org.biojava.bio.seq.db
Class AnnotatedSequenceDB
java.lang.Object
|
+--org.biojava.bio.seq.db.AnnotatedSequenceDB
- public class AnnotatedSequenceDB
- extends java.lang.Object
- implements SequenceDB, java.io.Serializable
SequenceDB implementation which lazily applies a SequenceAnnotator
to sequences retrieved from a SequenceDB.
- Author:
- Thomas Down
- See Also:
- Serialized Form
Methods inherited from class java.lang.Object |
clone,
equals,
finalize,
getClass,
hashCode,
notify,
notifyAll,
toString,
wait,
wait,
wait |
AnnotatedSequenceDB
public AnnotatedSequenceDB(SequenceDB parent,
SequenceAnnotator a)
getParent
public SequenceDB getParent()
- Get the original sequenceDB from this annotated sequenceDB.
getName
public java.lang.String getName()
- Description copied from interface: SequenceDB
- Get the name of this sequence database.
- Specified by:
- getName in interface SequenceDB
- Tags copied from interface: SequenceDB
- Returns:
- the name of the sequence database, which may be null.
getSequence
public Sequence getSequence(java.lang.String id)
throws BioException
- Description copied from interface: SequenceDB
- Retrieve a single sequence by its id.
- Specified by:
- getSequence in interface SequenceDB
- Tags copied from interface: SequenceDB
- Parameters:
the
- id to retrieve by- Returns:
- the Sequence with that id
- Throws:
- BioException - if for any reason the sequence could not be retrieved
ids
public java.util.Set ids()
- Description copied from interface: SequenceDB
- Get an imutable set of all of the IDs in the database. The ids are legal
arguments to getSequence.
- Specified by:
- ids in interface SequenceDB
- Tags copied from interface: SequenceDB
- Returns:
- a Set of ids - at the moment, strings
sequenceIterator
public SequenceIterator sequenceIterator()
- Description copied from interface: SequenceDB
- Returns a SequenceTterator over all sequences in the database. The order
of retrieval is undefined.
- Specified by:
- sequenceIterator in interface SequenceDB
- Tags copied from interface: SequenceDB
- Returns:
- a SequenceIterator over all sequences
doAnnotation
protected Sequence doAnnotation(Sequence seq)
throws BioException
- Apply the annotation to a sequence.
- Parameters:
seq
- the sequence to annotate.