Package org.snpeff.snpEffect.factory
Class SnpEffPredictorFactoryRand
java.lang.Object
org.snpeff.snpEffect.factory.SnpEffPredictorFactory
org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRand
This class creates a random set of chromosomes, genes, transcripts and exons
- Author:
- pcingola
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Field Summary
Fields inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
FASTA_DELIMITER
Fields inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
MARK, MIN_TOTAL_FRAME_COUNT
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Constructor Summary
ConstructorsConstructorDescriptionSnpEffPredictorFactoryRand
(Config config, Random random, int maxGeneLen, int maxTranscripts, int maxExons) -
Method Summary
Modifier and TypeMethodDescriptioncreate()
protected boolean
Parse a linevoid
setAddUtrs
(boolean addUtrs) void
setChromo
(Chromosome chromo) void
setForceNegativeStrand
(boolean forceNegativeStrand) void
setForcePositiveStrand
(boolean forcePositive) void
setMinExons
(int minExons) void
setNumGenes
(int numGenes) Methods inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
addExon, addExons, addGene, addGene, addIntergenicConserved, addInterval, addIntronConserved, addUtr3, addUtr5, findOrCreateExon, findOrCreateGene, findOrCreateTranscript, readExonSequences, readExonSequencesGff, readGff
Methods inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
add, add, add, add, add, add, addMarker, addSequences, adjustChromosomes, adjustTranscripts, beforeExonSequences, codingFromCds, collapseZeroLenIntrons, createRandSequences, deleteRedundant, exonsFromCds, exonsFromCds, findGene, findGene, findMarker, findTranscript, findTranscript, getOrCreateChromosome, getProteinByTrId, parsePosition, replaceTranscript, setCircularCorrectLargeGap, setCreateRandSequences, setDebug, setFastaFile, setFileName, setRandom, setReadSequences, setStoreSequences, setVerbose, showChromoNamesDifferences
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Constructor Details
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SnpEffPredictorFactoryRand
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Method Details
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create
- Overrides:
create
in classSnpEffPredictorFactoryGff
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getChromo
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getChromoSequence
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parse
Description copied from class:SnpEffPredictorFactoryGff
Parse a line- Overrides:
parse
in classSnpEffPredictorFactoryGff
- Returns:
- true if a line was parsed
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setAddUtrs
public void setAddUtrs(boolean addUtrs) -
setChromo
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setForceNegativeStrand
public void setForceNegativeStrand(boolean forceNegativeStrand) -
setForcePositiveStrand
public void setForcePositiveStrand(boolean forcePositive) -
setMinExons
public void setMinExons(int minExons) -
setNumGenes
public void setNumGenes(int numGenes)
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