Package org.biojava.nbio.core.search.io

Class Hsp<S extends Sequence<C>,C extends Compound>

java.lang.Object

org.biojava.nbio.core.search.io.Hsp<S,C>

Type Parameters:

S - the sequence type

C - the compound type

public abstract class Hsp<S extends Sequence<C>,C extends Compound>
extends Object

This class models a search Hsp. You will retrieve a list of this using iterator of a Hit

Designed by Paolo Pavan. You may want to find my contacts on Github and LinkedIn for code info or discuss major changes. https://github.com/paolopavan

Author:

Paolo Pavan

Constructor Summary

Constructors

Constructor	Description
Hsp(int hspNum, double hspBitScore, int hspScore, double hspEvalue, int hspQueryFrom, int hspQueryTo, int hspHitFrom, int hspHitTo, int hspQueryFrame, int hspHitFrame, int hspIdentity, int hspPositive, int hspGaps, int hspAlignLen, String hspQseq, String hspHseq, String hspIdentityString, Double percentageIdentity, Integer mismatchCount)

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object obj)	Experimental.
SequencePair<S,C>	getAlignment()
int	getHspAlignLen()
double	getHspBitScore()
double	getHspEvalue()
int	getHspGaps()
int	getHspHitFrame()
int	getHspHitFrom()
int	getHspHitTo()
String	getHspHseq()	HSP aligned hit sequence string
int	getHspIdentity()
String	getHspIdentityString()	Identity string representing correspondence between aligned residues
int	getHspNum()
int	getHspPositive()
String	getHspQseq()	HSP aligned query sequence string
int	getHspQueryFrame()
int	getHspQueryFrom()
int	getHspQueryTo()
int	getHspScore()
Integer	getMismatchCount()
Double	getPercentageIdentity()
int	hashCode()

Methods inherited from class java.lang.Object

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

Constructor Details

Hsp

public Hsp(int hspNum,
 double hspBitScore,
 int hspScore,
 double hspEvalue,
 int hspQueryFrom,
 int hspQueryTo,
 int hspHitFrom,
 int hspHitTo,
 int hspQueryFrame,
 int hspHitFrame,
 int hspIdentity,
 int hspPositive,
 int hspGaps,
 int hspAlignLen,
 String hspQseq,
 String hspHseq,
 String hspIdentityString,
 Double percentageIdentity,
 Integer mismatchCount)

Method Details

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

Experimental. Wants to implement conceptual comparisons of search results. Fields unrelated to search are deliberately not considered. In HSP case, alignment representation strings are considered.

Overrides:

equals in class Object

Returns:

true if HSP alignments are the same, false otherwise or if alignment strings are undetermined

getAlignment

public SequencePair<S,C> getAlignment()

getHspNum

public int getHspNum()

getHspBitScore

public double getHspBitScore()

getHspScore

public int getHspScore()

getHspEvalue

public double getHspEvalue()

getHspQueryFrom

public int getHspQueryFrom()

getHspQueryTo

public int getHspQueryTo()

getHspHitFrom

public int getHspHitFrom()

getHspHitTo

public int getHspHitTo()

getHspQueryFrame

public int getHspQueryFrame()

getHspHitFrame

public int getHspHitFrame()

getHspIdentity

public int getHspIdentity()

getHspPositive

public int getHspPositive()

getHspGaps

public int getHspGaps()

getHspAlignLen

public int getHspAlignLen()

getHspQseq

public String getHspQseq()

HSP aligned query sequence string

Returns:

getHspHseq

public String getHspHseq()

HSP aligned hit sequence string

Returns:

getHspIdentityString

public String getHspIdentityString()

Identity string representing correspondence between aligned residues

Returns:

getPercentageIdentity

public Double getPercentageIdentity()

getMismatchCount

public Integer getMismatchCount()