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 DATE 021 * 022 */ 023 024package org.biojava.nbio.core.sequence.compound; 025 026import java.io.Serializable; 027 028import org.biojava.nbio.core.sequence.template.AbstractCompound; 029import org.biojava.nbio.core.sequence.template.Compound; 030import org.biojava.nbio.core.sequence.template.CompoundSet; 031 032/** 033 * Used to describe an Amino Acid. 034 * @author Richard Holland 035 * @author Scooter Willis 036 * @author Andy Yates 037 */ 038public class AminoAcidCompound extends AbstractCompound implements Serializable { 039 040 /** 041 * 042 */ 043private static final long serialVersionUID = -1955116496725902319L; 044private final AminoAcidCompoundSet compoundSet; 045 046 047 public AminoAcidCompound(AminoAcidCompoundSet compoundSet, String shortName, 048 String longName, String description, Float molecularWeight) { 049 super(shortName); 050 setShortName(shortName); 051 setLongName(longName); 052 setDescription(description); 053 setMolecularWeight(molecularWeight); 054 this.compoundSet = compoundSet; 055 } 056 057 // TODO need to allow for modified name; that's not equality though is it? 058 @Override 059public boolean equals(Object obj) { 060 if (obj == null) { 061 return false; 062 } 063 if (!(obj instanceof AminoAcidCompound)) { 064 return false; 065 } 066 AminoAcidCompound them = (AminoAcidCompound) obj; 067 if (toString().equals(them.toString())) { 068 return true; 069 } 070 return getLongName().equals(them.getLongName()); 071 072 } 073 074 @Override 075public int hashCode() { 076 return toString().hashCode(); 077 } 078 079 @Override 080public boolean equalsIgnoreCase(Compound compound) { 081 if (compound == null) { 082 return false; 083 } 084 if (!(compound instanceof AminoAcidCompound)) { 085 return false; 086 } 087 AminoAcidCompound them = (AminoAcidCompound) compound; 088 if (toString().equalsIgnoreCase(them.toString())) { 089 return true; 090 } 091 return getLongName().equalsIgnoreCase(them.getLongName()); 092 } 093 094 public CompoundSet<AminoAcidCompound> getCompoundSet() { 095 return compoundSet; 096 } 097}