Class BioSQLRichSequenceDB

Method Details

• getName

  public String getName()

  Description copied from interface: SequenceDBLite

  Get the name of this sequence database.

  Returns:

  the name of the sequence database, which may be null.

• getHibernateSession

  public Object getHibernateSession()

• processFeatureFilter

  public FeatureHolder processFeatureFilter(FeatureFilter ff)

• 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 AbstractRichSequenceDB

  Parameters:

  ff - a FeatureFilter.

• 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.

  Returns:

  a Set of ids - at the moment, strings

• fullyLoadRichSequence

  public RichSequence fullyLoadRichSequence(RichSequence id) throws IllegalIDException, BioException

  Throws:

  IllegalIDException

  BioException

• getRichSequence

  public RichSequence getRichSequence(String id) throws IllegalIDException, BioException

  Description copied from interface: RichSequenceDBLite

  Retrieve a single RichSequence by its id.

  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

• getRichSequences

  public RichSequenceDB getRichSequences(Set ids) throws BioException, IllegalIDException

  Description copied from interface: RichSequenceDBLite

  Retrieve multiple RichSequence by its id.

  Parameters:

  ids - a set of ids to retrieve by

  Returns:

  the RichSequences with that id

  Throws:

  IllegalIDException - if the database doesn't know about the id

  BioException

• getRichSequences

  public RichSequenceDB getRichSequences(Set ids, RichSequenceDB db) throws BioException, IllegalIDException

  Description copied from interface: RichSequenceDBLite

  Retrieve multiple RichSequence into a specific sequence database. If that database is null, a new HashRichSequenceDB is used.

  Parameters:

  ids - a set of ids to retrieve by

  db - a database to load the seqs into

  Returns:

  the RichSequences with that id

  Throws:

  IllegalIDException - if the database doesn't know about the id

  BioException

• removeRichSequence

  public void removeRichSequence(String id) throws IllegalIDException, BioException, ChangeVetoException

  Description copied from interface: RichSequenceDBLite

  Remove the RichSequence associated with an ID from the database.

  Specified by:

  removeRichSequence in interface RichSequenceDBLite

  Overrides:

  removeRichSequence in class AbstractRichSequenceDB

  Parameters:

  id - the ID of the RichSequence to remove

  Throws:

  IllegalIDException - if there is no RichSequence for the ID

  BioException - if something failed while removing the RichSequence for that ID

  ChangeVetoException - if either the database does not allow RichSequences to be removed or the modification was vetoed

• addRichSequence

  public void addRichSequence(RichSequence seq) throws IllegalIDException, BioException, ChangeVetoException

  Description copied from interface: RichSequenceDBLite

  Adds a sequence to the database.

  Specified by:

  addRichSequence in interface RichSequenceDBLite

  Overrides:

  addRichSequence in class AbstractRichSequenceDB

  Parameters:

  seq - the RichSequence to add

  Throws:

  IllegalIDException - if a uniqe ID could not be generated for RichSequence

  BioException - if something goes wrong with adding the RichSequence

  ChangeVetoException - if either the database does not allow RichSequences to be added or the modification was vetoed