/* * BioJava development code * * This code may be freely distributed and modified under the * terms of the GNU Lesser General Public Licence. This should * be distributed with the code. If you do not have a copy, * see: * * http://www.gnu.org/copyleft/lesser.html * * Copyright for this code is held jointly by the individual * authors. These should be listed in @author doc comments. * * For more information on the BioJava project and its aims, * or to join the biojava-l mailing list, visit the home page * at: * * http://www.biojava.org/ * */ package org.biojava.bio.seq.db; import java.util.Set; import org.biojava.bio.seq.FeatureFilter; import org.biojava.bio.seq.FeatureHolder; import org.biojava.bio.seq.SequenceIterator; /** * 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
* @author Gerald Loeffler
* @author Thomas Down
*/
public interface SequenceDB extends SequenceDBLite {
/**
* Get an immutable set of all of the IDs in the database. The ids are legal
* arguments to getSequence.
*
* @return a Set of ids - at the moment, strings
*/
Set ids();
/**
* Returns a SequenceIterator over all sequences in the database. The order
* of retrieval is undefined.
*
* @return a SequenceIterator over all sequences
*/
SequenceIterator sequenceIterator();
/**
* Query features attached to all sequences in this database.
* This is equivalent to applying filter
to all
* sequences then merging the results.
*
* @param filter a FeatureFilter
.
* @since 1.3
*/
public FeatureHolder filter(FeatureFilter filter);
}