/seq-kernel/libsvm/java/libsvm/svm.java
  class Cache (line 16) | class Cache {
    class head_t (line 19) | private final class head_t
    method Cache (line 28) | Cache(int l_, long size_)
    method lru_delete (line 41) | private void lru_delete(head_t h)
    method lru_insert (line 48) | private void lru_insert(head_t h)
    method get_data (line 61) | int get_data(int index, float[][] data, int len)
    method swap_index (line 92) | void swap_index(int i, int j)
  class QMatrix (line 130) | abstract class QMatrix {
    method get_Q (line 131) | abstract float[] get_Q(int column, int len);
    method get_QD (line 132) | abstract double[] get_QD();
    method swap_index (line 133) | abstract void swap_index(int i, int j);
  class Kernel (line 136) | abstract class Kernel extends QMatrix {
    method get_Q (line 146) | abstract float[] get_Q(int column, int len);
    method get_QD (line 147) | abstract double[] get_QD();
    method swap_index (line 149) | void swap_index(int i, int j)
    method powi (line 155) | private static double powi(double base, int times)
    method kernel_function (line 167) | double kernel_function(int i, int j)
    method Kernel (line 186) | Kernel(int l, svm_node[][] x_, svm_parameter param)
    method dot (line 204) | static double dot(svm_node[] x, svm_node[] y)
    method k_function (line 226) | static double k_function(svm_node[] x, svm_node[] y,
  class Solver (line 303) | class Solver {
    method get_C (line 324) | double get_C(int i)
    method update_alpha_status (line 328) | void update_alpha_status(int i)
    method is_upper_bound (line 336) | boolean is_upper_bound(int i) { return alpha_status[i] == UPPER_BOUND; }
    method is_lower_bound (line 337) | boolean is_lower_bound(int i) { return alpha_status[i] == LOWER_BOUND; }
    method is_free (line 338) | boolean is_free(int i) {  return alpha_status[i] == FREE; }
    class SolutionInfo (line 342) | static class SolutionInfo {
    method swap_index (line 350) | void swap_index(int i, int j)
    method reconstruct_gradient (line 362) | void reconstruct_gradient()
    method Solve (line 404) | void Solve(int l, QMatrix Q, double[] p_, byte[] y_,
    method select_working_set (line 673) | int select_working_set(int[] working_set)
    method be_shrunk (line 772) | private boolean be_shrunk(int i, double Gmax1, double Gmax2)
    method do_shrinking (line 792) | void do_shrinking()
    method calculate_rho (line 852) | double calculate_rho()
  class Solver_NU (line 897) | final class Solver_NU extends Solver
    method Solve (line 901) | void Solve(int l, QMatrix Q, double[] p, byte[] y,
    method select_working_set (line 910) | int select_working_set(int[] working_set)
    method be_shrunk (line 1022) | private boolean be_shrunk(int i, double Gmax1, double Gmax2, double Gm...
    method do_shrinking (line 1042) | void do_shrinking()
    method calculate_rho (line 1094) | double calculate_rho()
  class SVC_Q (line 1148) | class SVC_Q extends Kernel
    method SVC_Q (line 1154) | SVC_Q(svm_problem prob, svm_parameter param, byte[] y_)
    method get_Q (line 1164) | float[] get_Q(int i, int len)
    method get_QD (line 1176) | double[] get_QD()
    method swap_index (line 1181) | void swap_index(int i, int j)
  class ONE_CLASS_Q (line 1190) | class ONE_CLASS_Q extends Kernel
    method ONE_CLASS_Q (line 1195) | ONE_CLASS_Q(svm_problem prob, svm_parameter param)
    method get_Q (line 1204) | float[] get_Q(int i, int len)
    method get_QD (line 1216) | double[] get_QD()
    method swap_index (line 1221) | void swap_index(int i, int j)
  class SVR_Q (line 1229) | class SVR_Q extends Kernel
    method SVR_Q (line 1239) | SVR_Q(svm_problem prob, svm_parameter param)
    method swap_index (line 1260) | void swap_index(int i, int j)
    method get_Q (line 1267) | float[] get_Q(int i, int len)
    method get_QD (line 1286) | double[] get_QD()
  class svm (line 1292) | public class svm {
    method print (line 1301) | public void print(String s)
    method info (line 1310) | static void info(String s)
    method solve_c_svc (line 1315) | private static void solve_c_svc(svm_problem prob, svm_parameter param,
    method solve_nu_svc (line 1347) | private static void solve_nu_svc(svm_problem prob, svm_parameter param,
    method solve_one_class (line 1398) | private static void solve_one_class(svm_problem prob, svm_parameter pa...
    method solve_epsilon_svr (line 1426) | private static void solve_epsilon_svr(svm_problem prob, svm_parameter ...
    method solve_nu_svr (line 1459) | private static void solve_nu_svr(svm_problem prob, svm_parameter param,
    class decision_function (line 1495) | static class decision_function
    method svm_train_one (line 1501) | static decision_function svm_train_one(
    method sigmoid_train (line 1559) | private static void sigmoid_train(int l, double[] dec_values, double[]...
    method sigmoid_predict (line 1672) | private static double sigmoid_predict(double decision_value, double A,...
    method multiclass_probability (line 1682) | private static void multiclass_probability(int k, double[][] r, double...
    method svm_binary_svc_probability (line 1742) | private static void svm_binary_svc_probability(svm_problem prob, svm_p...
    method svm_svr_probability (line 1823) | private static double svm_svr_probability(svm_problem prob, svm_parame...
    method svm_group_classes (line 1854) | private static void svm_group_classes(svm_problem prob, int[] nr_class...
    method svm_train (line 1935) | public static svm_model svm_train(svm_problem prob, svm_parameter param)
    method svm_cross_validation (line 2172) | public static void svm_cross_validation(svm_problem prob, svm_paramete...
    method svm_get_svm_type (line 2282) | public static int svm_get_svm_type(svm_model model)
    method svm_get_nr_class (line 2287) | public static int svm_get_nr_class(svm_model model)
    method svm_get_labels (line 2292) | public static void svm_get_labels(svm_model model, int[] label)
    method svm_get_sv_indices (line 2299) | public static void svm_get_sv_indices(svm_model model, int[] indices)
    method svm_get_nr_sv (line 2306) | public static int svm_get_nr_sv(svm_model model)
    method svm_get_svr_probability (line 2311) | public static double svm_get_svr_probability(svm_model model)
    method svm_predict_values (line 2323) | public static double svm_predict_values(svm_model model, svm_node[] x,...
    method svm_predict (line 2396) | public static double svm_predict(svm_model model, svm_node[] x)
    method svm_predict_probability (line 2410) | public static double svm_predict_probability(svm_model model, svm_node...
    method svm_save_model (line 2453) | public static void svm_save_model(String model_file_name, svm_model mo...
    method atof (line 2538) | private static double atof(String s)
    method atoi (line 2543) | private static int atoi(String s)
    method read_model_header (line 2548) | private static boolean read_model_header(BufferedReader fp, svm_model ...
    method svm_load_model (line 2661) | public static svm_model svm_load_model(String model_file_name) throws ...
    method svm_load_model (line 2666) | public static svm_model svm_load_model(BufferedReader fp) throws IOExc...
    method svm_check_parameter (line 2711) | public static String svm_check_parameter(svm_problem prob, svm_paramet...
    method svm_check_probability_model (line 2831) | public static int svm_check_probability_model(svm_model model)
    method svm_set_print_string_function (line 2842) | public static void svm_set_print_string_function(svm_print_interface p...

FILE: code/Model/seq-kernel/libsvm/java/libsvm/svm_model.java
  class svm_model (line 5) | public class svm_model implements java.io.Serializable

FILE: code/Model/seq-kernel/libsvm/java/libsvm/svm_node.java
  class svm_node (line 2) | public class svm_node implements java.io.Serializable

FILE: code/Model/seq-kernel/libsvm/java/libsvm/svm_parameter.java
  class svm_parameter (line 2) | public class svm_parameter implements Cloneable,java.io.Serializable
    method clone (line 36) | public Object clone()

FILE: code/Model/seq-kernel/libsvm/java/libsvm/svm_print_interface.java
  type svm_print_interface (line 2) | public interface svm_print_interface
    method print (line 4) | public void print(String s);

FILE: code/Model/seq-kernel/libsvm/java/libsvm/svm_problem.java
  class svm_problem (line 2) | public class svm_problem implements java.io.Serializable

FILE: code/Model/seq-kernel/libsvm/java/svm_predict.java
  class svm_predict (line 5) | class svm_predict {
    method print (line 8) | public void print(String s) {}
    method print (line 13) | public void print(String s)
    method info (line 21) | static void info(String s)
    method atof (line 26) | private static double atof(String s)
    method atoi (line 31) | private static int atoi(String s)
    method predict (line 36) | private static void predict(BufferedReader input, DataOutputStream out...
    method exit_with_help (line 121) | private static void exit_with_help()
    method main (line 130) | public static void main(String argv[]) throws IOException

FILE: code/Model/seq-kernel/libsvm/java/svm_scale.java
  class svm_scale (line 6) | class svm_scale
    method exit_with_help (line 22) | private static void exit_with_help()
    method rewind (line 36) | private BufferedReader rewind(BufferedReader fp, String filename) thro...
    method output_target (line 42) | private void output_target(double value)
    method output (line 58) | private void output(int index, double value)
    method readline (line 80) | private String readline(BufferedReader fp) throws IOException
    method run (line 86) | private void run(String []argv) throws IOException
    method main (line 345) | public static void main(String argv[]) throws IOException

FILE: code/Model/seq-kernel/libsvm/java/svm_toy.java
  class svm_toy (line 8) | public class svm_toy extends Applet {
    class point (line 32) | class point {
      method point (line 33) | point(double x, double y, byte value)
    method init (line 46) | public void init()
    method draw_point (line 114) | void draw_point(point p)
    method clear_all (line 125) | void clear_all()
    method draw_all_points (line 136) | void draw_all_points()
    method button_change_clicked (line 143) | void button_change_clicked()
    method atof (line 149) | private static double atof(String s)
    method atoi (line 154) | private static int atoi(String s)
    method button_run_clicked (line 159) | void button_run_clicked(String args)
    method button_clear_clicked (line 366) | void button_clear_clicked()
    method button_save_clicked (line 371) | void button_save_clicked(String args)
    method button_load_clicked (line 409) | void button_load_clicked()
    method processMouseEvent (line 445) | protected void processMouseEvent(MouseEvent e)
    method paint (line 458) | public void paint(Graphics g)
    method getPreferredSize (line 470) | public Dimension getPreferredSize() { return new Dimension(XLEN,YLEN+5...
    method setSize (line 472) | public void setSize(Dimension d) { setSize(d.width,d.height); }
    method setSize (line 473) | public void setSize(int w,int h) {
    method main (line 480) | public static void main(String[] argv)
  class AppletFrame (line 486) | class AppletFrame extends Frame {
    method AppletFrame (line 487) | AppletFrame(String title, Applet applet, int width, int height)

FILE: code/Model/seq-kernel/libsvm/java/svm_train.java
  class svm_train (line 5) | class svm_train {
    method print (line 17) | public void print(String s) {}
    method exit_with_help (line 20) | private static void exit_with_help()
    method do_cross_validation (line 54) | private void do_cross_validation()
    method run (line 92) | private void run(String argv[]) throws IOException
    method main (line 115) | public static void main(String argv[]) throws IOException
    method atof (line 121) | private static double atof(String s)
    method atoi (line 132) | private static int atoi(String s)
    method parse_command_line (line 137) | private void parse_command_line(String argv[])
    method read_problem (line 262) | private void read_problem() throws IOException

FILE: code/Model/seq-kernel/libsvm/matlab/libsvmread.c
  type mwIndex (line 11) | typedef int mwIndex;
  function exit_with_help (line 21) | void exit_with_help()
  function fake_answer (line 28) | static void fake_answer(int nlhs, mxArray *plhs[])
  function read_problem (line 57) | void read_problem(const char *filename, int nlhs, mxArray *plhs[])
  function mexFunction (line 188) | void mexFunction( int nlhs, mxArray *plhs[],

FILE: code/Model/seq-kernel/libsvm/matlab/libsvmwrite.c
  type mwIndex (line 8) | typedef int mwIndex;
  function exit_with_help (line 12) | void exit_with_help()
  function fake_answer (line 19) | static void fake_answer(int nlhs, mxArray *plhs[])
  function libsvmwrite (line 26) | void libsvmwrite(const char *filename, const mxArray *label_vec, const m...
  function mexFunction (line 84) | void mexFunction( int nlhs, mxArray *plhs[],

FILE: code/Model/seq-kernel/libsvm/matlab/svm_model_matlab.c
  type mwIndex (line 9) | typedef int mwIndex;
  type svm_model (line 31) | struct svm_model
  type svm_model (line 211) | struct svm_model
  type svm_node (line 216) | struct svm_node
  type svm_model (line 217) | struct svm_model
  type svm_node (line 351) | struct svm_node
  type svm_node (line 351) | struct svm_node
  type svm_node (line 352) | struct svm_node
  type svm_node (line 352) | struct svm_node

FILE: code/Model/seq-kernel/libsvm/matlab/svm_model_matlab.h
  type svm_model (line 1) | struct svm_model
  type svm_model (line 2) | struct svm_model

FILE: code/Model/seq-kernel/libsvm/matlab/svmpredict.c
  type mwIndex (line 11) | typedef int mwIndex;
  function print_null (line 17) | int print_null(const char *s,...) {}
  function read_sparse_instance (line 20) | void read_sparse_instance(const mxArray *prhs, int index, struct svm_nod...
  function fake_answer (line 42) | static void fake_answer(int nlhs, mxArray *plhs[])
  function predict (line 49) | void predict(int nlhs, mxArray *plhs[], const mxArray *prhs[], struct sv...
  function exit_with_help (line 255) | void exit_with_help()
  function mexFunction (line 272) | void mexFunction( int nlhs, mxArray *plhs[],

FILE: code/Model/seq-kernel/libsvm/matlab/svmtrain.c
  type mwIndex (line 12) | typedef int mwIndex;
  function print_null (line 19) | void print_null(const char *s) {}
  function print_string_matlab (line 20) | void print_string_matlab(const char *s) {mexPrintf(s);}
  function exit_with_help (line 22) | void exit_with_help()
  type svm_parameter (line 56) | struct svm_parameter
  type svm_problem (line 57) | struct svm_problem
  type svm_model (line 58) | struct svm_model
  type svm_node (line 59) | struct svm_node
  function do_cross_validation (line 64) | double do_cross_validation()
  function parse_command_line (line 108) | int parse_command_line(int nrhs, const mxArray *prhs[], char *model_file...
  function read_problem_dense (line 222) | int read_problem_dense(const mxArray *label_vec, const mxArray *instance...
  function read_problem_sparse (line 302) | int read_problem_sparse(const mxArray *label_vec, const mxArray *instanc...
  function fake_answer (line 375) | static void fake_answer(int nlhs, mxArray *plhs[])
  function mexFunction (line 384) | void mexFunction( int nlhs, mxArray *plhs[],

FILE: code/Model/seq-kernel/libsvm/python/svm.py
  function print_null (line 45) | def print_null(s):
  function genFields (line 48) | def genFields(names, types):
  function fillprototype (line 51) | def fillprototype(f, restype, argtypes):
  class svm_node (line 55) | class svm_node(Structure):
    method __str__ (line 60) | def __str__(self):
  function gen_svm_nodearray (line 63) | def gen_svm_nodearray(xi, feature_max=None, isKernel=None):
  class svm_problem (line 90) | class svm_problem(Structure):
    method __init__ (line 95) | def __init__(self, y, x, isKernel=None):
  class svm_parameter (line 114) | class svm_parameter(Structure):
    method __init__ (line 123) | def __init__(self, options = None):
    method __str__ (line 128) | def __str__(self):
    method set_to_default_values (line 138) | def set_to_default_values(self):
    method parse_options (line 158) | def parse_options(self, options):
  class svm_model (line 232) | class svm_model(Structure):
    method __init__ (line 241) | def __init__(self):
    method __del__ (line 244) | def __del__(self):
    method get_svm_type (line 249) | def get_svm_type(self):
    method get_nr_class (line 252) | def get_nr_class(self):
    method get_svr_probability (line 255) | def get_svr_probability(self):
    method get_labels (line 258) | def get_labels(self):
    method get_sv_indices (line 264) | def get_sv_indices(self):
    method get_nr_sv (line 270) | def get_nr_sv(self):
    method is_probability_model (line 273) | def is_probability_model(self):
    method get_sv_coef (line 276) | def get_sv_coef(self):
    method get_SV (line 280) | def get_SV(self):
  function toPyModel (line 295) | def toPyModel(model_ptr):

FILE: code/Model/seq-kernel/libsvm/python/svmutil.py
  function svm_read_problem (line 14) | def svm_read_problem(data_file_name):
  function svm_load_model (line 36) | def svm_load_model(model_file_name):
  function svm_save_model (line 49) | def svm_save_model(model_file_name, model):
  function evaluations (line 57) | def evaluations(ty, pv):
  function svm_train (line 86) | def svm_train(arg1, arg2=None, arg3=None):
  function svm_predict (line 173) | def svm_predict(y, x, m, options=""):

FILE: code/Model/seq-kernel/libsvm/svm-predict.c
  function print_null (line 8) | int print_null(const char *s,...) {return 0;}
  type svm_node (line 12) | struct svm_node
  type svm_model (line 15) | struct svm_model
  function exit_input_error (line 39) | void exit_input_error(int line_num)
  function predict (line 45) | void predict(FILE *input, FILE *output)
  function exit_with_help (line 159) | void exit_with_help()
  function main (line 170) | int main(int argc, char **argv)

FILE: code/Model/seq-kernel/libsvm/svm-scale.c
  function exit_with_help (line 7) | void exit_with_help()
  function main (line 42) | int main(int argc,char **argv)
  function output_target (line 350) | void output_target(double value)
  function output (line 364) | void output(int index, double value)
  function clean_up (line 386) | int clean_up(FILE *fp_restore, FILE *fp, const char* msg)

FILE: code/Model/seq-kernel/libsvm/svm-toy/gtk/callbacks.cpp
  function svm_toy_initialize (line 42) | void svm_toy_initialize()
  function redraw_area (line 61) | void redraw_area(GtkWidget* widget, int x, int y, int w, int h)
  function draw_point (line 69) | void draw_point(const point& p)
  function draw_all_points (line 76) | void draw_all_points()
  function clear_all (line 82) | void clear_all()
  function on_button_change_clicked (line 90) | void
  function on_button_run_clicked (line 98) | void
  function on_button_clear_clicked (line 302) | void
  function on_window1_destroy (line 309) | void
  function gboolean (line 316) | gboolean
  function gboolean (line 327) | gboolean
  function show_fileselection (line 341) | void show_fileselection()
  function on_button_save_clicked (line 357) | void
  function on_button_load_clicked (line 366) | void
  function on_filesel_ok_clicked (line 374) | void
  function on_fileselection_destroy (line 437) | void
  function on_filesel_cancel_clicked (line 443) | void

FILE: code/Model/seq-kernel/libsvm/svm-toy/gtk/interface.c
  function GtkWidget (line 16) | GtkWidget*
  function GtkWidget (line 130) | GtkWidget*

FILE: code/Model/seq-kernel/libsvm/svm-toy/gtk/main.c
  function main (line 10) | int main (int argc, char *argv[])

FILE: code/Model/seq-kernel/libsvm/svm-toy/qt/svm-toy.cpp
  class SvmToyWindow (line 25) | class SvmToyWindow : public QWidget
    type point (line 49) | struct point {
    method QPixmap (line 55) | const QPixmap& choose_icon(int v)
    method clear_all (line 61) | void clear_all()
    method draw_point (line 67) | void draw_point(const point& p)
    method draw_all_points (line 73) | void draw_all_points()
    method button_change_icon_clicked (line 79) | void button_change_icon_clicked()
    method button_run_clicked (line 85) | void button_run_clicked()
    method button_clear_clicked (line 280) | void button_clear_clicked()
    method button_save_clicked (line 284) | void button_save_clicked()
    method button_load_clicked (line 313) | void button_load_clicked()
  function main (line 428) | int main( int argc, char* argv[] )

FILE: code/Model/seq-kernel/libsvm/svm-toy/windows/svm-toy.cpp
  type point (line 48) | struct point {
  function WinMain (line 58) | int WINAPI WinMain(HINSTANCE hInstance, HINSTANCE hPrevInstance,
  function getfilename (line 128) | int getfilename( HWND hWnd , char *filename, int len, int save)
  function clear_all (line 143) | void clear_all()
  function HBRUSH (line 150) | HBRUSH choose_brush(int v)
  function draw_point (line 157) | void draw_point(const point & p)
  function draw_all_points (line 168) | void draw_all_points()
  function button_run_clicked (line 174) | void button_run_clicked()
  function LRESULT (line 372) | LRESULT CALLBACK WndProc(HWND hwnd, UINT iMsg, WPARAM wParam, LPARAM lPa...

FILE: code/Model/seq-kernel/libsvm/svm-train.c
  function print_null (line 9) | void print_null(const char *s) {}
  function exit_with_help (line 11) | void exit_with_help()
  function exit_input_error (line 45) | void exit_input_error(int line_num)
  type svm_parameter (line 55) | struct svm_parameter
  type svm_problem (line 56) | struct svm_problem
  type svm_model (line 57) | struct svm_model
  type svm_node (line 58) | struct svm_node
  function main (line 83) | int main(int argc, char **argv)
  function do_cross_validation (line 122) | void do_cross_validation()
  function parse_command_line (line 161) | void parse_command_line(int argc, char **argv, char *input_file_name, ch...
  function read_problem (line 278) | void read_problem(const char *filename)

FILE: code/Model/seq-kernel/libsvm/svm.cpp
  function T (line 15) | static inline T min(T x,T y) { return (x<y)?x:y; }
  function T (line 18) | static inline T max(T x,T y) { return (x>y)?x:y; }
  function swap (line 20) | static inline void swap(T& x, T& y) { T t=x; x=y; y=t; }
  function clone (line 21) | static inline void clone(T*& dst, S* src, int n)
  function powi (line 26) | static inline double powi(double base, int times)
  function print_string_stdout (line 41) | static void print_string_stdout(const char *s)
  function info (line 48) | static void info(const char *fmt,...)
  function info (line 58) | static void info(const char *fmt,...) {}
  class Cache (line 67) | class Cache
    type head_t (line 81) | struct head_t
  class QMatrix (line 194) | class QMatrix {
  class Kernel (line 202) | class Kernel: public QMatrix {
    method swap_index (line 211) | virtual void swap_index(int i, int j) const	// no so const...
    method kernel_linear (line 231) | double kernel_linear(int i, int j) const
    method kernel_poly (line 235) | double kernel_poly(int i, int j) const
    method kernel_rbf (line 239) | double kernel_rbf(int i, int j) const
    method kernel_sigmoid (line 243) | double kernel_sigmoid(int i, int j) const
    method kernel_precomputed (line 247) | double kernel_precomputed(int i, int j) const
  class Solver (line 393) | class Solver {
    method Solver (line 395) | Solver() {}
    type SolutionInfo (line 398) | struct SolutionInfo {
    method get_C (line 426) | double get_C(int i)
    method update_alpha_status (line 430) | void update_alpha_status(int i)
    method is_upper_bound (line 438) | bool is_upper_bound(int i) { return alpha_status[i] == UPPER_BOUND; }
    method is_lower_bound (line 439) | bool is_lower_bound(int i) { return alpha_status[i] == LOWER_BOUND; }
    method is_free (line 440) | bool is_free(int i) { return alpha_status[i] == FREE; }
  class Solver_NU (line 1009) | class Solver_NU: public Solver
    method Solver_NU (line 1012) | Solver_NU() {}
    method Solve (line 1013) | void Solve(int l, const QMatrix& Q, const double *p, const schar *y,
  class SVC_Q (line 1266) | class SVC_Q: public Kernel
    method SVC_Q (line 1269) | SVC_Q(const svm_problem& prob, const svm_parameter& param, const schar...
    method Qfloat (line 1279) | Qfloat *get_Q(int i, int len) const
    method swap_index (line 1296) | void swap_index(int i, int j) const
  class ONE_CLASS_Q (line 1316) | class ONE_CLASS_Q: public Kernel
    method ONE_CLASS_Q (line 1319) | ONE_CLASS_Q(const svm_problem& prob, const svm_parameter& param)
    method Qfloat (line 1328) | Qfloat *get_Q(int i, int len) const
    method swap_index (line 1345) | void swap_index(int i, int j) const
  class SVR_Q (line 1362) | class SVR_Q: public Kernel
    method SVR_Q (line 1365) | SVR_Q(const svm_problem& prob, const svm_parameter& param)
    method swap_index (line 1387) | void swap_index(int i, int j) const
    method Qfloat (line 1394) | Qfloat *get_Q(int i, int len) const
  function solve_c_svc (line 1440) | static void solve_c_svc(
  function solve_nu_svc (line 1475) | static void solve_nu_svc(
  function solve_one_class (line 1530) | static void solve_one_class(
  function solve_epsilon_svr (line 1562) | static void solve_epsilon_svr(
  function solve_nu_svr (line 1600) | static void solve_nu_svr(
  type decision_function (line 1641) | struct decision_function
  function decision_function (line 1647) | static decision_function svm_train_one(
  function sigmoid_train (line 1705) | static void sigmoid_train(
  function sigmoid_predict (line 1818) | static double sigmoid_predict(double decision_value, double A, double B)
  function multiclass_probability (line 1829) | static void multiclass_probability(int k, double **r, double *p)
  function svm_binary_svc_probability (line 1893) | static void svm_binary_svc_probability(
  function svm_svr_probability (line 1980) | static double svm_svr_probability(
  function svm_group_classes (line 2014) | static void svm_group_classes(const svm_problem *prob, int *nr_class_ret...
  function svm_model (line 2092) | svm_model *svm_train(const svm_problem *prob, const svm_parameter *param)
  function svm_cross_validation (line 2339) | void svm_cross_validation(const svm_problem *prob, const svm_parameter *...
  function svm_get_svm_type (line 2460) | int svm_get_svm_type(const svm_model *model)
  function svm_get_nr_class (line 2465) | int svm_get_nr_class(const svm_model *model)
  function svm_get_labels (line 2470) | void svm_get_labels(const svm_model *model, int* label)
  function svm_get_sv_indices (line 2477) | void svm_get_sv_indices(const svm_model *model, int* indices)
  function svm_get_nr_sv (line 2484) | int svm_get_nr_sv(const svm_model *model)
  function svm_get_svr_probability (line 2489) | double svm_get_svr_probability(const svm_model *model)
  function svm_predict_values (line 2501) | double svm_predict_values(const svm_model *model, const svm_node *x, dou...
  function svm_predict (line 2577) | double svm_predict(const svm_model *model, const svm_node *x)
  function svm_predict_probability (line 2592) | double svm_predict_probability(
  function svm_save_model (line 2641) | int svm_save_model(const char *model_file_name, const svm_model *model)
  function read_model_header (line 2767) | bool read_model_header(FILE *fp, svm_model* model)
  function svm_model (line 2876) | svm_model *svm_load_model(const char *model_file_name)
  function svm_free_model_content (line 2984) | void svm_free_model_content(svm_model* model_ptr)
  function svm_free_and_destroy_model (line 3019) | void svm_free_and_destroy_model(svm_model** model_ptr_ptr)
  function svm_destroy_param (line 3029) | void svm_destroy_param(svm_parameter* param)
  function svm_check_probability_model (line 3156) | int svm_check_probability_model(const svm_model *model)
  function svm_set_print_string_function (line 3164) | void svm_set_print_string_function(void (*print_func)(const char *))

FILE: code/Model/seq-kernel/libsvm/svm.h
  type svm_node (line 12) | struct svm_node
  type svm_problem (line 18) | struct svm_problem
  type svm_parameter (line 28) | struct svm_parameter
  type svm_model (line 52) | struct svm_model
  type svm_model (line 74) | struct svm_model
  type svm_problem (line 74) | struct svm_problem
  type svm_parameter (line 74) | struct svm_parameter
  type svm_problem (line 75) | struct svm_problem
  type svm_parameter (line 75) | struct svm_parameter
  type svm_model (line 77) | struct svm_model
  type svm_model (line 78) | struct svm_model
  type svm_model (line 80) | struct svm_model
  type svm_model (line 81) | struct svm_model
  type svm_model (line 82) | struct svm_model
  type svm_model (line 83) | struct svm_model
  type svm_model (line 84) | struct svm_model
  type svm_model (line 85) | struct svm_model
  type svm_model (line 87) | struct svm_model
  type svm_node (line 87) | struct svm_node
  type svm_model (line 88) | struct svm_model
  type svm_node (line 88) | struct svm_node
  type svm_model (line 89) | struct svm_model
  type svm_node (line 89) | struct svm_node
  type svm_model (line 91) | struct svm_model
  type svm_model (line 92) | struct svm_model
  type svm_parameter (line 93) | struct svm_parameter
  type svm_problem (line 95) | struct svm_problem
  type svm_parameter (line 95) | struct svm_parameter
  type svm_model (line 96) | struct svm_model

FILE: code/Model/seq-kernel/libsvm/tools/checkdata.py
  function err (line 18) | def err(line_no, msg):
  function my_float (line 22) | def my_float(x):
  function main (line 28) | def main():

FILE: code/Model/seq-kernel/libsvm/tools/grid.py
  class GridOption (line 17) | class GridOption:
    method __init__ (line 18) | def __init__(self, dataset_pathname, options):
    method parse_options (line 40) | def parse_options(self, options):
  function redraw (line 105) | def redraw(db,best_param,gnuplot,options,tofile=False):
  function calculate_jobs (line 159) | def calculate_jobs(options):
  class WorkerStopToken (line 241) | class WorkerStopToken:  # used to notify the worker to stop or if a work...
  class Worker (line 244) | class Worker(Thread):
    method __init__ (line 245) | def __init__(self,name,job_queue,result_queue,options):
    method run (line 252) | def run(self):
    method get_cmd (line 278) | def get_cmd(self,c,g):
  class LocalWorker (line 289) | class LocalWorker(Worker):
    method run_one (line 290) | def run_one(self,c,g):
  class SSHWorker (line 297) | class SSHWorker(Worker):
    method __init__ (line 298) | def __init__(self,name,job_queue,result_queue,host,options):
    method run_one (line 302) | def run_one(self,c,g):
  class TelnetWorker (line 310) | class TelnetWorker(Worker):
    method __init__ (line 311) | def __init__(self,name,job_queue,result_queue,host,username,password,o...
    method run (line 316) | def run(self):
    method run_one (line 331) | def run_one(self,c,g):
  function find_parameters (line 339) | def find_parameters(dataset_pathname, options=''):
  function exit_with_help (line 465) | def exit_with_help():

FILE: code/Model/seq-kernel/libsvm/tools/subset.py
  function exit_with_help (line 9) | def exit_with_help(argv):
  function process_options (line 25) | def process_options(argv):
  function random_selection (line 56) | def random_selection(dataset, subset_size):
  function stratified_selection (line 60) | def stratified_selection(dataset, subset_size):
  function main (line 89) | def main(argv=sys.argv):

FILE: code/Model/seq-kernel/ssk_core/libsvm/CustomKernel.java
  class CustomKernel (line 3) | public abstract class CustomKernel
    method kernel (line 5) | abstract public double kernel(svm_node[] x, svm_node[] y);
    method new_svm_node (line 6) | abstract public svm_node new_svm_node();

FILE: code/Model/seq-kernel/ssk_core/libsvm/svm.java
  class Cache (line 11) | class Cache {
    class head_t (line 14) | private final class head_t
    method Cache (line 23) | Cache(int l_, int size_)
    method lru_delete (line 35) | private void lru_delete(head_t h)
    method lru_insert (line 42) | private void lru_insert(head_t h)
    method get_data (line 55) | int get_data(int index, float[][] data, int len)
    method swap_index (line 86) | void swap_index(int i, int j)
  class QMatrix (line 124) | abstract class QMatrix {
    method get_Q (line 125) | abstract float[] get_Q(int column, int len);
    method swap_index (line 126) | abstract void swap_index(int i, int j);
  class Kernel (line 130) | abstract class Kernel extends QMatrix {
    method get_Q (line 140) | abstract float[] get_Q(int column, int len);
    method swap_index (line 142) | void swap_index(int i, int j)
    method tanh (line 148) | private static double tanh(double x)
    method kernel_function (line 154) | double kernel_function(int i, int j)
    method Kernel (line 173) | Kernel(int l, svm_node[][] x_, svm_parameter param)
    method dot (line 191) | static double dot(svm_node[] x, svm_node[] y)
    method k_function (line 213) | static double k_function(svm_node[] x, svm_node[] y,
  class Solver (line 292) | class Solver {
    method get_C (line 312) | double get_C(int i)
    method update_alpha_status (line 316) | void update_alpha_status(int i)
    method is_upper_bound (line 324) | boolean is_upper_bound(int i) { return alpha_status[i] == UPPER_BOUND; }
    method is_lower_bound (line 325) | boolean is_lower_bound(int i) { return alpha_status[i] == LOWER_BOUND; }
    method is_free (line 326) | boolean is_free(int i) {  return alpha_status[i] == FREE; }
    class SolutionInfo (line 330) | static class SolutionInfo {
    method swap_index (line 338) | void swap_index(int i, int j)
    method reconstruct_gradient (line 350) | void reconstruct_gradient()
    method Solve (line 370) | void Solve(int l, QMatrix Q, double[] b_, byte[] y_,
    method select_working_set (line 618) | int select_working_set(int[] working_set)
    method do_shrinking (line 680) | void do_shrinking()
    method calculate_rho (line 750) | double calculate_rho()
  class Solver_NU (line 795) | final class Solver_NU extends Solver
    method Solve (line 799) | void Solve(int l, QMatrix Q, double[] b, byte[] y,
    method select_working_set (line 807) | int select_working_set(int[] working_set)
    method do_shrinking (line 883) | void do_shrinking()
    method calculate_rho (line 974) | double calculate_rho()
  class SVC_Q (line 1028) | class SVC_Q extends Kernel
    method SVC_Q (line 1033) | SVC_Q(svm_problem prob, svm_parameter param, byte[] y_)
    method get_Q (line 1040) | float[] get_Q(int i, int len)
    method swap_index (line 1052) | void swap_index(int i, int j)
  class ONE_CLASS_Q (line 1060) | class ONE_CLASS_Q extends Kernel
    method ONE_CLASS_Q (line 1064) | ONE_CLASS_Q(svm_problem prob, svm_parameter param)
    method get_Q (line 1070) | float[] get_Q(int i, int len)
    method swap_index (line 1082) | void swap_index(int i, int j)
  class SVR_Q (line 1089) | class SVR_Q extends Kernel
    method SVR_Q (line 1098) | SVR_Q(svm_problem prob, svm_parameter param)
    method swap_index (line 1116) | void swap_index(int i, int j)
    method get_Q (line 1122) | float[] get_Q(int i, int len)
  class svm (line 1142) | public class svm {
    method setCustomKernel (line 1148) | public static void setCustomKernel(CustomKernel ck)
    method solve_c_svc (line 1156) | private static void solve_c_svc(svm_problem prob, svm_parameter param,
    method solve_nu_svc (line 1188) | private static void solve_nu_svc(svm_problem prob, svm_parameter param,
    method solve_one_class (line 1239) | private static void solve_one_class(svm_problem prob, svm_parameter pa...
    method solve_epsilon_svr (line 1266) | private static void solve_epsilon_svr(svm_problem prob, svm_parameter ...
    method solve_nu_svr (line 1299) | private static void solve_nu_svr(svm_problem prob, svm_parameter param,
    class decision_function (line 1335) | static class decision_function
    method svm_train_one (line 1341) | static decision_function svm_train_one(
    method sigmoid_train (line 1399) | private static void sigmoid_train(int l, double[] dec_values, double[]...
    method sigmoid_predict (line 1512) | private static double sigmoid_predict(double decision_value, double A,...
    method multiclass_probability (line 1522) | private static void multiclass_probability(int k, double[][] r, double...
    method svm_binary_svc_probability (line 1582) | private static void svm_binary_svc_probability(svm_problem prob, svm_p...
    method svm_svr_probability (line 1663) | private static double svm_svr_probability(svm_problem prob, svm_parame...
    method svm_group_classes (line 1694) | private static void svm_group_classes(svm_problem prob, int[] nr_class...
    method svm_train (line 1757) | public static svm_model svm_train(svm_problem prob, svm_parameter param)
    method svm_cross_validation (line 1991) | public static void svm_cross_validation(svm_problem prob, svm_paramete...
    method svm_get_svm_type (line 2100) | public static int svm_get_svm_type(svm_model model)
    method svm_get_nr_class (line 2105) | public static int svm_get_nr_class(svm_model model)
    method svm_get_labels (line 2110) | public static void svm_get_labels(svm_model model, int[] label)
    method svm_get_svr_probability (line 2117) | public static double svm_get_svr_probability(svm_model model)
    method svm_predict_values (line 2129) | public static void svm_predict_values(svm_model model, svm_node[] x, d...
    method svm_predict (line 2181) | public static double svm_predict(svm_model model, svm_node[] x)
    method svm_predict_probability (line 2223) | public static double svm_predict_probability(svm_model model, svm_node...
    method svm_save_model (line 2266) | public static void svm_save_model(String model_file_name, svm_model mo...
    method atof (line 2347) | public static double atof(String s)
    method atoi (line 2352) | public static int atoi(String s)
    method svm_load_model (line 2357) | public static svm_model svm_load_model(String model_file_name)
    method svm_check_parameter (line 2514) | public static String svm_check_parameter(svm_problem prob, svm_paramet...
    method svm_check_probability_model (line 2628) | public static int svm_check_probability_model(svm_model model)

FILE: code/Model/seq-kernel/ssk_core/libsvm/svm_model.java
  class svm_model (line 5) | public class svm_model implements java.io.Serializable

FILE: code/Model/seq-kernel/ssk_core/libsvm/svm_node.java
  class svm_node (line 4) | public class svm_node implements java.io.Serializable
    method read (line 9) | public void read(String line, double[][] coef, int m, int index)
    method write (line 13) | public void write(DataOutputStream fp) throws IOException

FILE: code/Model/seq-kernel/ssk_core/libsvm/svm_parameter.java
  class svm_parameter (line 2) | public class svm_parameter implements Cloneable,java.io.Serializable
    method clone (line 36) | public Object clone()

FILE: code/Model/seq-kernel/ssk_core/libsvm/svm_problem.java
  class svm_problem (line 2) | public class svm_problem implements java.io.Serializable

FILE: code/Model/seq-kernel/ssk_core/ssk/FeatureDictionary.java
  class FeatureDictionary (line 20) | public class FeatureDictionary {
    method FeatureDictionary (line 29) | public FeatureDictionary()
    method getAddFeature (line 38) | public String getAddFeature(int nType, String strFeature)

FILE: code/Model/seq-kernel/ssk_core/ssk/InstanceExample.java
  class InstanceExample (line 12) | public class InstanceExample implements java.io.Serializable {
    method InstanceExample (line 18) | public InstanceExample(String text, FeatureDictionary fd)
    method setLabel (line 48) | public void setLabel(int label)
    method getLabel (line 53) | public int getLabel()
    method toString (line 59) | public String toString()
    method write (line 74) | public void write(DataOutputStream fp) throws IOException

FILE: code/Model/seq-kernel/ssk_core/ssk/SubsequenceKernel.java
  class SubsequenceKernel (line 23) | public class SubsequenceKernel extends CustomKernel
    method SubsequenceKernel (line 41) | public SubsequenceKernel(int maxlen, double lambda,
    method SubsequenceKernel (line 54) | public SubsequenceKernel()
    method kernel (line 74) | public double kernel(InstanceExample ie1, InstanceExample ie2)
    method kernel (line 103) | public double kernel(svm_node[] x1, svm_node[] x2)
    method new_svm_node (line 112) | public svm_node new_svm_node()
    method selfKernel (line 118) | public double selfKernel(String[][] s)
    method singleKernel (line 135) | public double singleKernel(String[][] s1, String[][] s2)
    method stringKernel (line 163) | protected double[] stringKernel(String[][] s, String[][] t,
    method common (line 209) | protected int common(String[] s, String[] t)
    method main (line 221) | public static void main (String[] args)

FILE: code/Model/seq-kernel/ssk_core/ssk/intex_node.java
  class intex_node (line 14) | public class intex_node extends svm_node {
    method read (line 24) | public void read(String line, double[][] coef, int m, int index)
    method write (line 41) | public void write(DataOutputStream fp) throws IOException

FILE: code/Model/warp/warp.cpp
  function main (line 49) | int main(int argc, const char * argv[]) {
  function print_matrix (line 146) | void print_matrix(char * filename, double** array, int nrows, int ncolum...
  function load_data (line 163) | void load_data(char *filename, int** data, int* count){
  function print (line 189) | void print(char* message, double** array, int nrows, int ncolumns) {
  function count_lines (line 199) | int count_lines(char * filename) {
  function free_matrix_double (line 239) | void free_matrix_double(double** array, int nrows) {
  function compare (line 245) | int compare (const void * a, const void * b){
  function gradient (line 276) | double gradient(double ** A, double ** B, int* features, int* positive_t...
  function rank (line 360) | double rank(int k){
  function dot (line 369) | double dot(double*Ax , double* Bi, int len){