Package ubic.gemma.model.genome.sequenceAnalysis

Class BlatResult

java.lang.Object

ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult

ubic.gemma.model.genome.sequenceAnalysis.BlatResult

All Implemented Interfaces:

Serializable, Identifiable

public class BlatResult
extends SequenceSimilaritySearchResult

Represents the result of a BLAT search. The column names follow the convention of Kent et al.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	BlatResult.Factory

Constructor Summary

Constructors

Constructor	Description
BlatResult()

Method Summary

Modifier and Type	Method	Description
Integer	getBlockCount()
String	getBlockSizes()
Integer	getMatches()
Integer	getMismatches()
Integer	getNs()
Integer	getQueryEnd()
Integer	getQueryGapBases()
Integer	getQueryGapCount()
Integer	getQueryStart()
String	getQueryStarts()
Integer	getRepMatches()
String	getStrand()
Long	getTargetEnd()
Integer	getTargetGapBases()
Integer	getTargetGapCount()
Long	getTargetStart()
String	getTargetStarts()
Double	identity()	Fraction identity computation, as in psl.c.
Double	score()	Based on the JKSrc method in psl.c, but without double-penalizing for mismatches.
void	setBlockCount(Integer blockCount)
void	setBlockSizes(String blockSizes)
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	setQueryStart(Integer queryStart)
void	setQueryStarts(String queryStarts)
void	setRepMatches(Integer repMatches)
void	setStrand(String strand)
void	setTargetEnd(Long targetEnd)
void	setTargetGapBases(Integer targetGapBases)
void	setTargetGapCount(Integer targetGapCount)
void	setTargetStart(Long targetStart)
void	setTargetStarts(String targetStarts)
String	toString()

Methods inherited from class ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult

equals, getId, getQuerySequence, getSearchedDatabase, getTargetAlignedRegion, getTargetChromosome, getTargetSequence, hashCode, setId, setQuerySequence, setSearchedDatabase, setTargetAlignedRegion, setTargetChromosome, setTargetSequence

Methods inherited from class java.lang.Object

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

Constructor Detail

BlatResult

public BlatResult()

Method Detail

toString

public String toString()

Overrides:

toString in class SequenceSimilaritySearchResult

identity

public Double identity()

Fraction identity computation, as in psl.c. Modified to INCLUDE repeat matches in the match count. See Blat4 at UCSC.

Returns:

Value between 0 and 1.

score

public Double score()

Based on the JKSrc method in psl.c, but without double-penalizing for mismatches. We also consider repeat matches to be the same as regular matches.

Returns:

Value between 0 and 1, representing the fraction of matches, minus a gap penalty.

getBlockCount

public Integer getBlockCount()

setBlockCount

public void setBlockCount(Integer blockCount)

getBlockSizes

public String getBlockSizes()

setBlockSizes

public void setBlockSizes(String blockSizes)

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)

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)

getStrand

public String getStrand()

setStrand

public void setStrand(String strand)

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)