LocusMiner/Optimization API locusminer-39 (20090430155559)
A E G L M N R S T

A

add(Locus) - Method in class edu.cornell.med.icb.locusminer.Genome
 
add(Transcript) - Method in class edu.cornell.med.icb.locusminer.Genome
 
add(Transcript) - Method in class edu.cornell.med.icb.locusminer.Locus
 
addRelation(Transcript, RelationKind, double) - Method in class edu.cornell.med.icb.locusminer.Transcript
 
addTranscript(String) - Method in class edu.cornell.med.icb.locusminer.Locus
 

E

edu.cornell.med.icb.locusminer - package edu.cornell.med.icb.locusminer
 
evaluate(IChromosome) - Method in class edu.cornell.med.icb.locusminer.LocusMinerFitnessFunction
 
ExtractPairs - Class in edu.cornell.med.icb.locusminer
Extract pairs of transcript Ids from a reduced.tab file.
ExtractPairs() - Constructor for class edu.cornell.med.icb.locusminer.ExtractPairs
 

G

Genome - Class in edu.cornell.med.icb.locusminer
Represents a set of loci.
Genome() - Constructor for class edu.cornell.med.icb.locusminer.Genome
 
getDefaultScore(RelationKind) - Method in class edu.cornell.med.icb.locusminer.LocusMinerFitnessFunction
 
getIdentifier() - Method in class edu.cornell.med.icb.locusminer.Locus
 
getIdentifier() - Method in class edu.cornell.med.icb.locusminer.Transcript
 
getKind() - Method in class edu.cornell.med.icb.locusminer.Relation
 
getLoci() - Method in class edu.cornell.med.icb.locusminer.Genome
 
getLocus(String) - Method in class edu.cornell.med.icb.locusminer.Genome
 
getLocusAtIndex(int) - Method in class edu.cornell.med.icb.locusminer.Genome
 
getRelationScore(Transcript, RelationKind, LocusMinerFitnessFunction) - Method in class edu.cornell.med.icb.locusminer.Transcript
 
getScore() - Method in class edu.cornell.med.icb.locusminer.Relation
 
getSource() - Method in class edu.cornell.med.icb.locusminer.Relation
 
getTarget() - Method in class edu.cornell.med.icb.locusminer.Relation
 
getTranscript(String) - Method in class edu.cornell.med.icb.locusminer.Genome
 
getTranscript(String) - Method in class edu.cornell.med.icb.locusminer.Locus
 
getTranscriptActive(IChromosome, int) - Static method in class edu.cornell.med.icb.locusminer.LocusMinerFitnessFunction
 
getTranscriptAtIndex(Integer) - Method in class edu.cornell.med.icb.locusminer.Locus
 
getTranscriptAtLocus(IChromosome, int, Locus) - Static method in class edu.cornell.med.icb.locusminer.LocusMinerFitnessFunction
 
getTranscriptIndex(Transcript) - Method in class edu.cornell.med.icb.locusminer.Locus
 

L

Locus - Class in edu.cornell.med.icb.locusminer
Represents a genetic locus.
Locus() - Constructor for class edu.cornell.med.icb.locusminer.Locus
 
Locus(String) - Constructor for class edu.cornell.med.icb.locusminer.Locus
 
LocusMiner - Class in edu.cornell.med.icb.locusminer
 
LocusMiner() - Constructor for class edu.cornell.med.icb.locusminer.LocusMiner
 
LocusMinerFitnessFunction - Class in edu.cornell.med.icb.locusminer
 
LocusMinerFitnessFunction(Genome, Locus[], boolean) - Constructor for class edu.cornell.med.icb.locusminer.LocusMinerFitnessFunction
 

M

main(String[]) - Static method in class edu.cornell.med.icb.locusminer.ExtractPairs
 
main(String[]) - Static method in class edu.cornell.med.icb.locusminer.LocusMiner
 

N

numLoci() - Method in class edu.cornell.med.icb.locusminer.Genome
 
numTranscripts() - Method in class edu.cornell.med.icb.locusminer.Genome
 
numTranscripts() - Method in class edu.cornell.med.icb.locusminer.Locus
 

R

Relation - Class in edu.cornell.med.icb.locusminer
Records relations between transcripts.
Relation(RelationKind, double, Transcript, Transcript) - Constructor for class edu.cornell.med.icb.locusminer.Relation
 

S

setPopulationSize(int) - Method in class edu.cornell.med.icb.locusminer.LocusMiner
 
setSearchKind(RelationKind) - Method in class edu.cornell.med.icb.locusminer.LocusMiner
 
setSearchKind(RelationKind) - Method in class edu.cornell.med.icb.locusminer.LocusMinerFitnessFunction
 
setTargetLocusNumber(int) - Method in class edu.cornell.med.icb.locusminer.LocusMinerFitnessFunction
 

T

tighten() - Method in class edu.cornell.med.icb.locusminer.Genome
 
tighten() - Method in class edu.cornell.med.icb.locusminer.Locus
 
Transcript - Class in edu.cornell.med.icb.locusminer
 
Transcript(String) - Constructor for class edu.cornell.med.icb.locusminer.Transcript
 
Transcript() - Constructor for class edu.cornell.med.icb.locusminer.Transcript
 

A E G L M N R S T
LocusMiner/Optimization API locusminer-39 (20090430155559)

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