Package org.snpeff.snpEffect.factory
Class SnpEffPredictorFactoryRand
- java.lang.Object
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- org.snpeff.snpEffect.factory.SnpEffPredictorFactory
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- org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
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- org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRand
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public class SnpEffPredictorFactoryRand extends SnpEffPredictorFactoryGff
This class creates a random set of chromosomes, genes, transcripts and exons- Author:
- pcingola
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Field Summary
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Fields inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
FASTA_DELIMITER
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Fields inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
MARK, MIN_TOTAL_FRAME_COUNT
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Constructor Summary
Constructors Constructor Description SnpEffPredictorFactoryRand(Config config, java.util.Random random, int maxGeneLen, int maxTranscripts, int maxExons)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description SnpEffectPredictor
create()
Chromosome
getChromo()
java.lang.String
getChromoSequence()
protected boolean
parse(java.lang.String line)
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)
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Methods inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
addExon, addExons, addGene, addIntergenicConserved, addInterval, addIntronConserved, addUtr3, addUtr5, findOrCreateExon, findOrCreateGene, findOrCreateTranscript, readExonSequences, readExonSequencesGff, readGff
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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, setCreateRandSequences, setDebug, setFastaFile, setFileName, setRandom, setReadSequences, setStoreSequences, setVerbose, showChromoNamesDifferences
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Constructor Detail
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SnpEffPredictorFactoryRand
public SnpEffPredictorFactoryRand(Config config, java.util.Random random, int maxGeneLen, int maxTranscripts, int maxExons)
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Method Detail
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create
public SnpEffectPredictor create()
- Overrides:
create
in classSnpEffPredictorFactoryGff
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getChromo
public Chromosome getChromo()
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getChromoSequence
public java.lang.String getChromoSequence()
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parse
protected boolean parse(java.lang.String line)
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)
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setChromo
public void setChromo(Chromosome chromo)
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setForceNegativeStrand
public void setForceNegativeStrand(boolean forceNegativeStrand)
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setForcePositiveStrand
public void setForcePositiveStrand(boolean forcePositive)
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setMinExons
public void setMinExons(int minExons)
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setNumGenes
public void setNumGenes(int numGenes)
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