util.bio.annotation
Class Translation

java.lang.Object
  util.bio.annotation.Translation

All Implemented Interfaces:

java.io.Serializable

public class Translation

extends java.lang.Object

implements java.io.Serializable

Translation specific information, protein but referenced with genomic coordinates thus some bits code for protein, some don't physically exist.

See Also:

Serialized Form

Constructor Summary

Translation(Gff3Feature f)

Translation(int start, int end, int orientation)

Method Summary

java.util.ArrayList	getCodingSegments()
int	getEnd()
java.util.ArrayList	getIntrons()
int	getOrientation()
int	getStart()
void	makeSegments()
void	setTransGrp(TransGroup ref) Sets TransGroup ref but also fires the makeSegments method
java.lang.String	toString()
static java.lang.String	toStringALInts(java.util.ArrayList al)

Methods inherited from class java.lang.Object

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

Constructor Detail

Translation

public Translation(int start,
                   int end,
                   int orientation)

Translation

public Translation(Gff3Feature f)

Method Detail

setTransGrp

public void setTransGrp(TransGroup ref)

Sets TransGroup ref but also fires the makeSegments method

makeSegments

public void makeSegments()

toString

public java.lang.String toString()

toStringALInts

public static java.lang.String toStringALInts(java.util.ArrayList al)

getCodingSegments

public java.util.ArrayList getCodingSegments()

getOrientation

public int getOrientation()

getEnd

public int getEnd()

getStart

public int getStart()

getIntrons

public java.util.ArrayList getIntrons()