Interface SequenceDB

All Superinterfaces:
Changeable, SequenceDBLite
All Known Subinterfaces:
RichSequenceDB
All Known Implementing Classes:
AbstractRichSequenceDB, AbstractSequenceDB, AnnotatedSequenceDB, BioSQLRichSequenceDB, BioSQLSequenceDB, CachingSequenceDB, DistributedSequenceDB, DummySequenceDB, GenbankRichSequenceDB, GenpeptRichSequenceDB, HashRichSequenceDB, HashSequenceDB, IndexedSequenceDB, SequenceDBWrapper, SubSequenceDB, ViewingSequenceDB

public interface SequenceDB extends SequenceDBLite
A database of sequences with accessible keys and iterators over all sequences.

This may have several implementations with rich behaviour, but basically most of the time you will just use the interface methods to do stuff. A sequence database contains a finite number of sequences stored under unique keys.

Author:
Matthew Pocock, Gerald Loeffler, Thomas Down
  • Method Details

    • ids

      Set ids()
      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
    • sequenceIterator

      Returns a SequenceIterator over all sequences in the database. The order of retrieval is undefined.
      Returns:
      a SequenceIterator over all sequences
    • filter

      Query features attached to all sequences in this database. This is equivalent to applying filter to all sequences then merging the results.
      Parameters:
      filter - a FeatureFilter.
      Since:
      1.3