A B C D E F G H I L M N O P Q R S T V W

A

acceptorList - Static variable in class ec.app.sequence.ExonParser
 
ACTG - Static variable in class ec.app.sequence.ExonParser
 
addChild(FTNode) - Method in class ec.app.sequence.FTNode
 
addToMap(String, String, String) - Static method in class ec.app.sequence.ExonParser
 
addTopPopulationToHallOfFame(EvolutionState, GPIndividual[], int) - Method in class ec.app.sequence.HallOfFame
 
AG_SEQUENCE - Static variable in class ec.app.sequence.ExonParser
 
anotherMotif - Variable in class ec.app.sequence.MotifData
 

B

bp - Variable in class ec.app.sequence.FTNode
 

C

cleanOnly - Variable in class ec.app.sequence.SequenceFeatureGenerator
 
cleanOnly - Variable in class ec.app.sequence.ThreadedSequenceFeatureInterpreter
 
cleanse() - Method in class ec.app.sequence.FTNode
 
close() - Static method in class ec.app.sequence.FileUtil
 
close - Variable in class ec.app.sequence.MotifData
 
close() - Method in class ec.app.sequence.ThreadedSequenceFeatureInterpreter
 
copyNode(FTNode, FTNode) - Method in class ec.app.sequence.FTNode
 
copyTo(GPData) - Method in class ec.app.sequence.MotifData
 
currentMotif - Variable in class ec.app.sequence.MotifData
 
currentMotifLength - Static variable in class ec.app.sequence.MotifData
 
currentPosition - Variable in class ec.app.sequence.MotifData
 
currentSequence - Variable in class ec.app.sequence.SequenceClassificationProblem
 
currentTerminal - Variable in class ec.app.sequence.MotifData
 

D

donorList - Static variable in class ec.app.sequence.ExonParser
 

E

ec.app.sequence - package ec.app.sequence
 
emptyClone() - Method in class ec.app.sequence.SubpopulationExt
 
entropyConditionedOnColumns(double[][]) - Static method in class ec.app.sequence.SequenceClassificationProblem
Computes conditional entropy of the rows given the columns.
entropyConditionedOnRows(double[][]) - Static method in class ec.app.sequence.SequenceClassificationProblem
Computes conditional entropy of the columns given the rows.
eq(double, double) - Static method in class ec.app.sequence.SequenceClassificationProblem
Tests if a is equal to b.
evaluate(EvolutionState, Individual, int, int) - Method in class ec.app.sequence.SequenceClassificationProblem
 
ExonParser - Class in ec.app.sequence
This is generic Utility to parse RNA sequences, with exons data given, to find the exact locations of Acceptors and Donors.
ExonParser() - Constructor for class ec.app.sequence.ExonParser
 

F

factory - Static variable in class ec.app.sequence.SequenceFeatureGenerator
 
factory - Static variable in class ec.app.sequence.ThreadedSequenceFeatureInterpreter
 
falseExp(FTNode) - Method in class ec.app.sequence.FTNode
 
FastaFileChunker - Class in ec.app.sequence
 
FastaFileChunker() - Constructor for class ec.app.sequence.FastaFileChunker
 
FastaParserGenome - Class in ec.app.sequence
This Utility is used to extract Positive and Negative samples from Fasta files which have labels in properties.
FastaParserGenome() - Constructor for class ec.app.sequence.FastaParserGenome
 
FastaParserGenomeLabelGenerator - Class in ec.app.sequence
 
FastaParserGenomeLabelGenerator() - Constructor for class ec.app.sequence.FastaParserGenomeLabelGenerator
 
FeatureCollector - Class in ec.app.sequence
 
FeatureCollector() - Constructor for class ec.app.sequence.FeatureCollector
 
FeatureReader - Class in ec.app.sequence
 
FeatureReader() - Constructor for class ec.app.sequence.FeatureReader
 
FeatureSorter - Class in ec.app.sequence
 
FeatureSorter() - Constructor for class ec.app.sequence.FeatureSorter
 
FileUtil - Class in ec.app.sequence
 
FileUtil() - Constructor for class ec.app.sequence.FileUtil
 
finalStatistics(EvolutionState, int) - Method in class ec.app.sequence.StatisticPluginForHallofFame
 
flushToFile(EvolutionState, String) - Method in class ec.app.sequence.HallOfFame
 
FTNode - Class in ec.app.sequence
 
FTNode() - Constructor for class ec.app.sequence.FTNode
 

G

generateLibSVMFile(File) - Method in class ec.app.sequence.SequenceFeatureGenerator
 
generateLibSVMFile(File, int) - Method in class ec.app.sequence.ThreadedSequenceFeatureInterpreter
 
generateSequences(String, String, ArrayList, ArrayList, ArrayList, ArrayList) - Static method in class ec.app.sequence.RNASequenceParser
 
getCurrentSequence() - Method in class ec.app.sequence.SequenceClassificationProblem
 
getFactory(int) - Method in class ec.app.sequence.SequenceClassificationProblem
 
getFillers(int) - Static method in class ec.app.sequence.ExonParser
 
GT_SEQUENCE - Static variable in class ec.app.sequence.ExonParser
 

H

HallOfFame - Class in ec.app.sequence
This is our simple implementation of Hall of Fame to capture good individuals from the run.
HallOfFame() - Constructor for class ec.app.sequence.HallOfFame
 

I

isBoolOp(String) - Method in class ec.app.sequence.FTNode
 

L

lchild - Variable in class ec.app.sequence.FTNode
 
LibSvmToWekaFormatter - Class in ec.app.sequence
 
LibSvmToWekaFormatter() - Constructor for class ec.app.sequence.LibSvmToWekaFormatter
 
load_tree(String, int[], PatternFactory) - Static method in class ec.app.sequence.FTNode
 

M

main(String[]) - Static method in class ec.app.sequence.ExonParser
 
main(String[]) - Static method in class ec.app.sequence.FastaFileChunker
 
main(String[]) - Static method in class ec.app.sequence.FastaParserGenome
 
main(String[]) - Static method in class ec.app.sequence.FastaParserGenomeLabelGenerator
 
main(String[]) - Static method in class ec.app.sequence.FeatureReader
 
main(String[]) - Static method in class ec.app.sequence.FeatureSorter
 
main(String[]) - Static method in class ec.app.sequence.LibSvmToWekaFormatter
 
main(String[]) - Static method in class ec.app.sequence.RNASequenceParser
 
main(String[]) - Static method in class ec.app.sequence.SequenceFeatureGenerator
 
main(String[]) - Static method in class ec.app.sequence.ThreadedSequenceFeatureInterpreter
 
matches - Variable in class ec.app.sequence.MotifData
 
MEDIUM - Static variable in class ec.app.sequence.SequenceClassificationProblem
 
MotifData - Class in ec.app.sequence
This is the basic evolutionary data bucket sent across and each one puts his results in the bucket.
MotifData() - Constructor for class ec.app.sequence.MotifData
 

N

negativeSequences - Static variable in class ec.app.sequence.SequenceClassificationProblem
 
negativeSequencesList - Static variable in class ec.app.sequence.SequenceClassificationProblem
 

O

organismToExonPositions - Static variable in class ec.app.sequence.ExonParser
 

P

parent - Variable in class ec.app.sequence.FTNode
 
parseSequence(String, String) - Static method in class ec.app.sequence.ExonParser
 
populate(EvolutionState, int) - Method in class ec.app.sequence.SubpopulationExt
 
position - Variable in class ec.app.sequence.FTNode
 
POSITIVE_FILE_NAME_PARAM - Static variable in class ec.app.sequence.SequenceClassificationProblem
 
positiveSequences - Static variable in class ec.app.sequence.SequenceClassificationProblem
 
positiveSequencesList - Static variable in class ec.app.sequence.SequenceClassificationProblem
 
postEvaluationStatistics(EvolutionState) - Method in class ec.app.sequence.StatisticPluginForHallofFame
 

Q

quickWrite(String) - Static method in class ec.app.sequence.FileUtil
 
quickWrite(String) - Method in class ec.app.sequence.ThreadedSequenceFeatureInterpreter
All threads use this, so better be synchronized

R

random - Static variable in class ec.app.sequence.ExonParser
 
rchild - Variable in class ec.app.sequence.FTNode
 
read(File) - Method in class ec.app.sequence.FeatureReader
 
readTextFileToStringList(File, boolean) - Static method in class ec.app.sequence.FileUtil
Reads the lines of a text file.
RNASequenceParser - Class in ec.app.sequence
 
RNASequenceParser() - Constructor for class ec.app.sequence.RNASequenceParser
 

S

s - Variable in class ec.app.sequence.FTNode
 
SequenceClassificationProblem - Class in ec.app.sequence
Basic Fitness assessment code.
SequenceClassificationProblem() - Constructor for class ec.app.sequence.SequenceClassificationProblem
 
SequenceFeatureGenerator - Class in ec.app.sequence
 
SequenceFeatureGenerator() - Constructor for class ec.app.sequence.SequenceFeatureGenerator
 
setup(String) - Method in class ec.app.sequence.HallOfFame
 
setup(EvolutionState, Parameter) - Method in class ec.app.sequence.SequenceClassificationProblem
 
setup(String) - Method in class ec.app.sequence.SequenceFeatureGenerator
This method reads the sequences from File with labels +1, -1 and tries to put it in right buckets.
setup(EvolutionState, Parameter) - Method in class ec.app.sequence.StatisticPluginForHallofFame
 
setup(String) - Method in class ec.app.sequence.ThreadedSequenceFeatureInterpreter
This method reads the sequences from File with labels +1, -1 and tries to put it in right buckets.
SMALL - Static variable in class ec.app.sequence.SequenceClassificationProblem
The small deviation allowed in double comparisons.
splitEqually(String, String, int) - Static method in class ec.app.sequence.FastaFileChunker
 
StatisticPluginForHallofFame - Class in ec.app.sequence
This class is meant for getting plugin for HallOfFame.
StatisticPluginForHallofFame() - Constructor for class ec.app.sequence.StatisticPluginForHallofFame
 
SubpopulationExt - Class in ec.app.sequence
This class extends Subpopulation and decreases the size of it every time by 25% for example.
SubpopulationExt() - Constructor for class ec.app.sequence.SubpopulationExt
 

T

ThreadedSequenceFeatureInterpreter - Class in ec.app.sequence
This code is meant to read the Features stored in file (hall of fame output) and generate LibSVM specific format files.
ThreadedSequenceFeatureInterpreter() - Constructor for class ec.app.sequence.ThreadedSequenceFeatureInterpreter
 
toString() - Method in class ec.app.sequence.FTNode
 

V

value(SymbolList) - Method in class ec.app.sequence.FTNode
 

W

writeFeature(GPIndividual, EvolutionState) - Static method in class ec.app.sequence.FeatureCollector
 
writeStringToTextFile(File, String, boolean) - Static method in class ec.app.sequence.FileUtil
Writes a string into a text file.

A B C D E F G H I L M N O P Q R S T V W