Package org.biojava.bio.seq.db

Class CachingSequenceDB

java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.seq.db.AbstractSequenceDB
org.biojava.bio.seq.db.SequenceDBWrapper
org.biojava.bio.seq.db.CachingSequenceDB
All Implemented Interfaces:
Serializable, SequenceDB, SequenceDBLite, Changeable
public class CachingSequenceDB extends SequenceDBWrapper
SequenceDB implementation that caches the results of another SequenceDB.
Author:
Matthew Pocock
See Also:

  • Constructor Details

    • CachingSequenceDB

      public CachingSequenceDB(SequenceDB parent)
      Create a new CachingSequenceDB that caches the sequences in parent.
      Parameters:
      parent - the SequenceDB to cache

  • 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

      public Sequence getSequence(String id) throws BioException
      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:
      IllegalIDException - if the database doesn't know about the id
      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