com.pacbio.secondary.vis.data.read

Class ReadInfo

java.lang.Object

com.pacbio.secondary.vis.data.read.ReadInfo

Direct Known Subclasses:

EpiProReadInfo

public class ReadInfo
extends java.lang.Object

Local storage class for read info

Author:

mmilletti

Field Summary

Fields

Modifier and Type	Field and Description
protected int	molid
protected int	structid

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	ReadInfo() serialization only
	ReadInfo(WsRead read)

Method Summary

Methods

Modifier and Type	Method and Description
protected void	copyWsRead(java.lang.String name, int lane, int score, java.lang.String sequence, byte[] annotations, byte[] qv, int molid, int structid)
byte[]	getAnnotations()
int	getAvgQV()
int	getLane()
int	getMedianQV()
java.lang.String	getMetricsInfo(int mode)
int	getMolID()
java.lang.String	getName()
byte[]	getQV()
int	getScore()
java.lang.String	getSequence()
int	getStructID()
boolean	isVariantPosInsertionAt(int index)
void	setAnnotations(byte[] annotations)
void	setLane(int lane)
void	setMolID(int molid)
void	setName(java.lang.String name)
void	setQV(byte[] qv)
void	setScore(int score)
void	setSequence(java.lang.String sequence)
void	setStructID(int structid)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

molid

protected int molid

structid

protected int structid

Constructor Detail

ReadInfo

protected ReadInfo()

serialization only

ReadInfo

public ReadInfo(WsRead read)

Method Detail

copyWsRead

protected void copyWsRead(java.lang.String name,
              int lane,
              int score,
              java.lang.String sequence,
              byte[] annotations,
              byte[] qv,
              int molid,
              int structid)

getName

public java.lang.String getName()

setName

public void setName(java.lang.String name)

getLane

public int getLane()

setLane

public void setLane(int lane)

getMolID

public int getMolID()

setMolID

public void setMolID(int molid)

getStructID

public int getStructID()

setStructID

public void setStructID(int structid)

getScore

public int getScore()

setScore

public void setScore(int score)

getSequence

public java.lang.String getSequence()

setSequence

public void setSequence(java.lang.String sequence)

getAnnotations

public byte[] getAnnotations()

setAnnotations

public void setAnnotations(byte[] annotations)

getQV

public byte[] getQV()

setQV

public void setQV(byte[] qv)

getAvgQV

public int getAvgQV()

getMedianQV

public int getMedianQV()

getMetricsInfo

public java.lang.String getMetricsInfo(int mode)

isVariantPosInsertionAt

public boolean isVariantPosInsertionAt(int index)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object