org.biojava.bio.search
Class SimpleSeqSimilaritySearchResult

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

All Implemented Interfaces:

Annotatable, Changeable, SeqSimilaritySearchResult

public class SimpleSeqSimilaritySearchResult

extends AbstractChangeable

implements SeqSimilaritySearchResult

SimpleSeqSimilaritySearchResult objects represent a result of a search of a SymbolList against the sequences within a SequenceDB object. The core data (query sequence, database, search parameters, hits) have accessors, while supplementary data are stored in the Annotation object. Supplementary data are typically the more loosely formatted details which vary from one search program to another (and between versions of those programs).

Since:

1.1

Author:

Keith James, Gerald Loeffler

See Also:

AbstractChangeable, SeqSimilaritySearchResult, Annotatable

Nested Class Summary

Nested classes inherited from class org.biojava.bio.Annotatable

Annotatable.AnnotationForwarder

Field Summary

protected Annotatable.AnnotationForwarder

annotationForwarder

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Constructor Summary

SimpleSeqSimilaritySearchResult(Sequence querySequence, SequenceDB sequenceDB, java.util.Map searchParameters, java.util.List hits, Annotation annotation)
Creates a new SimpleSeqSimilaritySearchResult.

Method Summary

boolean	equals(java.lang.Object other)
Annotation	getAnnotation() getAnnotation returns the Annotation associated with this hit.
protected ChangeSupport	getChangeSupport(ChangeType ct) Called to retrieve the ChangeSupport for this object
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.
int	hashCode()
java.lang.String	toString()

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

annotationForwarder

protected transient Annotatable.AnnotationForwarder annotationForwarder

Constructor Detail

SimpleSeqSimilaritySearchResult

public SimpleSeqSimilaritySearchResult(Sequence querySequence,
                                       SequenceDB sequenceDB,
                                       java.util.Map searchParameters,
                                       java.util.List hits,
                                       Annotation annotation)

Creates a new SimpleSeqSimilaritySearchResult.

Parameters:

querySequence - a Sequence.

sequenceDB - a SequenceDB.

searchParameters - a Map.

annotation - an Annotation.

hits - a List.

Method Detail

getQuerySequence

public Sequence getQuerySequence()

Description copied from interface: SeqSimilaritySearchResult

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

Specified by:

getQuerySequence in interface SeqSimilaritySearchResult

Returns:

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

getSequenceDB

public SequenceDB getSequenceDB()

Description copied from interface: SeqSimilaritySearchResult

Returns the sequence database against which the search was performed.

Specified by:

getSequenceDB in interface SeqSimilaritySearchResult

Returns:

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

getSearchParameters

public java.util.Map getSearchParameters()

Description copied from interface: SeqSimilaritySearchResult

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

Specified by:

getSearchParameters in interface SeqSimilaritySearchResult

Returns:

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

getHits

public java.util.List getHits()

Description copied from interface: SeqSimilaritySearchResult

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

Specified by:

getHits in 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.

getAnnotation

public Annotation getAnnotation()

getAnnotation returns the Annotation associated with this hit.

Specified by:

getAnnotation in interface Annotatable

Returns:

an Annotation.

equals

public boolean equals(java.lang.Object other)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getChangeSupport

protected ChangeSupport getChangeSupport(ChangeType ct)

Description copied from class: AbstractChangeable

Called to retrieve the ChangeSupport for this object

Overrides:

getChangeSupport in class AbstractChangeable