org.acedb.seq
Class AceSequenceDB
java.lang.Object
|
+--org.acedb.seq.AceSequenceDB
- public class AceSequenceDB
- extends java.lang.Object
- implements SequenceDB
An implementation of SequenceDB that lets either an entire ACeDB database,
or some sub-set of its sequences be viewed as a native BioJava sequence
database.
- Author:
- Matthew Pocock, Gerald Loeffler
Method Summary |
java.lang.String |
getName()
Get the name of this sequence database. |
Sequence |
getSequence(java.lang.String id)
Retrieve a single sequence by its id. |
java.util.Set |
ids()
Get an imutable set of all of the IDs in the database. |
SequenceIterator |
sequenceIterator()
Returns a SequenceTterator over all sequences in the database. |
Methods inherited from class java.lang.Object |
clone,
equals,
finalize,
getClass,
hashCode,
notify,
notifyAll,
toString,
wait,
wait,
wait |
seqSet
protected AceSet seqSet
AceSequenceDB
public AceSequenceDB(AceURL dbURL,
java.lang.String pattern)
throws AceException
AceSequenceDB
public AceSequenceDB(AceURL dbURL)
throws AceException
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