org.biojava.nbio.core.search.io

Class Hit

java.lang.Object

org.biojava.nbio.core.search.io.Hit

All Implemented Interfaces:

Iterable<Hsp>

public abstract class Hit
extends Object
implements Iterable<Hsp>

This class models a search Hit. You will retrieve a list of this using iterator of a Result 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
Hit(int hitNum, String hitId, String hitDef, String hitAccession, int hitLen, List<Hsp> hsps, Sequence hitSequence)

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(Object obj) Implements conceptual comparisons of search results.
String	getHitAccession()
String	getHitDef()
String	getHitId()
int	getHitLen()
int	getHitNum()
Sequence	getHitSequence() returns the reference to the original and whole sequence hit in the database.
int	hashCode()
Iterator<Hsp>	iterator()

Methods inherited from class java.lang.Object

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

Constructor Detail

Hit

public Hit(int hitNum,
   String hitId,
   String hitDef,
   String hitAccession,
   int hitLen,
   List<Hsp> hsps,
   Sequence hitSequence)

Method Detail

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

Implements conceptual comparisons of search results. Fields unrelated to search are deliberately not considered.

Overrides:

equals in class Object

Returns:

getHitNum

public int getHitNum()

getHitId

public String getHitId()

getHitDef

public String getHitDef()

getHitAccession

public String getHitAccession()

getHitLen

public int getHitLen()

getHitSequence

public Sequence getHitSequence()

returns the reference to the original and whole sequence hit in the database. Available only if the ResultFactory implements setHitReferences and it was used before the parsing with SearchIO

Returns:

Sequence object

iterator

public Iterator<Hsp> iterator()

Specified by:

iterator in interface Iterable<Hsp>