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

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

All Implemented Interfaces:

Serializable, Comparable<Interval>, GenomeRange

Direct Known Subclasses:

BlastResult, BSSRead, BSSReadView.BSSAlignment, ChromosomeMap.ReadLocus, DASResult.DASFeature, Gene, MethylViewer.MethlEntry

public class Read
extends Interval

An interval with starnd information

Author:

leo

See Also:

Serialized Form

Nested Class Summary

static class

Read.ReadType

Constructor Summary

	Read()
	Read(int start, int end)
protected	Read(Read other)
	Read(String name, int start, int end)

Method Summary

void	accept(GenomeRangeVisitor visitor)
Interval	downstreamRegion(int length)
String	getColor()
String	getName()
char	getStrand()
boolean	isAntiSense()
boolean	isSense()
void	setColor(String color)
void	setName(String name)
void	setStrand(String strand)
Interval	upstreamRegion(int length)

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

Constructor Detail

Read

public Read()

Read

public Read(int start,
            int end)

Read

public Read(String name,
            int start,
            int end)

Read

protected Read(Read other)

Method Detail

getName

public String getName()

Specified by:

getName in interface GenomeRange

Overrides:

getName in class Interval

setName

public void setName(String name)

getColor

public String getColor()

Overrides:

getColor in class Interval

setColor

public void setColor(String color)

getStrand

public char getStrand()

isSense

public boolean isSense()

Specified by:

isSense in interface GenomeRange

Overrides:

isSense in class Interval

isAntiSense

public boolean isAntiSense()

Specified by:

isAntiSense in interface GenomeRange

Overrides:

isAntiSense in class Interval

setStrand

public void setStrand(String strand)

accept

public void accept(GenomeRangeVisitor visitor)

Specified by:

accept in interface GenomeRange

Overrides:

accept in class Interval

upstreamRegion

public Interval upstreamRegion(int length)

downstreamRegion

public Interval downstreamRegion(int length)