org.jbei.ice.storage.model

Class TraceSequenceAlignment

java.lang.Object

org.jbei.ice.storage.model.TraceSequenceAlignment

All Implemented Interfaces:

DataModel

@Entity
public class TraceSequenceAlignment
extends Object
implements DataModel

Store computed trace alignment information.

Author:

Zinovii Dmytrv, Timothy Ham

Constructor Summary

Constructors

Constructor and Description
TraceSequenceAlignment()
TraceSequenceAlignment(TraceSequence traceSequence, int score, int strand, int queryStart, int queryEnd, int subjectStart, int subjectEnd, String queryAlignment, String subjectAlignment, String sequenceHash, Date modificationTime)

Method Summary

Modifier and Type	Method and Description
long	getId()
Date	getModificationTime()
String	getQueryAlignment()
int	getQueryEnd()
int	getQueryStart()
int	getScore()
String	getSequenceHash()
int	getStrand()
String	getSubjectAlignment()
int	getSubjectEnd()
int	getSubjectStart()
TraceSequence	getTraceSequence()
void	setId(long id)
void	setModificationTime(Date modificationTime)
void	setQueryAlignment(String queryAlignment)
void	setQueryEnd(int queryEnd)
void	setQueryStart(int queryStart)
void	setScore(int score)
void	setSequenceHash(String sequenceHash)
void	setStrand(int strand)
void	setSubjectAlignment(String subjectAlignment)
void	setSubjectEnd(int subjectEnd)
void	setSubjectStart(int subjectStart)
void	setTraceSequence(TraceSequence traceSequence)
TraceSequenceAlignmentInfo	toDataTransferObject()

Methods inherited from class java.lang.Object

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

Constructor Detail

TraceSequenceAlignment

public TraceSequenceAlignment()

TraceSequenceAlignment

public TraceSequenceAlignment(TraceSequence traceSequence,
                              int score,
                              int strand,
                              int queryStart,
                              int queryEnd,
                              int subjectStart,
                              int subjectEnd,
                              String queryAlignment,
                              String subjectAlignment,
                              String sequenceHash,
                              Date modificationTime)

Method Detail

getTraceSequence

public TraceSequence getTraceSequence()

setTraceSequence

public void setTraceSequence(TraceSequence traceSequence)

getId

public long getId()

Specified by:

getId in interface DataModel

setId

public void setId(long id)

getScore

public int getScore()

getStrand

public int getStrand()

setStrand

public void setStrand(int strand)

setScore

public void setScore(int score)

getQueryStart

public int getQueryStart()

setQueryStart

public void setQueryStart(int queryStart)

getQueryEnd

public int getQueryEnd()

setQueryEnd

public void setQueryEnd(int queryEnd)

getSubjectStart

public int getSubjectStart()

setSubjectStart

public void setSubjectStart(int subjectStart)

getSubjectEnd

public int getSubjectEnd()

setSubjectEnd

public void setSubjectEnd(int subjectEnd)

getQueryAlignment

public String getQueryAlignment()

setQueryAlignment

public void setQueryAlignment(String queryAlignment)

getSubjectAlignment

public String getSubjectAlignment()

setSubjectAlignment

public void setSubjectAlignment(String subjectAlignment)

getSequenceHash

public String getSequenceHash()

setSequenceHash

public void setSequenceHash(String sequenceHash)

getModificationTime

public Date getModificationTime()

setModificationTime

public void setModificationTime(Date modificationTime)

toDataTransferObject

public TraceSequenceAlignmentInfo toDataTransferObject()

Specified by:

toDataTransferObject in interface DataModel