Package org.biojava.bio.search
Class SimpleSeqSimilaritySearchResult
java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.search.SimpleSeqSimilaritySearchResult
- All Implemented Interfaces:
Annotatable
,SeqSimilaritySearchResult
,Changeable
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:
-
Nested Class Summary
Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
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Field Summary
FieldsFields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
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Constructor Summary
ConstructorsConstructorDescriptionSimpleSeqSimilaritySearchResult
(Sequence querySequence, SequenceDB sequenceDB, Map searchParameters, List hits, Annotation annotation) Creates a newSimpleSeqSimilaritySearchResult
. -
Method Summary
Modifier and TypeMethodDescriptionboolean
getAnnotation
returns the Annotation associated with this hit.protected ChangeSupport
Called to retrieve the ChangeSupport for this object.getHits()
Return all hits in this sequence similarity search result.Returns the query sequence which was used to perform the search.Returns the search parameters used in the search that produced this search result.Returns the sequence database against which the search was performed.int
hashCode()
toString()
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
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Field Details
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annotationForwarder
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Constructor Details
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SimpleSeqSimilaritySearchResult
public SimpleSeqSimilaritySearchResult(Sequence querySequence, SequenceDB sequenceDB, Map searchParameters, List hits, Annotation annotation) Creates a newSimpleSeqSimilaritySearchResult
.- Parameters:
querySequence
- aSequence
.sequenceDB
- aSequenceDB
.searchParameters
- aMap
.hits
- aList
.annotation
- anAnnotation
.
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Method Details
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getQuerySequence
Description copied from interface:SeqSimilaritySearchResult
Returns the query sequence which was used to perform the search.- Specified by:
getQuerySequence
in interfaceSeqSimilaritySearchResult
- Returns:
- the
Sequence
object used to search theSequenceDB
. Never returns null.
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getSequenceDB
Description copied from interface:SeqSimilaritySearchResult
Returns the sequence database against which the search was performed.- Specified by:
getSequenceDB
in interfaceSeqSimilaritySearchResult
- Returns:
- the
SequenceDB object
against which the search was carried out. Never returns null.
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getSearchParameters
Description copied from interface:SeqSimilaritySearchResult
Returns the search parameters used in the search that produced this search result.- Specified by:
getSearchParameters
in interfaceSeqSimilaritySearchResult
- Returns:
- the (immutable) search parameter
Map object
. May return null.
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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 interfaceSeqSimilaritySearchResult
- Returns:
- an (immutable)
List
ofSeqSimilaritySearchHit
objects containing all hits in the search result. Never returns null but may return an empty list.
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getAnnotation
getAnnotation
returns the Annotation associated with this hit.- Specified by:
getAnnotation
in interfaceAnnotatable
- Returns:
- an
Annotation
.
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equals
-
hashCode
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toString
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getChangeSupport
Description copied from class:AbstractChangeable
Called to retrieve the ChangeSupport for this object.Your implementation of this method should have the following structure:
It is usual for the forwarding listeners (someForwarder in this example) to be transient and lazily instantiated. Be sure to register invalid input: '&' unregister the forwarder in the code that does the ChangeEvent handling in setter methods.ChangeSupport cs = super.getChangeSupport(ct); if(someForwarder == null invalid input: '&'invalid input: '&' ct.isMatching(SomeInterface.SomeChangeType)) { someForwarder = new ChangeForwarder(... this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange); } return cs;
- Overrides:
getChangeSupport
in classAbstractChangeable
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