001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 * Created on 01-21-2010
021 */
022
023package org.biojava.nbio.core.sequence.io.template;
024
025import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
026import org.biojava.nbio.core.sequence.template.AbstractSequence;
027import org.biojava.nbio.core.sequence.template.Compound;
028import org.biojava.nbio.core.sequence.template.ProxySequenceReader;
029
030import java.io.IOException;
031import java.util.List;
032
033/**
034 *
035 * @author Scooter Willis 
036 * @param <C> the compound type
037 */
038public interface SequenceCreatorInterface<C extends Compound> {
039        /**
040         *
041         * @param sequence
042         * @param index
043         * @return
044         * @throws CompoundNotFoundException
045         * @throws IOException
046         */
047        public AbstractSequence<C> getSequence(String sequence, long index) throws CompoundNotFoundException, IOException;
048
049        /**
050         *
051         * @param proxyLoader
052         * @param index
053         * @return
054         */
055        public AbstractSequence<C> getSequence(ProxySequenceReader<C> proxyLoader, long index);
056
057        /**
058         *
059         * @param list
060         * @return
061         */
062        public AbstractSequence<C> getSequence(List<C> list);
063
064}