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 * @author Richard Holland
023 *
024 *
025 */
026package org.biojava.nbio.core.sequence.template;
027
028import java.util.List;
029import java.util.Set;
030
031
032public interface CompoundSet<C extends Compound> {
033
034        /**
035         * Returns the maximum size of a compound String this set holds
036         */
037        public int getMaxSingleCompoundStringLength();
038
039        /**
040         * Returns true if all String representations of Compounds are of the
041         * same length.
042         */
043        public boolean isCompoundStringLengthEqual();
044
045        /**
046         * Return null if not recognised. Throw IllegalArgumentException if string
047         * is longer than maximum allowed by {@link #getStringForCompound(Compound)}.
048         */
049        public C getCompoundForString(String string);
050
051        public String getStringForCompound(C compound);
052
053        public boolean compoundsEquivalent(C compoundOne, C compoundTwo);
054
055        public boolean isValidSequence(Sequence<C> sequence);
056
057        public Set<C> getEquivalentCompounds(C compound);
058
059        public boolean hasCompound(C compound);
060
061        public List<C> getAllCompounds();
062
063        boolean isComplementable();
064}