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.alignment;
023
024import java.util.List;
025
026import org.biojava.bio.symbol.Location;
027
028/**
029 * <p>
030 * UnequalLengthAlignment has the following behavior. Two or more SymbolLists
031 * may align in such a way that their ends do not overlap.
032 * </p>
033 * 
034 * <pre>
035 *      example
036 *         1         aaaaaatttcttt
037 *         2               tttgtttggggggc
038 * </pre>
039 * 
040 * <p>
041 * length returns ?? <br>
042 * symbolAt(1,1) returns 20 <br>
043 * symbolAt(2,1) returns null -- NOT an exception <br>
044 * symbolAt(2,99) throws NoSuchElementException <br>
045 * leftMost returns 1 <br>
046 * rightMost returns 2 <br>
047 * locInAlignment (1) returns (1,13) <br>
048 * locInAlignment (2) returns (7,20) <br>
049 * alignmentRange() returns (7,13) <br>
050 * </p>
051 * 
052 * @author David Waring
053 */
054
055public interface UnequalLengthAlignment extends Alignment {
056
057        /**
058         * The location of an individual SymbolList relative to overall Alignment
059         */
060        public Location locInAlignment(Object label);
061
062        /**
063         * Returns a list labels, of all seqs that cover that column
064         */
065        public List<String> labelsAt(int column);
066
067        /**
068         * Returns list of all the labels that intersect that range
069         */
070        public List<String> labelsInRange(Location loc);
071
072}