org.biojava.bridge.Biocorba.Seqcore
Class SequenceDBAdapter

java.lang.Object
  |
  +--org.biojava.bridge.Biocorba.Seqcore.SequenceDBAdapter

public class SequenceDBAdapter
extends java.lang.Object
implements SequenceDB

Author:
Matthew Pocock, Gerald Loeffler

Constructor Summary
SequenceDBAdapter(PrimarySeqDB primarySeqDB)
           
 
Method Summary
 java.lang.String getName()
          Get the name of this sequence database.
 PrimarySeqDB getPrimarySeqDB()
           
 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
 

Constructor Detail

SequenceDBAdapter

public SequenceDBAdapter(PrimarySeqDB primarySeqDB)
Method Detail

getPrimarySeqDB

public PrimarySeqDB getPrimarySeqDB()

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