org.biojava.bio.search
Interface SeqSimilaritySearchResult

All Known Implementing Classes:
SimpleSeqSimilaritySearchResult

public interface SeqSimilaritySearchResult
extends java.lang.Cloneable

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

Author:
Gerald Loeffler for the IMP

Method Summary
 java.lang.Object clone()
           
 java.util.List getHits()
          return all hits in this sequence similarity search result.
 SymbolList getQuerySequence()
          return the sequence with which the search that produced this search result was performed.
 SeqSimilaritySearcher getSearcher()
          return the sequence similarity searcher that produced this sequence similarity search result.
 java.util.Map getSearchParameters()
          return the search parameters used in the search that produced this search result.
 SequenceDB getSequenceDB()
          return the sequence database against which the search that produced this search result was performed.
 

Method Detail

getSearcher

public SeqSimilaritySearcher getSearcher()
return the sequence similarity searcher that produced this sequence similarity search result.
Returns:
the SeqSimilaritySearcher object whose search() method produced this object. Never returns null.

getQuerySequence

public SymbolList getQuerySequence()
return the sequence with which the search that produced this search result was performed.
Returns:
the SymbolList object passed to the searchers search() method that produced this object. Never returns null.

getSequenceDB

public SequenceDB getSequenceDB()
return the sequence database against which the search that produced this search result was performed.
Returns:
the SequenceDB object passed to the searchers search() method that produced this object. Never returns null.

getSearchParameters

public java.util.Map getSearchParameters()
return the search parameters used in the search that produced this search result.
Returns:
the (immutable) search parameter Map object passed to the searchers search() method that produced this object. May return null because SeqSimilaritySearcher.search() must accept a null value for searchParameters.

getHits

public 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.

clone

public java.lang.Object clone()
Overrides:
clone in class java.lang.Object