util.bio.parsers.gff
Class GffParser

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

public class GffParser

extends java.lang.Object

Parses GFF files extracting the annotation according to GFF(2). http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml tabtabtabtabtabtab tabtab[space delimited key=value; key=value; attributes] Uses some hashes to count the sources, features, and attributes Generates an array of GffFeature objects, see to learn about what's used to parse the Attributes. This parser needs to be tested on each new GFF file, the GFF format is so flexible as to cause all kinds of problems. Works with flybase, and the drosophila release 3.1 gff annotation.

Constructor Summary

GffParser(java.io.File file, int startNt, int stopNt)

Method Summary

GffFeature[]	getGffFeatures()
void	quantifyItems()

Methods inherited from class java.lang.Object

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

Constructor Detail

GffParser

public GffParser(java.io.File file,
                 int startNt,
                 int stopNt)

Method Detail

getGffFeatures

public GffFeature[] getGffFeatures()

quantifyItems

public void quantifyItems()