util.bio.parsers.gff
Class ExtractGffFeatures

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

public class ExtractGffFeatures

extends java.lang.Object

Constructor Summary

ExtractGffFeatures(java.lang.String[] args)

Method Summary

void	extractGffFeatures()
static void	main(java.lang.String[] args)
void	printClusters(java.util.LinkedHashMap map) Prints all the gff lines.
static void	printDocs()
void	printUCSCFormat(java.util.LinkedHashMap map) Print each cluster in ucsc table format refGene.name refGene.chrom refGene.strand refGene.txStart refGene.txEnd refGene.cdsStart refGene.cdsEnd refGene.exonCount refGene.exonStarts refGene.exonEnds refLink.product geneName.name refSeqSummary.summary NM_198576 chr1 + 995569 1031415 995619 1030284 36 995569,997647,1010723,1016111,1016522,1016827,1017258,1018541,1018840,1019125,1019411,1019636,1020463,1020661,1021035,1021266,1021462,1021699,1022122,1022629,1022875,1023078,1023314,1024169,1024538,1024868,1025205,1025535,1025729,1026028,1026555,1026755,1027030,1029055,1029750,1030126, 995820,997909,1010771,1016327,1016747,1017052,1017465,1018760,1019035,1019326,1019560,1019742,1020580,1020826,1021179,1021391,1021568,1022038,1022260,1022757,1022990,1023198,1023668,1024362,1024754,1025098,1025340,1025632,1025894,1026140,1026672,1026948,1027118,1029280,1029854,1031415, agrin AGRIN Agrin is a neuronal aggregating factor that induces the aggregation of ...
void	processArgs(java.lang.String[] args) This method will process each argument and assign new varibles

Methods inherited from class java.lang.Object

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

Constructor Detail

ExtractGffFeatures

public ExtractGffFeatures(java.lang.String[] args)

Method Detail

extractGffFeatures

public void extractGffFeatures()

printClusters

public void printClusters(java.util.LinkedHashMap map)

Prints all the gff lines.

printUCSCFormat

public void printUCSCFormat(java.util.LinkedHashMap map)

Print each cluster in ucsc table format refGene.name refGene.chrom refGene.strand refGene.txStart refGene.txEnd refGene.cdsStart refGene.cdsEnd refGene.exonCount refGene.exonStarts refGene.exonEnds refLink.product geneName.name refSeqSummary.summary NM_198576 chr1 + 995569 1031415 995619 1030284 36 995569,997647,1010723,1016111,1016522,1016827,1017258,1018541,1018840,1019125,1019411,1019636,1020463,1020661,1021035,1021266,1021462,1021699,1022122,1022629,1022875,1023078,1023314,1024169,1024538,1024868,1025205,1025535,1025729,1026028,1026555,1026755,1027030,1029055,1029750,1030126, 995820,997909,1010771,1016327,1016747,1017052,1017465,1018760,1019035,1019326,1019560,1019742,1020580,1020826,1021179,1021391,1021568,1022038,1022260,1022757,1022990,1023198,1023668,1024362,1024754,1025098,1025340,1025632,1025894,1026140,1026672,1026948,1027118,1029280,1029854,1031415, agrin AGRIN Agrin is a neuronal aggregating factor that induces the aggregation of ...

main

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

processArgs

public void processArgs(java.lang.String[] args)

This method will process each argument and assign new varibles

printDocs

public static void printDocs()