Hsp

java.lang.Object
- org.biojava.nbio.core.search.io.Hsp<S,C>

```
public abstract class Hsp<S extends Sequence<C>,C extends Compound>
extends java.lang.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 and 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)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and 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()`

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

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,
           java.lang.String hspQseq,
           java.lang.String hspHseq,
           java.lang.String hspIdentityString,
           java.lang.Double percentageIdentity,
           java.lang.Integer mismatchCount)

Method Detail
- hashCode
```
public int hashCode()
```
  Overrides:
  
  hashCode in class java.lang.Object
- equals
```
public boolean equals(java.lang.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 java.lang.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 java.lang.String getHspQseq()
```
  HSP aligned query sequence string
  
  Returns:
- getHspHseq
```
public java.lang.String getHspHseq()
```
  HSP aligned hit sequence string
  
  Returns:
- getHspIdentityString
```
public java.lang.String getHspIdentityString()
```
  Identity string representing correspondence between aligned residues
  
  Returns:
- getPercentageIdentity
```
public java.lang.Double getPercentageIdentity()
```
- getMismatchCount
```
public java.lang.Integer getMismatchCount()
```

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

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Hsp

Method Detail

hashCode

equals

getAlignment

getHspNum

getHspBitScore

getHspScore

getHspEvalue

getHspQueryFrom

getHspQueryTo

getHspHitFrom

getHspHitTo

getHspQueryFrame

getHspHitFrame

getHspIdentity

getHspPositive

getHspGaps

getHspAlignLen

getHspQseq

getHspHseq

getHspIdentityString

getPercentageIdentity

getMismatchCount