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
 java.util.List getHits()
          Return all hits in this sequence similarity search result.
 Sequence getQuerySequence()
          Returns the query sequence which was used to perform the search.
 java.util.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

java.util.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

java.util.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.