Class GffParser

  extended byutil.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


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


public GffFeature[] getGffFeatures()


public void quantifyItems()