Package org.snpeff.snpEffect.factory

Class SnpEffPredictorFactoryGtf22

java.lang.Object

org.snpeff.snpEffect.factory.SnpEffPredictorFactory

org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff

org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGtf22

public class SnpEffPredictorFactoryGtf22
extends SnpEffPredictorFactoryGff

This class creates a SnpEffectPredictor from a GTF 2.2 file References: http://mblab.wustl.edu/GTF22.html

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
SnpEffPredictorFactoryGtf22(Config config)

Method Summary

Modifier and Type	Method	Description
protected boolean	parse(java.lang.String line)	Parse a line

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

addExon, addExons, addGene, addGene, addIntergenicConserved, addInterval, addIntronConserved, addUtr3, addUtr5, create, 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

SnpEffPredictorFactoryGtf22

public SnpEffPredictorFactoryGtf22(Config config)

Method Detail

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