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.SymbolList;
025
026/**
027 * Interface for things that perform matches.
028 *
029 * <p>
030 * These will almost always be produced by a factory method on a BioPattern
031 * object.
032 * </p>
033 *
034 * @author Matthew Pocock
035 */
036public interface BioMatcher {
037  /**
038   * Attempt to find the next match.
039   *
040   * <p>
041   * If the pattern can be found, then this will return true. If it could not,
042   * then it will return false. This is convenient within for or while loops.
043   * </p>
044   *
045   * <p>
046   * Each time this is called, the next match will be found. The start() and
047   * end() values will increase each time, regardless of wether you called any
048   * other methods.
049   * </p>
050   *
051   * @return true if there is another match
052   */
053  boolean find();
054
055  /**
056   * Get the first symbol index that matches the pattern.
057   *
058   * @return the start of the current match
059   * @throws java.lang.IllegalStateException if there is no current match
060   */
061  int start();
062
063  /**
064   * Get the last symbol index that matches the pattern.
065   *
066   * @return the end of the current match
067   * @throws java.lang.IllegalStateException if there is no current match
068   */
069  int end();
070
071  /**
072   * Get the matching region as a SymbolList.
073   *
074   * @return the matching symbols
075   * @throws java.lang.IllegalStateException if there is no current match
076   */
077  SymbolList group();
078
079}