3 // FORESTER -- software libraries and applications
4 // for evolutionary biology research and applications.
6 // Copyright (C) 2008-2009 Christian M. Zmasek
7 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
10 // This library is free software; you can redistribute it and/or
11 // modify it under the terms of the GNU Lesser General Public
12 // License as published by the Free Software Foundation; either
13 // version 2.1 of the License, or (at your option) any later version.
15 // This library is distributed in the hope that it will be useful,
16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
18 // Lesser General Public License for more details.
20 // You should have received a copy of the GNU Lesser General Public
21 // License along with this library; if not, write to the Free Software
22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
24 // Contact: phylosoft @ gmail . com
25 // WWW: www.phylosoft.org/forester
27 package org.forester.surfacing;
29 import org.forester.protein.BinaryDomainCombination;
30 import org.forester.protein.DomainId;
31 import org.forester.util.ForesterUtil;
33 public class BasicBinaryDomainCombination implements BinaryDomainCombination {
41 BasicBinaryDomainCombination() {
47 public BasicBinaryDomainCombination( final String id_0, final String id_1 ) {
48 if ( ( id_0 == null ) || ( id_1 == null ) ) {
49 throw new IllegalArgumentException( "attempt to create binary domain combination using null" );
51 final String my_id_0 = id_0.trim();
52 final String my_id_1 = id_1.trim();
53 if ( my_id_0.toLowerCase().compareTo( my_id_1.toLowerCase() ) < 0 ) {
56 _data = my_id_0 + BinaryDomainCombination.SEPARATOR + my_id_1;
61 _data = my_id_1 + BinaryDomainCombination.SEPARATOR + my_id_0;
65 public BasicBinaryDomainCombination( final DomainId id_0, final DomainId id_1 ) {
66 this( id_0.getId(), id_1.getId() );
70 public int compareTo( final BinaryDomainCombination binary_domain_combination ) {
71 if ( binary_domain_combination.getClass() != this.getClass() ) {
72 throw new IllegalArgumentException( "attempt to compare [" + binary_domain_combination.getClass() + "] to "
73 + "[" + this.getClass() + "]" );
75 if ( equals( binary_domain_combination ) ) {
78 final int x = getId0().compareTo( binary_domain_combination.getId0() );
83 return getId1().compareTo( binary_domain_combination.getId1() );
88 public boolean equals( final Object o ) {
92 else if ( o == null ) {
93 throw new IllegalArgumentException( "attempt to check [" + this.getClass() + "] equality to null" );
95 else if ( o.getClass() != this.getClass() ) {
96 throw new IllegalArgumentException( "attempt to check [" + this.getClass() + "] equality to ["
97 + o.getClass() + "]" );
100 return ( getId0().equals( ( ( BinaryDomainCombination ) o ).getId0() ) )
101 && ( getId1().equals( ( ( BinaryDomainCombination ) o ).getId1() ) );
106 public DomainId getId0() {
107 return new DomainId( _data.split( BinaryDomainCombination.SEPARATOR )[ 0 ] );
111 public DomainId getId1() {
112 // return new DomainId( _id_1 );
113 return new DomainId( _data.split( BinaryDomainCombination.SEPARATOR )[ 1 ] );
117 public int hashCode() {
118 // return getId0().hashCode() + ( 19 * getId1().hashCode() );
119 // return ( _id_0 + _id_1 ).hashCode();
120 return _data.hashCode();
124 public StringBuffer toGraphDescribingLanguage( final OutputFormat format,
125 final String node_attribute,
126 final String edge_attribute ) {
127 final StringBuffer sb = new StringBuffer();
130 if ( ForesterUtil.isEmpty( node_attribute ) ) {
131 sb.append( getId0() );
133 sb.append( getId1() );
134 if ( !ForesterUtil.isEmpty( edge_attribute ) ) {
136 sb.append( edge_attribute );
141 sb.append( getId0() );
143 sb.append( node_attribute );
145 sb.append( ForesterUtil.LINE_SEPARATOR );
146 sb.append( getId1() );
148 sb.append( node_attribute );
150 sb.append( ForesterUtil.LINE_SEPARATOR );
151 sb.append( getId0() );
153 sb.append( getId1() );
154 if ( !ForesterUtil.isEmpty( edge_attribute ) ) {
156 sb.append( edge_attribute );
162 throw new AssertionError( "unknown format:" + format );
168 public String toString() {
170 // final StringBuffer sb = new StringBuffer();
171 // sb.append( _id_0 );
172 // sb.append( BinaryDomainCombination.SEPARATOR );
173 // sb.append( _id_1 );
174 // return sb.toString();
177 public static BinaryDomainCombination createInstance( final String ids ) {
178 if ( ids.indexOf( BinaryDomainCombination.SEPARATOR ) < 1 ) {
179 throw new IllegalArgumentException( "Unexpected format for binary domain combination [" + ids + "]" );
181 final String[] ids_ary = ids.split( BinaryDomainCombination.SEPARATOR );
182 if ( ids_ary.length != 2 ) {
183 throw new IllegalArgumentException( "Unexpected format for binary domain combination [" + ids + "]" );
185 return new BasicBinaryDomainCombination( ids_ary[ 0 ], ids_ary[ 1 ] );