Interface BioEntryDB

All Superinterfaces:
BioEntryDBLite
All Known Subinterfaces:
RichSequenceDB
All Known Implementing Classes:
AbstractBioEntryDB, AbstractRichSequenceDB, BioSQLBioEntryDB, BioSQLRichSequenceDB, GenbankRichSequenceDB, GenpeptRichSequenceDB, HashBioEntryDB, HashRichSequenceDB

public interface BioEntryDB extends BioEntryDBLite
. A database of RichSequences 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.

Since:
1.5
Author:
Matthew Pocock, Gerald Loeffler, Thomas Down, Richard Holland
  • Method Details

    • ids

      Set ids()
      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
    • getBioEntryIterator

      Returns a BioEntryIterator over all BioEntrys in the database. The order of retrieval is undefined.
      Returns:
      a BioEntryIterator over all BioEntrys