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

java.lang.Object
  extended by org.utgenome.gwt.utgb.client.bio.Interval
      extended by org.utgenome.gwt.utgb.client.bio.SAMReadPairFragment
All Implemented Interfaces:
Serializable, Comparable<Interval>, GenomeRange

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(GenomeRangeVisitor 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 GenomeRange
Overrides:
getName in class Interval

getGap

public Gap getGap()

accept

public void accept(GenomeRangeVisitor visitor)
Specified by:
accept in interface GenomeRange
Overrides:
accept in class Interval


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