util.bio.parsers.gff
Class DmelRel4Extractor

java.lang.Object
  util.bio.parsers.gff.DmelRel4Extractor

public class DmelRel4Extractor

extends java.lang.Object

Class for building gene models from GFF3Features, specifically tailored to release 4.0 drosophila melanogaster GFF. The start is always less than the end. The actual length of an element is end+1-start. Orientation is 1,-1, or 0 corresponding to +,-, or .

Constructor Summary

DmelRel4Extractor()

Method Summary

void	buildGeneGrp(Gff3Feature f) Creates a new gene group, call this last after having loaded the exons, transcripts, and translations.
void	buildGenericFeature(Gff3Feature f)
void	buildTransGroups()
void	extract(java.io.File gffFile, boolean stripIt)
java.util.ArrayList	getGeneGroupArrayList()
GeneGroup[]	getGeneGroups() Final product from the extractor.
java.util.LinkedHashSet	getGenericFeatureHash() Contains all the feature types that were not recognized by the Extractor.
java.util.ArrayList	getGenericFeatures()
java.util.ArrayList	getGenericFeaturesAL()
java.util.LinkedHashSet	getGenericFeaturesHash()
java.lang.String	getRegExGeneTypes()
boolean	isGenericFeaturesFound()
static void	main(java.lang.String[] args)
void	setChromosomeNameAppender(java.lang.String chromosomeNameAppender)
void	setRegExGeneTypes(java.lang.String regExGeneTypes)
static java.lang.String	stripIt(java.util.regex.Pattern patCG, java.util.regex.Pattern patTE, java.util.regex.Pattern patCR, java.lang.String toStrip)

Methods inherited from class java.lang.Object

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

Constructor Detail

DmelRel4Extractor

public DmelRel4Extractor()

Method Detail

main

public static void main(java.lang.String[] args)

extract

public void extract(java.io.File gffFile,
                    boolean stripIt)

stripIt

public static java.lang.String stripIt(java.util.regex.Pattern patCG,
                                       java.util.regex.Pattern patTE,
                                       java.util.regex.Pattern patCR,
                                       java.lang.String toStrip)

getGenericFeatureHash

public java.util.LinkedHashSet getGenericFeatureHash()

Contains all the feature types that were not recognized by the Extractor. Should be user added items like CRMs, enhancers, etc.

getGenericFeatures

public java.util.ArrayList getGenericFeatures()

buildGenericFeature

public void buildGenericFeature(Gff3Feature f)

buildTransGroups

public void buildTransGroups()

buildGeneGrp

public void buildGeneGrp(Gff3Feature f)

Creates a new gene group, call this last after having loaded the exons, transcripts, and translations.

getGeneGroupArrayList

public java.util.ArrayList getGeneGroupArrayList()

getGeneGroups

public GeneGroup[] getGeneGroups()

Final product from the extractor. Use in downstream analysis.

isGenericFeaturesFound

public boolean isGenericFeaturesFound()

getRegExGeneTypes

public java.lang.String getRegExGeneTypes()

setRegExGeneTypes

public void setRegExGeneTypes(java.lang.String regExGeneTypes)

getGenericFeaturesAL

public java.util.ArrayList getGenericFeaturesAL()

getGenericFeaturesHash

public java.util.LinkedHashSet getGenericFeaturesHash()

setChromosomeNameAppender

public void setChromosomeNameAppender(java.lang.String chromosomeNameAppender)