object.common
Class BlastHit

java.lang.Object
  object.common.BlastHit

public class BlastHit
extends java.lang.Object

Description
When a Blast program is launch, the results are parsed and stored as BlastHit objects in an Hashtable results, data member of a Blast object
Infos : KLB - IPMC - 08/2003

See Also:

Blast

Field Summary

private java.lang.String	alignmentSize Alignment size
private java.lang.String	expectValue Expect value of the alignment
private java.lang.String	hitId Hit id for the corresponding alignment
private java.lang.String	hitSequence Hit sequence
private java.lang.String	hitStartPosition Start position on the hit sequence
private java.lang.String	hitStopPosition Stop position on the hit sequence
private java.lang.String	numberOfIdentities Number of identities
private java.lang.String	percentageIdentity Percentage of identity
private java.lang.String	queryId Query id for the corresponding alignment
private java.lang.String	querySequence Query sequence
private java.lang.String	queryStartPosition Start position on the query sequence
private java.lang.String	queryStopPosition Stop position on the query sequence
private java.lang.String	score Score of the corresponding alignment

Constructor Summary

BlastHit()
Default constructor

BlastHit(java.lang.String queryId, java.lang.String hitId, java.lang.String score, java.lang.String alignmentSize, java.lang.String percentageIdentity, java.lang.String expectValue, java.lang.String queryStartPosition, java.lang.String queryStopPosition, java.lang.String hitStartPosition, java.lang.String hitStopPosition, java.lang.String querySequence, java.lang.String hitSequence)

Method Summary

java.lang.String	getAlignmentSize() Alignment size
java.lang.String	getExpectValue() Expect value of the alignment
java.lang.String	getHitId() Hit id for the corresponding alignment
java.lang.String	getHitSequence() Hit sequence
java.lang.String	getHitStartPosition() Start position on the hit sequence
java.lang.String	getHitStopPosition() Stop position on the hit sequence
java.lang.String	getNumberOfIdentities() Number of identities
java.lang.String	getPercentageIdentity() Percentage of identity
java.lang.String	getQueryId() Query id for the corresponding alignment
java.lang.String	getQuerySequence() Query sequence
java.lang.String	getQueryStartPosition() Start position on the query sequence
java.lang.String	getQueryStopPosition() Stop position on the query sequence
java.lang.String	getScore() Score of the corresponding alignment
void	setAlignmentSize(java.lang.String alignmentSize)
void	setExpectValue(java.lang.String expectValue)
void	setHitId(java.lang.String hitId)
void	setHitSequence(java.lang.String hitSequence)
void	setHitStartPosition(java.lang.String hitStartPosition)
void	setHitStopPosition(java.lang.String hitStopPosition)
void	setNumberOfIdentities(java.lang.String numberOfIdentities)
void	setPercentageIdentity(java.lang.String percentageIdentity)
void	setQueryId(java.lang.String queryId)
void	setQuerySequence(java.lang.String querySequence)
void	setQueryStartPosition(java.lang.String queryStartPosition)
void	setQueryStopPosition(java.lang.String queryStopPosition)
void	setScore(java.lang.String score)

Methods inherited from class java.lang.Object

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

Field Detail

queryId

private java.lang.String queryId

Query id for the corresponding alignment

hitId

private java.lang.String hitId

Hit id for the corresponding alignment

score

private java.lang.String score

Score of the corresponding alignment

alignmentSize

private java.lang.String alignmentSize

Alignment size

percentageIdentity

private java.lang.String percentageIdentity

Percentage of identity

numberOfIdentities

private java.lang.String numberOfIdentities

Number of identities

expectValue

private java.lang.String expectValue

Expect value of the alignment

queryStartPosition

private java.lang.String queryStartPosition

Start position on the query sequence

queryStopPosition

private java.lang.String queryStopPosition

Stop position on the query sequence

hitStartPosition

private java.lang.String hitStartPosition

Start position on the hit sequence

hitStopPosition

private java.lang.String hitStopPosition

Stop position on the hit sequence

querySequence

private java.lang.String querySequence

Query sequence

hitSequence

private java.lang.String hitSequence

Hit sequence

Constructor Detail

BlastHit

public BlastHit()

Default constructor

BlastHit

public BlastHit(java.lang.String queryId,
                java.lang.String hitId,
                java.lang.String score,
                java.lang.String alignmentSize,
                java.lang.String percentageIdentity,
                java.lang.String expectValue,
                java.lang.String queryStartPosition,
                java.lang.String queryStopPosition,
                java.lang.String hitStartPosition,
                java.lang.String hitStopPosition,
                java.lang.String querySequence,
                java.lang.String hitSequence)

Method Detail

getQueryId

public java.lang.String getQueryId()

Query id for the corresponding alignment

setQueryId

public void setQueryId(java.lang.String queryId)

getHitId

public java.lang.String getHitId()

Hit id for the corresponding alignment

setHitId

public void setHitId(java.lang.String hitId)

getScore

public java.lang.String getScore()

Score of the corresponding alignment

setScore

public void setScore(java.lang.String score)

getAlignmentSize

public java.lang.String getAlignmentSize()

Alignment size

setAlignmentSize

public void setAlignmentSize(java.lang.String alignmentSize)

getPercentageIdentity

public java.lang.String getPercentageIdentity()

Percentage of identity

setPercentageIdentity

public void setPercentageIdentity(java.lang.String percentageIdentity)

getNumberOfIdentities

public java.lang.String getNumberOfIdentities()

Number of identities

setNumberOfIdentities

public void setNumberOfIdentities(java.lang.String numberOfIdentities)

getExpectValue

public java.lang.String getExpectValue()

Expect value of the alignment

setExpectValue

public void setExpectValue(java.lang.String expectValue)

getQueryStartPosition

public java.lang.String getQueryStartPosition()

Start position on the query sequence

setQueryStartPosition

public void setQueryStartPosition(java.lang.String queryStartPosition)

getQueryStopPosition

public java.lang.String getQueryStopPosition()

Stop position on the query sequence

setQueryStopPosition

public void setQueryStopPosition(java.lang.String queryStopPosition)

getHitStartPosition

public java.lang.String getHitStartPosition()

Start position on the hit sequence

setHitStartPosition

public void setHitStartPosition(java.lang.String hitStartPosition)

getHitStopPosition

public java.lang.String getHitStopPosition()

Stop position on the hit sequence

setHitStopPosition

public void setHitStopPosition(java.lang.String hitStopPosition)

getQuerySequence

public java.lang.String getQuerySequence()

Query sequence

setQuerySequence

public void setQuerySequence(java.lang.String querySequence)

getHitSequence

public java.lang.String getHitSequence()

Hit sequence

setHitSequence

public void setHitSequence(java.lang.String hitSequence)