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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.
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