org.biojava.bio.seq.distributed
Class DistributedSequenceDB
java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.seq.db.AbstractSequenceDB
org.biojava.bio.seq.distributed.DistributedSequenceDB
- All Implemented Interfaces:
- Changeable, SequenceDB, SequenceDBLite
- public class DistributedSequenceDB
- extends AbstractSequenceDB
- implements SequenceDB
Sequence database from the meta-DAS system.
- Since:
- 1.2
- Author:
- Thomas Down, Matthew Pocock
- For general use:
- Once you've made one of these and populated it with a few DistDataSource instances,
you should be able to prety much forget about it and use it directly as a normal
SequenceDB implementation.
- For advanced users:
- DataSources can be added and removed while the object is live.
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
DATASOURCE
public static final ChangeType DATASOURCE
DATASOURCE_SELECTION
public static final ChangeType DATASOURCE_SELECTION
DistributedSequenceDB
public DistributedSequenceDB()
hasChangeSupport
protected boolean hasChangeSupport()
getChangeSupport
protected ChangeSupport getChangeSupport()
getDataSources
public java.util.Set getDataSources()
addDataSource
public void addDataSource(DistDataSource dds)
throws ChangeVetoException
- Throws:
ChangeVetoException
removeDataSource
public void removeDataSource(DistDataSource dds)
throws ChangeVetoException
- Throws:
ChangeVetoException
getName
public java.lang.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.
addSequence
public void addSequence(Sequence seq)
throws ChangeVetoException
- Description copied from interface:
SequenceDBLite
- Adds a sequence to the database.
- Specified by:
addSequence
in interface SequenceDBLite
- Overrides:
addSequence
in class AbstractSequenceDB
- Throws:
ChangeVetoException
removeSequence
public void removeSequence(java.lang.String id)
throws ChangeVetoException
- Description copied from interface:
SequenceDBLite
- Remove the sequence associated with an ID from the database.
- Specified by:
removeSequence
in interface SequenceDBLite
- Overrides:
removeSequence
in class AbstractSequenceDB
- Throws:
ChangeVetoException
getSequence
public Sequence getSequence(java.lang.String id)
throws IllegalIDException,
BioException
- Description copied from interface:
SequenceDBLite
- Retrieve a single sequence by its id.
- Specified by:
getSequence
in interface SequenceDBLite
- 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
ids
public java.util.Set ids()
- Description copied from interface:
SequenceDB
- Get an immutable set of all of the IDs in the database. The ids are legal
arguments to getSequence.
- Specified by:
ids
in interface SequenceDB
- Returns:
- a Set of ids - at the moment, strings
filter
public FeatureHolder filter(FeatureFilter ff)
- Description copied from interface:
SequenceDB
- Query features attached to all sequences in this database.
This is equivalent to applying
filter
to all
sequences then merging the results.
- Specified by:
filter
in interface SequenceDB
- Overrides:
filter
in class AbstractSequenceDB