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

Field Summary
protected  AceSet seqSet
           
 
Constructor Summary
AceSequenceDB(AceURL dbURL)
           
AceSequenceDB(AceURL dbURL, java.lang.String pattern)
           
 
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
 

Field Detail

seqSet

protected AceSet seqSet
Constructor Detail

AceSequenceDB

public AceSequenceDB(AceURL dbURL,
                     java.lang.String pattern)
              throws AceException

AceSequenceDB

public AceSequenceDB(AceURL dbURL)
              throws AceException
Method Detail

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