Class AnnotatedSequenceDB

Method Details

• 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