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

java.lang.Object
  org.utgenome.gwt.utgb.client.bio.Interval
      org.utgenome.gwt.utgb.client.bio.SAMReadLight
          org.utgenome.gwt.utgb.client.bio.SAMRead

All Implemented Interfaces:

Serializable, Comparable<Interval>, OnGenome

public class SAMRead
extends SAMReadLight

Genome Read data

Author:

yoshimura

See Also:

Serialized Form

Field Summary

int	iSize
int	mapq
String	mrnm
int	mStart
String	qual
String	refSeq
String	rname
String	seq
Properties	tag

Fields inherited from class org.utgenome.gwt.utgb.client.bio.SAMReadLight

cigar, flag, qname, unclippedEnd, unclippedStart

Constructor Summary

SAMRead()

SAMRead(int start, int end)

Method Summary

void	accept(OnGenomeDataVisitor visitor)
String	getName()
String	getQV()
String	getSequence()
boolean	isAntiSense()
boolean	isMate(SAMRead other)
boolean	isSense()
boolean	mateIsMappedToTheSameChr()
String	toString()

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

isFirstRead, isMappedInProperPair, isMate, isPairedRead, isSecondRead, isUnmapped, unclippedSequenceContains, unclippedSequenceHasOverlapWith

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

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

Methods inherited from class java.lang.Object

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

Field Detail

rname

public String rname

mapq

public int mapq

mrnm

public String mrnm

mStart

public int mStart

iSize

public int iSize

seq

public String seq

qual

public String qual

tag

public Properties tag

refSeq

public String refSeq

Constructor Detail

SAMRead

public SAMRead()

SAMRead

public SAMRead(int start,
               int end)

Method Detail

toString

public String toString()

Overrides:

toString in class SAMReadLight

isMate

public boolean isMate(SAMRead other)

getSequence

public String getSequence()

Overrides:

getSequence in class SAMReadLight

getQV

public String getQV()

Overrides:

getQV in class SAMReadLight

getName

public String getName()

Specified by:

getName in interface OnGenome

Overrides:

getName in class SAMReadLight

isSense

public boolean isSense()

Overrides:

isSense in class SAMReadLight

isAntiSense

public boolean isAntiSense()

Overrides:

isAntiSense in class SAMReadLight

accept

public void accept(OnGenomeDataVisitor visitor)

Specified by:

accept in interface OnGenome

Overrides:

accept in class SAMReadLight

mateIsMappedToTheSameChr

public boolean mateIsMappedToTheSameChr()