Package org.biojava.bio.seq.db
Interface SequenceDB
- All Superinterfaces:
Changeable
,SequenceDBLite
- All Known Subinterfaces:
RichSequenceDB
- All Known Implementing Classes:
AbstractRichSequenceDB
,AbstractSequenceDB
,AnnotatedSequenceDB
,BioSQLRichSequenceDB
,BioSQLSequenceDB
,CachingSequenceDB
,DistributedSequenceDB
,DummySequenceDB
,GenbankRichSequenceDB
,GenpeptRichSequenceDB
,HashRichSequenceDB
,HashSequenceDB
,IndexedSequenceDB
,SequenceDBWrapper
,SubSequenceDB
,ViewingSequenceDB
A database of sequences with accessible keys and iterators over all
sequences.
This may have several implementations with rich behaviour, but basically most of the time you will just use the interface methods to do stuff. A sequence database contains a finite number of sequences stored under unique keys.
- Author:
- Matthew Pocock, Gerald Loeffler, Thomas Down
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Field Summary
Fields inherited from interface org.biojava.bio.seq.db.SequenceDBLite
SEQUENCES
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Method Summary
Modifier and TypeMethodDescriptionfilter
(FeatureFilter filter) Query features attached to all sequences in this database.ids()
Get an immutable set of all of the IDs in the database.Returns a SequenceIterator over all sequences in the database.Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
Methods inherited from interface org.biojava.bio.seq.db.SequenceDBLite
addSequence, getName, getSequence, removeSequence
-
Method Details
-
ids
Get an immutable set of all of the IDs in the database. The ids are legal arguments to getSequence.- Returns:
- a Set of ids - at the moment, strings
-
sequenceIterator
Returns a SequenceIterator over all sequences in the database. The order of retrieval is undefined.- Returns:
- a SequenceIterator over all sequences
-
filter
Query features attached to all sequences in this database. This is equivalent to applyingfilter
to all sequences then merging the results.- Parameters:
filter
- aFeatureFilter
.- Since:
- 1.3
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