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.symbol; 023 024import java.io.Serializable; 025 026import org.biojava.utils.SingletonList; 027 028/** 029 * <p> 030 * Encapsulates an edit operation on a SymbolList. 031 * See {@link org.biojava.bio.symbol.SymbolList 032 * SymbolList} for a full description. 033 * </p> 034 * 035 * @author Matthew Pocock 036 */ 037public final class Edit implements Serializable { 038 public final int pos; 039 public final int length; 040 public final SymbolList replacement; 041 042 /** 043 * Create a new Edit. 044 * 045 * @param pos the start of the edit 046 * @param length the length of the edit 047 * @param replacement a SymbolList representing the symbols that replace those from pos to 048 * pos + length-1 inclusive 049 */ 050 public Edit(int pos, int length, SymbolList replacement) { 051 this.pos = pos; 052 this.length = length; 053 this.replacement = replacement; 054 } 055 056 /** 057 * Convenience construtor for making single residue changes 058 * 059 * @param pos the position of the change 060 * @param alpha the <code>Alphabet</code> of the replacement <code>Symbol</code> 061 * @param replacement the replacement <code>Symbol</code> 062 * @throws IllegalSymbolException if the replacement <code>Symbol</code> is not contained in <code>alpha</code> 063 */ 064 public Edit(int pos, Alphabet alpha, Symbol replacement) throws IllegalSymbolException{ 065 this.pos = pos; 066 this.length = 1; 067 SymbolList sl = new SimpleSymbolList( 068 alpha, new SingletonList(replacement)); 069 this.replacement = sl; 070 } 071}