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java.lang.Objectorg.biojava.utils.AbstractChangeable
org.biojava.bio.search.SequenceDBSearchResult
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).
AbstractChangeable
,
SeqSimilaritySearchResult
,
Annotatable
Nested Class Summary |
Nested classes inherited from class org.biojava.bio.Annotatable |
Annotatable.AnnotationForwarder |
Field Summary | |
protected Annotatable.AnnotationForwarder |
annotationForwarder
Deprecated. |
Fields inherited from interface org.biojava.bio.Annotatable |
ANNOTATION |
Constructor Summary | |
SequenceDBSearchResult(Sequence querySequence,
SequenceDB sequenceDB,
java.util.Map searchParameters,
java.util.List hits,
Annotation annotation)
Deprecated. Creates a new SequenceDBSearchResult . |
Method Summary | |
boolean |
equals(java.lang.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 |
java.util.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. |
java.util.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. |
java.lang.String |
toString()
Deprecated. |
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 |
protected transient Annotatable.AnnotationForwarder annotationForwarder
Constructor Detail |
public SequenceDBSearchResult(Sequence querySequence, SequenceDB sequenceDB, java.util.Map searchParameters, java.util.List hits, Annotation annotation)
SequenceDBSearchResult
.
querySequence
- a Sequence
.sequenceDB
- a SequenceDB
.searchParameters
- a Map
.annotation
- an Annotation
.hits
- a List
.Method Detail |
public Sequence getQuerySequence()
SeqSimilaritySearchResult
getQuerySequence
in interface SeqSimilaritySearchResult
Sequence
object used to search the
SequenceDB
. Never returns null.public SequenceDB getSequenceDB()
SeqSimilaritySearchResult
getSequenceDB
in interface SeqSimilaritySearchResult
SequenceDB object
against which the
search was carried out. Never returns null.public java.util.Map getSearchParameters()
SeqSimilaritySearchResult
getSearchParameters
in interface SeqSimilaritySearchResult
Map
object
. May return null.public java.util.List getHits()
SeqSimilaritySearchResult
getHits
in interface SeqSimilaritySearchResult
List
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 Annotatable
Annotation
.public boolean equals(java.lang.Object other)
public int hashCode()
public java.lang.String toString()
protected ChangeSupport getChangeSupport(ChangeType ct)
AbstractChangeable
getChangeSupport
in class AbstractChangeable
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