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, Random random, int maxGeneLen, int maxTranscripts, int maxExons)
Method Summary

Modifier and Type

Method

Description

SnpEffectPredictor

create()

Chromosome

getChromo()

String

getChromoSequence()

protected boolean

parse(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 Details
- SnpEffPredictorFactoryRand
  
  public SnpEffPredictorFactoryRand(Config config, Random random, int maxGeneLen, int maxTranscripts, int maxExons)
Method Details
- create
  
  public SnpEffectPredictor create()
  
  Overrides:
  
  create in class SnpEffPredictorFactoryGff
- getChromo
  
  public Chromosome getChromo()
- getChromoSequence
  
  public String getChromoSequence()
- parse
  
  protected boolean parse(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)

Class SnpEffPredictorFactoryRand

Field Summary

Fields inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff

Fields inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactory

Constructor Summary

Method Summary

Methods inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff

Methods inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactory

Methods inherited from class java.lang.Object

Constructor Details

SnpEffPredictorFactoryRand

Method Details

create

getChromo

getChromoSequence

parse

setAddUtrs

setChromo

setForceNegativeStrand

setForcePositiveStrand

setMinExons

setNumGenes