org.utgenome.gwt.utgb.client.bio
Class SAMReadPairFragment

java.lang.Object
  org.utgenome.gwt.utgb.client.bio.Interval
      org.utgenome.gwt.utgb.client.bio.SAMReadPairFragment

All Implemented Interfaces:

Serializable, Comparable<Interval>, OnGenome

public class SAMReadPairFragment
extends Interval

Paired-end reads without the other mate data

Author:

leo

See Also:

Serialized Form

Field Summary

int	mateStart
SAMReadLight	oneEnd

Constructor Summary

SAMReadPairFragment()

SAMReadPairFragment(SAMReadLight oneEnd, int mateStart)

Method Summary

void	accept(OnGenomeDataVisitor visitor)
Gap	getGap()
String	getName()

Methods inherited from class org.utgenome.gwt.utgb.client.bio.Interval

adjustToOneOrigin, atomicSetStartAndEnd, compareTo, contains, contains, correctInterval, follows, getColor, getEnd, getStart, hasOverlap, intersect, intersectsWith, isAntiSense, isSense, length, precedes, setEnd, setStart, toJSONArray, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

oneEnd

public SAMReadLight oneEnd

mateStart

public int mateStart

Constructor Detail

SAMReadPairFragment

public SAMReadPairFragment()

SAMReadPairFragment

public SAMReadPairFragment(SAMReadLight oneEnd,
                           int mateStart)

Method Detail

getName

public String getName()

Specified by:

getName in interface OnGenome

Overrides:

getName in class Interval

getGap

public Gap getGap()

accept

public void accept(OnGenomeDataVisitor visitor)

Specified by:

accept in interface OnGenome

Overrides:

accept in class Interval