Class ViewSequenceFactory

Method Details

• getQuerySeqHolder

  public SequenceDB getQuerySeqHolder()

  getQuerySeqHolder returns the database of query sequences used to retrieve sequences for creation of the various result objects.

  Returns:

  a SequenceDB value.

• setQuerySeqHolder

  public void setQuerySeqHolder(SequenceDB querySeqHolder)

  setQuerySeqHolder sets the query sequence holder to a specific database.

  Parameters:

  querySeqHolder - a SequenceDB containing the query sequence(s).

• getSubjectDBInstallation

  public SequenceDBInstallation getSubjectDBInstallation()

  getSubjectDBInstallation returns the installation in which all the databases searched may be found. SequenceDBs are retrieved for creation of the various result objects.

  Returns:

  a SequenceDBInstallation containing the subject database(s).

• setSubjectDBInstallation

  public void setSubjectDBInstallation(SequenceDBInstallation subjectDBs)

  setSubjectDBInstallation sets the subject database holder to a specific installation.

  Parameters:

  subjectDBs - a SequenceDBInstallation containing the subject database(s)

• setDatabaseID

  public void setDatabaseID(String databaseID)

• makeQueryViewSequence

  protected Sequence makeQueryViewSequence(String queryID) throws BioException

  Throws:

  BioException

• makeSubjectViewSequence

  protected Sequence makeSubjectViewSequence(String subjectID) throws BioException

  Throws:

  BioException