org.biojava.bio.seq.db
Class AnnotatedSequenceDB
java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.seq.db.AbstractSequenceDB
org.biojava.bio.seq.db.AnnotatedSequenceDB
- All Implemented Interfaces:
- Serializable, SequenceDB, SequenceDBLite, Changeable
public class AnnotatedSequenceDB
- extends AbstractSequenceDB
- implements SequenceDB, Serializable
SequenceDB implementation which lazily applies a SequenceAnnotator
to sequences retrieved from a SequenceDB.
- Author:
- Thomas Down, Matthew Pocock
- See Also:
- Serialized Form
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
AnnotatedSequenceDB
public AnnotatedSequenceDB(SequenceDB parent,
SequenceAnnotator a)
getParent
public SequenceDB getParent()
- Get the original sequenceDB from this annotated sequenceDB.
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 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
ids
public 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
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
- Overrides:
sequenceIterator
in class AbstractSequenceDB
- Returns:
- a SequenceIterator over all sequences
doAnnotation
protected Sequence doAnnotation(Sequence seq)
throws BioException
- Apply the annotation to a sequence.
- Parameters:
seq
- the sequence to annotate.
- Throws:
BioException