Package ubic.gemma.model.genome.sequenceAnalysis

Class BlatResultValueObject

java.lang.Object

ubic.gemma.model.common.IdentifiableValueObject<BlatResult>

ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject

All Implemented Interfaces:

Serializable, Identifiable

public class BlatResultValueObject
extends IdentifiableValueObject<BlatResult>

Author:

paul

See Also:

• Serialized Form

Field Summary

Fields inherited from class ubic.gemma.model.common.IdentifiableValueObject

id

Constructor Summary

Constructors

Constructor	Description
BlatResultValueObject()	Required when using the class as a spring bean.
BlatResultValueObject(Long id)
BlatResultValueObject(Long id, TaxonValueObject taxon, Integer blockCount, String blockSizes, Integer matches, Integer mismatches, Integer ns, Integer queryEnd, Integer queryGapBases, Integer queryGapCount, BioSequenceValueObject querySequence, Integer queryStart, String queryStarts, Integer repMatches, Double score, Double identity, String strand, String targetChromosomeName, String targetDatabase, Long targetEnd, Integer targetGapBases, Integer targetGapCount, Long targetStart, String targetStarts)
BlatResultValueObject(BlatResult br, Double score, Double identity)

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object obj)
Integer	getBlockCount()
String	getBlockSizes()
Double	getIdentity()
Integer	getMatches()
Integer	getMismatches()
Integer	getNs()
Integer	getQueryEnd()
Integer	getQueryGapBases()
Integer	getQueryGapCount()
BioSequenceValueObject	getQuerySequence()
Integer	getQueryStart()
String	getQueryStarts()
Integer	getRepMatches()
Double	getScore()
String	getStrand()
String	getTargetChromosomeName()
String	getTargetDatabase()
Long	getTargetEnd()
Integer	getTargetGapBases()
Integer	getTargetGapCount()
Long	getTargetStart()
String	getTargetStarts()
TaxonValueObject	getTaxon()
int	hashCode()
void	setBlockCount(Integer blockCount)
void	setBlockSizes(String blockSizes)
void	setIdentity(Double identity)
void	setMatches(Integer matches)
void	setMismatches(Integer mismatches)
void	setNs(Integer ns)
void	setQueryEnd(Integer queryEnd)
void	setQueryGapBases(Integer queryGapBases)
void	setQueryGapCount(Integer queryGapCount)
void	setQuerySequence(BioSequenceValueObject querySequence)
void	setQueryStart(Integer queryStart)
void	setQueryStarts(String queryStarts)
void	setRepMatches(Integer repMatches)
void	setScore(Double score)
void	setStrand(String strand)
void	setTargetChromosomeName(String targetChromosomeName)
void	setTargetDatabase(String targetDatabase)
void	setTargetEnd(Long targetEnd)
void	setTargetGapBases(Integer targetGapBases)
void	setTargetGapCount(Integer targetGapCount)
void	setTargetStart(Long targetStart)
void	setTargetStarts(String targetStarts)
void	setTaxon(TaxonValueObject taxon)

Methods inherited from class ubic.gemma.model.common.IdentifiableValueObject

getId, setId, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Details

BlatResultValueObject

public BlatResultValueObject()

Required when using the class as a spring bean.

BlatResultValueObject

public BlatResultValueObject(Long id)

BlatResultValueObject

public BlatResultValueObject(BlatResult br,
 Double score,
 Double identity)

BlatResultValueObject

public BlatResultValueObject(Long id,
 TaxonValueObject taxon,
 Integer blockCount,
 String blockSizes,
 Integer matches,
 Integer mismatches,
 Integer ns,
 Integer queryEnd,
 Integer queryGapBases,
 Integer queryGapCount,
 BioSequenceValueObject querySequence,
 Integer queryStart,
 String queryStarts,
 Integer repMatches,
 Double score,
 Double identity,
 String strand,
 String targetChromosomeName,
 String targetDatabase,
 Long targetEnd,
 Integer targetGapBases,
 Integer targetGapCount,
 Long targetStart,
 String targetStarts)

Method Details

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

getBlockCount

public Integer getBlockCount()

setBlockCount

public void setBlockCount(Integer blockCount)

getBlockSizes

public String getBlockSizes()

setBlockSizes

public void setBlockSizes(String blockSizes)

getIdentity

public Double getIdentity()

setIdentity

public void setIdentity(Double identity)

Parameters:

identity - the identity to set (0-1)

getMatches

public Integer getMatches()

setMatches

public void setMatches(Integer matches)

getMismatches

public Integer getMismatches()

setMismatches

public void setMismatches(Integer mismatches)

getNs

public Integer getNs()

setNs

public void setNs(Integer ns)

getQueryEnd

public Integer getQueryEnd()

setQueryEnd

public void setQueryEnd(Integer queryEnd)

getQueryGapBases

public Integer getQueryGapBases()

setQueryGapBases

public void setQueryGapBases(Integer queryGapBases)

getQueryGapCount

public Integer getQueryGapCount()

setQueryGapCount

public void setQueryGapCount(Integer queryGapCount)

getQuerySequence

public BioSequenceValueObject getQuerySequence()

Returns:

the querySequence

setQuerySequence

public void setQuerySequence(BioSequenceValueObject querySequence)

Parameters:

querySequence - the querySequence to set

getQueryStart

public Integer getQueryStart()

setQueryStart

public void setQueryStart(Integer queryStart)

getQueryStarts

public String getQueryStarts()

setQueryStarts

public void setQueryStarts(String queryStarts)

getRepMatches

public Integer getRepMatches()

setRepMatches

public void setRepMatches(Integer repMatches)

getScore

public Double getScore()

setScore

public void setScore(Double score)

getStrand

public String getStrand()

setStrand

public void setStrand(String strand)

getTargetChromosomeName

public String getTargetChromosomeName()

setTargetChromosomeName

public void setTargetChromosomeName(String targetChromosomeName)

getTargetDatabase

public String getTargetDatabase()

setTargetDatabase

public void setTargetDatabase(String targetDatabase)

getTargetEnd

public Long getTargetEnd()

setTargetEnd

public void setTargetEnd(Long targetEnd)

getTargetGapBases

public Integer getTargetGapBases()

setTargetGapBases

public void setTargetGapBases(Integer targetGapBases)

getTargetGapCount

public Integer getTargetGapCount()

setTargetGapCount

public void setTargetGapCount(Integer targetGapCount)

getTargetStart

public Long getTargetStart()

setTargetStart

public void setTargetStart(Long targetStart)

getTargetStarts

public String getTargetStarts()

setTargetStarts

public void setTargetStarts(String targetStarts)

getTaxon

public TaxonValueObject getTaxon()

setTaxon

public void setTaxon(TaxonValueObject taxon)