util.bio.parsers.gff
Class Gff3Parser

java.lang.Object
  util.bio.parsers.gff.Gff3Parser

public class Gff3Parser

extends java.lang.Object

For parsing a GFF3 text file into GFF3Feature objects, be sure to set the regExTypes String filter to match which types you want to save!

Constructor Summary

Gff3Parser()

Gff3Parser(java.io.File GFF3File)

Method Summary

Gff3Feature[][]	getChromSplitFeatures() Returns the features split by chromosome.
Gff3Feature[]	getFeatures()
java.io.File	getGFFFile()
java.lang.String	getRegExTypes()
static void	main(java.lang.String[] args)
boolean	parseIt(java.io.File GFF3File)
boolean	printNotes()
void	setGFFFile(java.io.File file)
void	setPrintNotes(boolean printNotes)
void	setRegExTypes(java.lang.String regExTypes) Use something like -> gene|ncRNA|snoRNA|tRNA|rRNA|transposable_element|pseudogene|CDS|mRNA|exon Only those gff lines with a type matching this regular expression will be made into GFF3Feature's.
void	setRelax(boolean relax)
void	subtractOneFromFeatures() Subract one from start and end of each feature.

Methods inherited from class java.lang.Object

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

Constructor Detail

Gff3Parser

public Gff3Parser(java.io.File GFF3File)

Gff3Parser

public Gff3Parser()

Method Detail

parseIt

public boolean parseIt(java.io.File GFF3File)

subtractOneFromFeatures

public void subtractOneFromFeatures()

Subract one from start and end of each feature. Use for converting to zero base coordinates.

getChromSplitFeatures

public Gff3Feature[][] getChromSplitFeatures()

Returns the features split by chromosome.

main

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

getFeatures

public Gff3Feature[] getFeatures()

getGFFFile

public java.io.File getGFFFile()

setGFFFile

public void setGFFFile(java.io.File file)

printNotes

public boolean printNotes()

setPrintNotes

public void setPrintNotes(boolean printNotes)

getRegExTypes

public java.lang.String getRegExTypes()

setRegExTypes

public void setRegExTypes(java.lang.String regExTypes)

Use something like -> gene|ncRNA|snoRNA|tRNA|rRNA|transposable_element|pseudogene|CDS|mRNA|exon Only those gff lines with a type matching this regular expression will be made into GFF3Feature's. If you want everything set this to '.+' . If you don't know what types are present in the gff file, run this parser and it will print all of the types.

setRelax

public void setRelax(boolean relax)