util.bio.parsers.gff
Class GffFeature

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

public class GffFeature

extends java.lang.Object

A container for each of the values in a GFF 2 line. tabtabtabtabtabtab tabtab[space delimited key=value; key=value; attributes] Each param is split into a String[] on \t Attributes are further processed splitting on ;\s into another String[] each of theses Strings are then split into key value pairs on an = or \s and stuffed into a LinkedHashMap Note Stop = End +1, needed to convert to real coordinates!

Constructor Summary

GffFeature(java.lang.String unParsedGffLine)

Method Summary

java.util.LinkedHashMap	getAttsHash()
java.lang.String	getAttsString()
int	getEnd()
java.lang.String	getFeature()
java.lang.String	getGffLine()
double	getScore()
java.lang.String	getSeqName()
java.lang.String	getSource()
int	getStart()
java.lang.String	getStrand()
boolean	isGffGood()
static double	parseStringToDouble(java.lang.String text)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

GffFeature

public GffFeature(java.lang.String unParsedGffLine)

Method Detail

toString

public java.lang.String toString()

parseStringToDouble

public static double parseStringToDouble(java.lang.String text)

getGffLine

public java.lang.String getGffLine()

getSeqName

public java.lang.String getSeqName()

getSource

public java.lang.String getSource()

getFeature

public java.lang.String getFeature()

getStart

public int getStart()

getEnd

public int getEnd()

getScore

public double getScore()

getStrand

public java.lang.String getStrand()

getAttsHash

public java.util.LinkedHashMap getAttsHash()

getAttsString

public java.lang.String getAttsString()

isGffGood

public boolean isGffGood()