All Superinterfaces:

BioEntryDB, BioEntryDBLite, Changeable, RichSequenceDBLite, SequenceDB, SequenceDBLite

All Known Implementing Classes:

AbstractRichSequenceDB, BioSQLRichSequenceDB, GenbankRichSequenceDB, GenpeptRichSequenceDB, HashRichSequenceDB

public interface RichSequenceDB
extends SequenceDB, BioEntryDB, RichSequenceDBLite 

Since:

1.5

Author:

Matthew Pocock, Gerald Loeffler, Thomas Down, Richard Holland

• Field Summary

  • Fields inherited from interface org.biojavax.bio.db.BioEntryDBLite

    BIOENTRYS

  • Fields inherited from interface org.biojava.bio.seq.db.SequenceDBLite

    SEQUENCES

• Method Summary

  All Methods

  Modifier and Type	Method and Description
  RichSequenceIterator	getRichSequenceIterator () Returns a RichSequenceIterator over all sequences in the database.
  SequenceIterator	sequenceIterator () Returns a SequenceIterator over all sequences in the database.

  • Methods inherited from interface org.biojava.bio.seq.db.SequenceDB

    filter, ids

  • Methods inherited from interface org.biojavax.bio.db.BioEntryDB

    getBioEntryIterator, ids

  • Methods inherited from interface org.biojavax.bio.db.RichSequenceDBLite

    addRichSequence, getRichSequence, getRichSequences, getRichSequences, removeRichSequence

  • Methods inherited from interface org.biojavax.bio.db.BioEntryDBLite

    addBioEntry, getBioEntry, getBioEntrys, getBioEntrys, getName, removeBioEntry

  • Methods inherited from interface org.biojava.bio.seq.db.SequenceDBLite

    addSequence, getName, getSequence, removeSequence

  • Methods inherited from interface org.biojava.utils.Changeable

    addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

• Method Detail

  • sequenceIterator

    SequenceIterator sequenceIterator()

    Returns a SequenceIterator over all sequences in the database. The order of retrieval is undefined. Will always return an instance of RichSequenceIterator.

    Specified by:

    sequenceIterator in interface SequenceDB

    Returns:

    a SequenceIterator over all sequences

  • getRichSequenceIterator

    RichSequenceIterator getRichSequenceIterator()

    Returns a RichSequenceIterator over all sequences in the database. The order of retrieval is undefined.

    Returns:

    a RichSequenceIterator over all sequences