com.pacbio.secondary.vis.data.read

Class EpiProReadInfo

java.lang.Object

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

com.pacbio.secondary.vis.data.read.EpiProReadInfo

public class EpiProReadInfo
extends ReadInfo

Datum for each segment of a subread: prolog, primary, epilog

Author:

mmilletti

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	EpiProReadInfo.EpiProInfo

Field Summary

Fields

Modifier and Type	Field and Description
protected EpiProReadInfo.EpiProInfo	epilog
protected EpiProReadInfo.EpiProInfo	primary
protected EpiProReadInfo.EpiProInfo	prolog
protected int	subread_length

Fields inherited from class com.pacbio.secondary.vis.data.read.ReadInfo

molid, structid

Constructor Summary

Constructors

Constructor and Description
EpiProReadInfo(int subread_length)

Method Summary

Methods

Modifier and Type	Method and Description
EpiProReadInfo.EpiProInfo	getEpilogInfo()
EpiProReadInfo.EpiProInfo	getPrimaryInfo()
EpiProReadInfo.EpiProInfo	getPrologInfo()
int	getSubreadLength()
void	setEpilogInfo(int contig, long from, long to, int strand, int subread_start, int subread_end)
void	setPrimaryInfo(int contig, long from, long to, int strand, int subread_start, int subread_end)
void	setPrologInfo(int contig, long from, long to, int strand, int subread_start, int subread_end)

Methods inherited from class com.pacbio.secondary.vis.data.read.ReadInfo

copyWsRead, getAnnotations, getAvgQV, getLane, getMedianQV, getMetricsInfo, getMolID, getName, getQV, getScore, getSequence, getStructID, isVariantPosInsertionAt, setAnnotations, setLane, setMolID, setName, setQV, setScore, setSequence, setStructID, toString

Methods inherited from class java.lang.Object

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

Field Detail

subread_length

protected int subread_length

primary

protected EpiProReadInfo.EpiProInfo primary

prolog

protected EpiProReadInfo.EpiProInfo prolog

epilog

protected EpiProReadInfo.EpiProInfo epilog

Constructor Detail

EpiProReadInfo

public EpiProReadInfo(int subread_length)

Method Detail

getSubreadLength

public int getSubreadLength()

getPrimaryInfo

public EpiProReadInfo.EpiProInfo getPrimaryInfo()

getPrologInfo

public EpiProReadInfo.EpiProInfo getPrologInfo()

getEpilogInfo

public EpiProReadInfo.EpiProInfo getEpilogInfo()

setPrimaryInfo

public void setPrimaryInfo(int contig,
                  long from,
                  long to,
                  int strand,
                  int subread_start,
                  int subread_end)

setPrologInfo

public void setPrologInfo(int contig,
                 long from,
                 long to,
                 int strand,
                 int subread_start,
                 int subread_end)

setEpilogInfo

public void setEpilogInfo(int contig,
                 long from,
                 long to,
                 int strand,
                 int subread_start,
                 int subread_end)