com.pacbio.secondary.vis.svc.server.data

Class WsRead

java.lang.Object

com.pacbio.secondary.vis.svc.server.data.WsRead

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<WsRead>

Direct Known Subclasses:

WsReadEx

public class WsRead
extends java.lang.Object
implements java.lang.Comparable<WsRead>, java.io.Serializable

Author:

mmilletti

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected byte[]	ann
protected WsIntervalSvc	intv
protected int	lane
protected int	molid
protected java.lang.String	name
protected byte[]	qv
protected int	scor
protected java.lang.String	seq
protected int	structid

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	WsRead()
	WsRead(java.lang.String name, int contig, int start, int stop, byte strand, double score, int read_length, boolean createQV, int molid, int structid) called by CMPH5FileWrapper::getAnnotatedResultsFromFile
	WsRead(java.lang.String name, int contig, int start, int stop, byte strand, java.lang.String sequence, double score, byte[] qv, byte[] annotation, int molid, int structid) called by CMPH5FileWrapper::getAlignedResultsFromFile

Method Summary

Methods

Modifier and Type	Method and Description
void	clipReadTo(int start, int length) assumes length > 0
int	compareTo(WsRead obj)
byte[]	getAnn()
WsIntervalSvc	getIntv()
int	getLane()
int	getMolid()
java.lang.String	getName()
long	getNumBasesFromMarkerRead() Helper function for marker read with stats
byte[]	getQv()
protected short	getQv(int idx)
int	getScor()
java.lang.String	getSeq()
int	getStructid()
double	getTimeFromMarkerRead() Helper function for marker read with stats
void	setAnn(byte[] ann)
void	setIntv(WsIntervalSvc intv)
void	setLane(int lane)
void	setMolid(int molid)
void	setName(java.lang.String name)
void	setQv(byte[] qv)
void	setScor(int scor)
void	setSeq(java.lang.String seq)
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

name

protected java.lang.String name

intv

protected WsIntervalSvc intv

lane

protected int lane

scor

protected int scor

seq

protected java.lang.String seq

ann

protected byte[] ann

qv

protected byte[] qv

molid

protected int molid

structid

protected int structid

Constructor Detail

WsRead

protected WsRead()

WsRead

public WsRead(java.lang.String name,
      int contig,
      int start,
      int stop,
      byte strand,
      java.lang.String sequence,
      double score,
      byte[] qv,
      byte[] annotation,
      int molid,
      int structid)

called by CMPH5FileWrapper::getAlignedResultsFromFile

Parameters:

name -

contig -

start -

stop -

strand -

sequence -

score -

qv -

annotation -

molid -

structid -

WsRead

public WsRead(java.lang.String name,
      int contig,
      int start,
      int stop,
      byte strand,
      double score,
      int read_length,
      boolean createQV,
      int molid,
      int structid)

called by CMPH5FileWrapper::getAnnotatedResultsFromFile

Parameters:

name -

contig -

start -

stop -

strand -

score -

read_length -

createQV -

molid -

structid -

Method Detail

getName

public java.lang.String getName()

setName

public void setName(java.lang.String name)

getIntv

public WsIntervalSvc getIntv()

setIntv

public void setIntv(WsIntervalSvc intv)

getLane

public int getLane()

setLane

public void setLane(int lane)

getScor

public int getScor()

setScor

public void setScor(int scor)

getSeq

public java.lang.String getSeq()

setSeq

public void setSeq(java.lang.String seq)

getAnn

public byte[] getAnn()

setAnn

public void setAnn(byte[] ann)

getQv

public byte[] getQv()

setQv

public void setQv(byte[] qv)

getMolid

public int getMolid()

setMolid

public void setMolid(int molid)

getStructid

public int getStructid()

setStructid

public void setStructid(int structid)

compareTo

public int compareTo(WsRead obj)

Specified by:

compareTo in interface java.lang.Comparable<WsRead>

getNumBasesFromMarkerRead

public long getNumBasesFromMarkerRead()

Helper function for marker read with stats

Returns:

number of bases

getTimeFromMarkerRead

public double getTimeFromMarkerRead()

Helper function for marker read with stats

Returns:

time to execute operation

clipReadTo

public void clipReadTo(int start,
              int length)

assumes length > 0

Parameters:

start -

length -

getQv

protected short getQv(int idx)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object