org.utgenome.gwt.utgb.server.app
Class BSSReadView.BSSAlignment

java.lang.Object
  org.utgenome.gwt.utgb.client.bio.Interval
      org.utgenome.gwt.utgb.client.bio.Read
          org.utgenome.gwt.utgb.server.app.BSSReadView.BSSAlignment

All Implemented Interfaces:

Serializable, Comparable<Interval>, GenomeRange

Enclosing class:

BSSReadView

public static class BSSReadView.BSSAlignment
extends Read

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class org.utgenome.gwt.utgb.client.bio.Read

Read.ReadType

Field Summary

String	alignment
int	bitScore
String	evalue
double	queryCoverage
int	queryLength
String	querySequence
double	similarity
String	target
String	targetSequence

Constructor Summary

BSSReadView.BSSAlignment()

Method Summary

void	setAlignment(String alignment)
void	setBitScore(int bitScore)
void	setEvalue(String evalue)
void	setQueryCoverage(double queryCoverage)
void	setQueryLength(int queryLength)
void	setQuerySequence(String querySequence)
void	setSimilarity(double similarity)
void	setTarget(String target)
void	setTargetSequence(String targetSequence)
String	toAlignmentView()

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

accept, downstreamRegion, getColor, getName, getStrand, isAntiSense, isSense, setColor, setName, setStrand, upstreamRegion

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

adjustToOneOrigin, atomicSetStartAndEnd, compareTo, contains, contains, correctInterval, follows, getEnd, getStart, hasOverlap, intersect, intersectsWith, 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

similarity

public double similarity

queryCoverage

public double queryCoverage

queryLength

public int queryLength

evalue

public String evalue

bitScore

public int bitScore

targetSequence

public String targetSequence

querySequence

public String querySequence

alignment

public String alignment

target

public String target

Constructor Detail

BSSReadView.BSSAlignment

public BSSReadView.BSSAlignment()

Method Detail

setTarget

public void setTarget(String target)

setQueryLength

public void setQueryLength(int queryLength)

setSimilarity

public void setSimilarity(double similarity)

setQueryCoverage

public void setQueryCoverage(double queryCoverage)

setEvalue

public void setEvalue(String evalue)

setBitScore

public void setBitScore(int bitScore)

setTargetSequence

public void setTargetSequence(String targetSequence)

setQuerySequence

public void setQuerySequence(String querySequence)

setAlignment

public void setAlignment(String alignment)

toAlignmentView

public String toAlignmentView()