org.biojava.bio.search

Interface SeqSimilaritySearchResult

All Superinterfaces:

Annotatable, Changeable

All Known Implementing Classes:

SequenceDBSearchResult, SimpleSeqSimilaritySearchResult

public interface SeqSimilaritySearchResult
extends Annotatable

Objects of this type represent one particular result of a sequence similarity search.

Author:

Gerald Loeffler, Keith James

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

Annotatable.AnnotationForwarder

Field Summary

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Method Summary

Modifier and Type	Method and Description
List	getHits() Return all hits in this sequence similarity search result.
Sequence	getQuerySequence() Returns the query sequence which was used to perform the search.
Map	getSearchParameters() Returns the search parameters used in the search that produced this search result.
SequenceDB	getSequenceDB() Returns the sequence database against which the search was performed.

Methods inherited from interface org.biojava.bio.Annotatable

getAnnotation

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Method Detail

getQuerySequence

Sequence getQuerySequence()

Returns the query sequence which was used to perform the search.

Returns:

the Sequence object used to search the SequenceDB. Never returns null.

getSequenceDB

SequenceDB getSequenceDB()

Returns the sequence database against which the search was performed.

Returns:

the SequenceDB object against which the search was carried out. Never returns null.

getSearchParameters

Map getSearchParameters()

Returns the search parameters used in the search that produced this search result.

Returns:

the (immutable) search parameter Map object. May return null.

getHits

List getHits()

Return all hits in this sequence similarity search result. The hits are sorted from best to worst.

Returns:

an (immutable) List of SeqSimilaritySearchHit objects containing all hits in the search result. Never returns null but may return an empty list.