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).AbstractChangeable,
SeqSimilaritySearchResult,
AnnotatableAnnotatable.AnnotationForwarder| Modifier and Type | Field and Description |
|---|---|
protected ChangeForwarder |
annotationForwarder |
ANNOTATION| Constructor and Description |
|---|
SimpleSeqSimilaritySearchResult(Sequence querySequence,
SequenceDB sequenceDB,
Map searchParameters,
List hits,
Annotation annotation)
Creates a new
SimpleSeqSimilaritySearchResult. |
| Modifier and Type | Method and Description |
|---|---|
boolean |
equals(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.
|
List |
getHits()
Return all hits in this sequence similarity search result.
|
Sequence |
getQuerySequence()
Returns the query sequence which was used to perform the search.
|
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() |
String |
toString() |
addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListenerclone, finalize, getClass, notify, notifyAll, wait, wait, waitaddChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListenerprotected transient ChangeForwarder annotationForwarder
public SimpleSeqSimilaritySearchResult(Sequence querySequence, SequenceDB sequenceDB, Map searchParameters, List hits, Annotation annotation)
SimpleSeqSimilaritySearchResult.querySequence - a Sequence.sequenceDB - a SequenceDB.searchParameters - a Map.annotation - an Annotation.hits - a List.public Sequence getQuerySequence()
SeqSimilaritySearchResultgetQuerySequence in interface SeqSimilaritySearchResultSequence object used to search the
SequenceDB. Never returns null.public SequenceDB getSequenceDB()
SeqSimilaritySearchResultgetSequenceDB in interface SeqSimilaritySearchResultSequenceDB object against which the
search was carried out. Never returns null.public Map getSearchParameters()
SeqSimilaritySearchResultgetSearchParameters in interface SeqSimilaritySearchResultMap
object. May return null.public List getHits()
SeqSimilaritySearchResultgetHits in interface SeqSimilaritySearchResultList of
SeqSimilaritySearchHit objects containing all hits
in the search result. Never returns null but may return an
empty list.public Annotation getAnnotation()
getAnnotation returns the Annotation associated
with this hit.getAnnotation in interface AnnotatableAnnotation.protected ChangeSupport getChangeSupport(ChangeType ct)
AbstractChangeable
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;
getChangeSupport in class AbstractChangeableCopyright © 2014 BioJava. All rights reserved.