org.biojava.bio.search

Class SequenceDBSearchResult

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.search.SequenceDBSearchResult

All Implemented Interfaces:

Annotatable, SeqSimilaritySearchResult, Changeable

Deprecated.

SimpleSeqSimilaritySearchResult has been made Annotatable and is now functionally identical.

public class SequenceDBSearchResult
extends AbstractChangeable
implements SeqSimilaritySearchResult, Annotatable

SequenceDBSearchResult 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, Matthew Pocock

See Also:

AbstractChangeable, SeqSimilaritySearchResult, Annotatable

Nested Class Summary

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

Annotatable.AnnotationForwarder

Field Summary

Fields

Modifier and Type	Field and Description
protected ChangeForwarder	annotationForwarder Deprecated.

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Constructor Summary

Constructors

Constructor and Description
SequenceDBSearchResult(Sequence querySequence, SequenceDB sequenceDB, Map searchParameters, List hits, Annotation annotation) Deprecated. Creates a new SequenceDBSearchResult.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(Object other) Deprecated.
Annotation	getAnnotation() Deprecated. getAnnotation returns the Annotation associated with this hit.
protected ChangeSupport	getChangeSupport(ChangeType ct) Deprecated. Called to retrieve the ChangeSupport for this object.
List	getHits() Deprecated. Return all hits in this sequence similarity search result.
Sequence	getQuerySequence() Deprecated. Returns the query sequence which was used to perform the search.
Map	getSearchParameters() Deprecated. Returns the search parameters used in the search that produced this search result.
SequenceDB	getSequenceDB() Deprecated. Returns the sequence database against which the search was performed.
int	hashCode() Deprecated.
String	toString() Deprecated.

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, hasListeners, 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 ChangeForwarder annotationForwarder

Deprecated.

Constructor Detail

SequenceDBSearchResult

public SequenceDBSearchResult(Sequence querySequence,
                      SequenceDB sequenceDB,
                      Map searchParameters,
                      List hits,
                      Annotation annotation)

Deprecated.

Creates a new SequenceDBSearchResult.

Parameters:

querySequence - a Sequence.

sequenceDB - a SequenceDB.

searchParameters - a Map.

annotation - an Annotation.

hits - a List.

Method Detail

getQuerySequence

public Sequence getQuerySequence()

Deprecated.

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()

Deprecated.

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 Map getSearchParameters()

Deprecated.

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 List getHits()

Deprecated.

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()

Deprecated.

getAnnotation returns the Annotation associated with this hit.

Specified by:

getAnnotation in interface Annotatable

Returns:

an Annotation.

equals

public boolean equals(Object other)

Deprecated.

Overrides:

equals in class Object

hashCode

public int hashCode()

Deprecated.

Overrides:

hashCode in class Object

toString

public String toString()

Deprecated.

Overrides:

toString in class Object

getChangeSupport

protected ChangeSupport getChangeSupport(ChangeType ct)

Deprecated.

Description copied from class: AbstractChangeable

Called to retrieve the ChangeSupport for this object.

Your implementation of this method should have the following structure:

 ChangeSupport cs = super.getChangeSupport(ct);

 if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
   someForwarder = new ChangeForwarder(...

   this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
 }

 return cs;
 

It is usual for the forwarding listeners (someForwarder in this example) to be transient and lazily instantiated. Be sure to register & unregister the forwarder in the code that does the ChangeEvent handling in setter methods.

Overrides:

getChangeSupport in class AbstractChangeable