Class BioSQLBioEntryDB

Method Details

• getName

  public String getName()

  Description copied from interface: BioEntryDBLite

  Get the name of this sequence database.

  Returns:

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

• getHibernateSession

  public Object getHibernateSession()

• ids

  public Set ids()

  Description copied from interface: BioEntryDB

  Get an immutable set of all of the IDs in the database. The ids are legal arguments to getBioEntry.

  Returns:

  a Set of ids - at the moment, strings

• getBioEntry

  public BioEntry getBioEntry(String id) throws IllegalIDException, BioException

  Description copied from interface: BioEntryDBLite

  Retrieve a single BioEntry by its id.

  Parameters:

  id - the id to retrieve by

  Returns:

  the BioEntry with that id

  Throws:

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

  BioException - if there was a failure in retrieving the BioEntry

• getBioEntrys

  public BioEntryDB getBioEntrys(Set ids) throws BioException, IllegalIDException

  Description copied from interface: BioEntryDBLite

  Retrieve multiple BioEntry by their ids.

  Parameters:

  ids - a set of ids to retrieve by

  Returns:

  the BioEntrys with those ids

  Throws:

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

  BioException

• getBioEntrys

  public BioEntryDB getBioEntrys(Set ids, BioEntryDB db) throws BioException, IllegalIDException

  Description copied from interface: BioEntryDBLite

  Retrieve multiple BioEntry into a specific sequence database. If that database is null, a new HashBioEntryDB is used.

  Parameters:

  ids - a set of ids to retrieve by

  db - a database to load the seqs into

  Returns:

  the BioEntrys with that id

  Throws:

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

  BioException

• removeBioEntry

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

  Description copied from interface: BioEntryDBLite

  Remove the BioEntry associated with an ID from the database.

  Specified by:

  removeBioEntry in interface BioEntryDBLite

  Overrides:

  removeBioEntry in class AbstractBioEntryDB

  Parameters:

  id - the ID of the BioEntry to remove

  Throws:

  IllegalIDException - if there is no BioEntry for the ID

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

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

• addBioEntry

  public void addBioEntry(BioEntry seq) throws IllegalIDException, BioException, ChangeVetoException

  Description copied from interface: BioEntryDBLite

  Adds a sequence to the database.

  Specified by:

  addBioEntry in interface BioEntryDBLite

  Overrides:

  addBioEntry in class AbstractBioEntryDB

  Parameters:

  seq - the BioEntry to add

  Throws:

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

  BioException - if something goes wrong with adding the BioEntry

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

• _addBioEntry

  public void _addBioEntry(BioEntry seq) throws IllegalIDException, BioException, ChangeVetoException

  Throws:

  IllegalIDException

  BioException

  ChangeVetoException