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

public class SnpEffPredictorFactoryRand
extends SnpEffPredictorFactoryGff

This class creates a random set of chromosomes, genes, transcripts and exons

Author:

pcingola

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

Constructor Summary

Constructors

Constructor	Description
SnpEffPredictorFactoryRand(Config config, java.util.Random random, int maxGeneLen, int maxTranscripts, int maxExons)

Method Summary

Modifier and Type	Method	Description
SnpEffectPredictor	create()
Chromosome	getChromo()
java.lang.String	getChromoSequence()
protected boolean	parse(java.lang.String line)	Parse a line
void	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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SnpEffPredictorFactoryRand

public SnpEffPredictorFactoryRand(Config config,
                                  java.util.Random random,
                                  int maxGeneLen,
                                  int maxTranscripts,
                                  int maxExons)

Method Detail

create

public SnpEffectPredictor create()

Overrides:

create in class SnpEffPredictorFactoryGff

getChromo

public Chromosome getChromo()

getChromoSequence

public java.lang.String getChromoSequence()

parse

protected boolean parse(java.lang.String line)

Description copied from class: SnpEffPredictorFactoryGff

Parse a line

Overrides:

parse in class SnpEffPredictorFactoryGff

Returns:

true if a line was parsed

setAddUtrs

public void setAddUtrs(boolean addUtrs)

setChromo

public void setChromo(Chromosome chromo)

setForceNegativeStrand

public void setForceNegativeStrand(boolean forceNegativeStrand)

setForcePositiveStrand

public void setForcePositiveStrand(boolean forcePositive)

setMinExons

public void setMinExons(int minExons)

setNumGenes

public void setNumGenes(int numGenes)