org.biojava.bio.search
Class SimpleSeqSimilaritySearchResult

java.lang.Object
  |
  +--org.biojava.bio.search.SimpleSeqSimilaritySearchResult

public class SimpleSeqSimilaritySearchResult
extends java.lang.Object
implements SeqSimilaritySearchResult, java.lang.Cloneable

an class that implements the trivial (housekeeping) responsibilities of interface SeqSimilaritySearchResult. Objects of this class are immutable.

Author:
Gerald Loeffler for the IMP

Constructor Summary
SimpleSeqSimilaritySearchResult(SeqSimilaritySearcher searcher, SymbolList querySequence, SequenceDB sequenceDB, java.util.Map searchParameters, java.util.List hits)
          construct an immutable object by giving all its properties.
 
Method Summary
 java.lang.Object clone()
           
 boolean equals(java.lang.Object o)
           
 java.util.List getHits()
          return an unmodifiable view of the hits list.
 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 an unmodifiable view of the search parameters map.
 SequenceDB getSequenceDB()
          return the sequence database against which the search that produced this search result was performed.
 int hashCode()
           
 java.lang.String toString()
           
 
Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait
 

Constructor Detail

SimpleSeqSimilaritySearchResult

public SimpleSeqSimilaritySearchResult(SeqSimilaritySearcher searcher,
                                       SymbolList querySequence,
                                       SequenceDB sequenceDB,
                                       java.util.Map searchParameters,
                                       java.util.List hits)
construct an immutable object by giving all its properties.
Parameters:
searcher - the sequence similarity searcher that produced this search result. Not null.
querySequence - the query sequence that gave rise to this search result. Not null.
sequenceDB - the sequence database against the search that produced this results was done. Not null.
searchParameters - the search parameters used in the search that produced this result. May be null. If not null, the getter for this property returns an unmodifiable view of this object.
hits - the list of SeqSimilaritySearchHit objects that make up this result. Not null. The getter for this property returns an unmodifiable view of this object.
Method Detail

getSearcher

public SeqSimilaritySearcher getSearcher()
Description copied from interface: SeqSimilaritySearchResult
return the sequence similarity searcher that produced this sequence similarity search result.
Specified by:
getSearcher in interface SeqSimilaritySearchResult
Tags copied from interface: SeqSimilaritySearchResult
Returns:
the SeqSimilaritySearcher object whose search() method produced this object. Never returns null.

getQuerySequence

public SymbolList getQuerySequence()
Description copied from interface: SeqSimilaritySearchResult
return the sequence with which the search that produced this search result was performed.
Specified by:
getQuerySequence in interface SeqSimilaritySearchResult
Tags copied from interface: SeqSimilaritySearchResult
Returns:
the SymbolList object passed to the searchers search() method that produced this object. Never returns null.

getSequenceDB

public SequenceDB getSequenceDB()
Description copied from interface: SeqSimilaritySearchResult
return the sequence database against which the search that produced this search result was performed.
Specified by:
getSequenceDB in interface SeqSimilaritySearchResult
Tags copied from interface: SeqSimilaritySearchResult
Returns:
the SequenceDB object passed to the searchers search() method that produced this object. Never returns null.

getSearchParameters

public java.util.Map getSearchParameters()
return an unmodifiable view of the search parameters map.
Specified by:
getSearchParameters in interface SeqSimilaritySearchResult
Tags copied from interface: SeqSimilaritySearchResult
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 an unmodifiable view of the hits list.
Specified by:
getHits in interface SeqSimilaritySearchResult
Tags copied from interface: SeqSimilaritySearchResult
Returns:
an (immutable) List of SeqSimilaritySearchHit objects containing all hits in the search result. Never returns null but may return an empty list.

toString

public java.lang.String toString()
Overrides:
toString in class java.lang.Object

equals

public boolean equals(java.lang.Object o)
Overrides:
equals in class java.lang.Object

hashCode

public int hashCode()
Overrides:
hashCode in class java.lang.Object

clone

public java.lang.Object clone()
Specified by:
clone in interface SeqSimilaritySearchResult
Overrides:
clone in class java.lang.Object