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 */
021
022package org.biojava.bio.search;
023
024import org.biojava.bio.symbol.IllegalAlphabetException;
025import org.biojava.bio.symbol.SymbolList;
026
027/**
028 *
029 *
030 * @author Matthew Pocock
031 */
032public interface BioPattern {
033  /**
034   * Get a matcher that will use these parameters to search a SymbolList.
035   *
036   * <p>
037   * The resulting BioMatcher is independant of this BioPattern.
038   * In particular, calling any mutator methods on this pattern will not affect
039   * the matcher.
040   * </p>
041   *
042   * @param symList  the SymbolList to match against
043   * @return a BioMatcher that will perform the search
044   * @throws IllegalAlphabetException if symList is not over the right alphabet
045   */
046  BioMatcher matcher(SymbolList symList)
047  throws IllegalAlphabetException;
048}