util.bio.annotation
Class GeneRep

java.lang.Object
  util.bio.annotation.GeneRep

All Implemented Interfaces:

java.io.Serializable

public class GeneRep

extends java.lang.Object

implements java.io.Serializable

A GeneRep resentation contains a genomic sequence designating a gene broken into various segments. This takes the most conservative approach. Any annotation that says something is coding is shown as coding. Exons are maximized, introns and UTRs minimalized (actually UTR refers to RNA, not genomic). Different translations/transcriptions will give various versions of these segments. There is no orientation for these features! Use the GeneGroup to get the real start/stop and thus the orientation and strand.

See Also:

Serialized Form

Constructor Summary

GeneRep(TransGroup[] transGrps, GeneGroup geneGrpRef)

Method Summary

java.util.ArrayList	getCodingSegments() Conservative estimate of coding segments.
int[]	getFivePrimeNonCodingRegion() Conservative estimate returning smallest non coding region.
GeneGroup	getGeneGrp()
java.util.ArrayList	getNonCodingSegments() Conservative estimate of non coding segments between coding exons.
int	getStartATGPosition() Conservative estimate of the start ATG position, from the longest transcript
int[]	getThreePrimeNonCodingRegion() Conservative estimate returning smallest non coding region.
boolean	isTranslationFlag()
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

GeneRep

public GeneRep(TransGroup[] transGrps,
               GeneGroup geneGrpRef)

Method Detail

toString

public java.lang.String toString()

getGeneGrp

public GeneGroup getGeneGrp()

isTranslationFlag

public boolean isTranslationFlag()

getCodingSegments

public java.util.ArrayList getCodingSegments()

Conservative estimate of coding segments. Returns biggest from all translations.

getNonCodingSegments

public java.util.ArrayList getNonCodingSegments()

Conservative estimate of non coding segments between coding exons. Not introns!

getFivePrimeNonCodingRegion

public int[] getFivePrimeNonCodingRegion()

Conservative estimate returning smallest non coding region. Not the UTR!

getThreePrimeNonCodingRegion

public int[] getThreePrimeNonCodingRegion()

Conservative estimate returning smallest non coding region. Not the UTR!

getStartATGPosition

public int getStartATGPosition()

Conservative estimate of the start ATG position, from the longest transcript