public abstract class Hsp<S extends Sequence<C>,C extends Compound>
extends java.lang.Object
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,
java.lang.String hspQseq,
java.lang.String hspHseq,
java.lang.String hspIdentityString,
java.lang.Double percentageIdentity,
java.lang.Integer mismatchCount) |
Modifier and Type | Method | Description |
---|---|---|
boolean |
equals(java.lang.Object obj) |
Experimental.
|
SequencePair<S,C> |
getAlignment() |
|
int |
getHspAlignLen() |
|
double |
getHspBitScore() |
|
double |
getHspEvalue() |
|
int |
getHspGaps() |
|
int |
getHspHitFrame() |
|
int |
getHspHitFrom() |
|
int |
getHspHitTo() |
|
java.lang.String |
getHspHseq() |
HSP aligned hit sequence string
|
int |
getHspIdentity() |
|
java.lang.String |
getHspIdentityString() |
Identity string representing correspondence between aligned residues
|
int |
getHspNum() |
|
int |
getHspPositive() |
|
java.lang.String |
getHspQseq() |
HSP aligned query sequence string
|
int |
getHspQueryFrame() |
|
int |
getHspQueryFrom() |
|
int |
getHspQueryTo() |
|
int |
getHspScore() |
|
java.lang.Integer |
getMismatchCount() |
|
java.lang.Double |
getPercentageIdentity() |
|
int |
hashCode() |
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, java.lang.String hspQseq, java.lang.String hspHseq, java.lang.String hspIdentityString, java.lang.Double percentageIdentity, java.lang.Integer mismatchCount)
public int hashCode()
hashCode
in class java.lang.Object
public boolean equals(java.lang.Object obj)
equals
in class java.lang.Object
public SequencePair<S,C> getAlignment()
public int getHspNum()
public double getHspBitScore()
public int getHspScore()
public double getHspEvalue()
public int getHspQueryFrom()
public int getHspQueryTo()
public int getHspHitFrom()
public int getHspHitTo()
public int getHspQueryFrame()
public int getHspHitFrame()
public int getHspIdentity()
public int getHspPositive()
public int getHspGaps()
public int getHspAlignLen()
public java.lang.String getHspQseq()
public java.lang.String getHspHseq()
public java.lang.String getHspIdentityString()
public java.lang.Double getPercentageIdentity()
public java.lang.Integer getMismatchCount()