org.biojava.bio.seq.db
Class AbstractSequenceDB
java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.seq.db.AbstractSequenceDB
- All Implemented Interfaces:
- SequenceDB, SequenceDBLite, Changeable
- Direct Known Subclasses:
- AnnotatedSequenceDB, DistributedSequenceDB, DummySequenceDB, HashSequenceDB, IndexedSequenceDB, SequenceDBWrapper
public abstract class AbstractSequenceDB
- extends AbstractChangeable
- implements SequenceDB
An abstract implementation of SequenceDB that provides the sequenceIterator
method.
- Author:
- Matthew Pocock, Thomas Down
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface org.biojava.bio.seq.db.SequenceDB |
ids |
AbstractSequenceDB
public AbstractSequenceDB()
sequenceIterator
public SequenceIterator sequenceIterator()
- Description copied from interface:
SequenceDB
- Returns a SequenceIterator over all sequences in the database. The order
of retrieval is undefined.
- Specified by:
sequenceIterator
in interface SequenceDB
- Returns:
- a SequenceIterator over all sequences
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
- Parameters:
ff
- a FeatureFilter
.
addSequence
public void addSequence(Sequence seq)
throws BioException,
ChangeVetoException
- Description copied from interface:
SequenceDBLite
- Adds a sequence to the database.
- Specified by:
addSequence
in interface SequenceDBLite
- Parameters:
seq
- the Sequence to add
- Throws:
IllegalIDException
- if a uniqe ID could not be generated for seq
BioException
- if something goes wrong with adding the sequence
ChangeVetoException
- if either the database does not allow
sequences to be added or the modification was vetoed
removeSequence
public void removeSequence(String id)
throws BioException,
ChangeVetoException
- Description copied from interface:
SequenceDBLite
- Remove the sequence associated with an ID from the database.
- Specified by:
removeSequence
in interface SequenceDBLite
- Parameters:
id
- the ID of the sequence to remove
- Throws:
IllegalIDException
- if there is no sequence for the ID
BioException
- if something failed while removing the sequence for
that ID
ChangeVetoException
- if either the database does not allow
sequences to be removed or the modification was vetoed