Class ViewingSequenceDB

All Implemented Interfaces:
Serializable, SequenceDB, SequenceDBLite, Changeable

SequenceDB implementation that returns new SequenceView instances wrapping the sequences in an underlying database. One appropriate use of this would be to wrap a DB in one of these and then wrap this in an annotating db so that the annotation is added to views, not the underlying sequences.
Since:
1.2
Author:
Matthew Pocock
See Also:
  • Constructor Details

    • ViewingSequenceDB

      public ViewingSequenceDB(SequenceDB parent)
      Create a new ViewingSequenceDB that views the sequences in parent.
      Parameters:
      parent - the SequenceDB to view
  • 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.
    • getSequence

      Description copied from interface: SequenceDBLite
      Retrieve a single sequence by its id.
      Parameters:
      id - the id to retrieve by
      Returns:
      the Sequence with that id
      Throws:
      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.
      Returns:
      a Set of ids - at the moment, strings