Class AbstractSequenceDB

Method Details

• 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