org.biojava.bio.seq.db.flat
Class FlatSequenceDB
java.lang.Object
org.biojava.utils.Unchangeable
org.biojava.bio.seq.db.flat.FlatSequenceDB
- All Implemented Interfaces:
- SequenceDBLite, Changeable
public class FlatSequenceDB
- extends Unchangeable
- implements SequenceDBLite
FlatSequenceDB
is an OBDA flatfile sequence databank
implementation. It is backed by an index created using the
org.biojava.bio.program.indexdb
package.
- Author:
- Keith James
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
FlatSequenceDB
public FlatSequenceDB(String location,
String dbName)
throws IOException,
BioException
- Throws:
IOException
BioException
getName
public String getName()
- Description copied from interface:
SequenceDBLite
- Get the name of this sequence database.
- Specified by:
getName
in interface SequenceDBLite
- Returns:
- the name of the sequence database, which may be null.
getSequence
public Sequence getSequence(String id)
throws IllegalIDException,
BioException
- Description copied from interface:
SequenceDBLite
- Retrieve a single sequence by its id.
- Specified by:
getSequence
in interface SequenceDBLite
- Parameters:
id
- the id to retrieve by
- Returns:
- the Sequence with that id
- Throws:
IllegalIDException
- if the database doesn't know about the id
BioException
- if there was a failure in retrieving the sequence
addSequence
public void addSequence(Sequence sequence)
throws ChangeVetoException
addSequence
always throws a
ChangeVetoException
as this implementation is
immutable.
- Specified by:
addSequence
in interface SequenceDBLite
- Parameters:
sequence
- a Sequence
.
- Throws:
ChangeVetoException
removeSequence
public void removeSequence(String id)
throws ChangeVetoException
removeSequence
always throws a
ChangeVetoException
as this implementation is
immutable.
- Specified by:
removeSequence
in interface SequenceDBLite
- Parameters:
id
- a String
.
- Throws:
ChangeVetoException