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: https://sites.google.com/site/cmzmasek/home/software/forester
27 package org.forester.surfacing;
29 import org.forester.protein.BinaryDomainCombination;
30 import org.forester.util.ForesterUtil;
32 public class BasicBinaryDomainCombination implements BinaryDomainCombination {
36 public BasicBinaryDomainCombination( final String id0, final String id1 ) {
37 if ( ( id0 == null ) || ( id1 == null ) ) {
38 throw new IllegalArgumentException( "attempt to create binary domain combination using null" );
40 if ( ( id0.indexOf( SEPARATOR ) != -1 ) || ( id1.indexOf( SEPARATOR ) != -1 ) ) {
41 throw new IllegalArgumentException( "ill formatted domain id: " + id0 + ", " + id1 );
43 if ( id0.toLowerCase().compareTo( id1.toLowerCase() ) < 0 ) {
44 _data = id0 + SEPARATOR + id1;
47 _data = id1 + SEPARATOR + id0;
51 BasicBinaryDomainCombination() {
56 public int compareTo( final BinaryDomainCombination binary_domain_combination ) {
57 if ( binary_domain_combination.getClass() != this.getClass() ) {
58 throw new IllegalArgumentException( "attempt to compare [" + binary_domain_combination.getClass() + "] to "
59 + "[" + this.getClass() + "]" );
61 if ( equals( binary_domain_combination ) ) {
64 final int x = getId0().compareTo( binary_domain_combination.getId0() );
69 return getId1().compareTo( binary_domain_combination.getId1() );
74 public boolean equals( final Object o ) {
78 else if ( o == null ) {
79 throw new IllegalArgumentException( "attempt to check [" + this.getClass() + "] equality to null" );
81 else if ( o.getClass() != this.getClass() ) {
82 throw new IllegalArgumentException( "attempt to check [" + this.getClass() + "] equality to ["
83 + o.getClass() + "]" );
86 return ( getId0().equals( ( ( BinaryDomainCombination ) o ).getId0() ) )
87 && ( getId1().equals( ( ( BinaryDomainCombination ) o ).getId1() ) );
92 public String getId0() {
93 return _data.substring( 0, _data.indexOf( SEPARATOR ) );
97 public String getId1() {
98 return _data.substring( _data.indexOf( SEPARATOR ) + 1 );
102 public int hashCode() {
103 return getAsStr().hashCode();
107 public StringBuffer toGraphDescribingLanguage( final OutputFormat format,
108 final String node_attribute,
109 final String edge_attribute ) {
110 final StringBuffer sb = new StringBuffer();
113 if ( ForesterUtil.isEmpty( node_attribute ) ) {
114 sb.append( getId0() );
116 sb.append( getId1() );
117 if ( !ForesterUtil.isEmpty( edge_attribute ) ) {
119 sb.append( edge_attribute );
124 sb.append( getId0() );
126 sb.append( node_attribute );
128 sb.append( ForesterUtil.LINE_SEPARATOR );
129 sb.append( getId1() );
131 sb.append( node_attribute );
133 sb.append( ForesterUtil.LINE_SEPARATOR );
134 sb.append( getId0() );
136 sb.append( getId1() );
137 if ( !ForesterUtil.isEmpty( edge_attribute ) ) {
139 sb.append( edge_attribute );
145 throw new AssertionError( "unknown format:" + format );
151 public String toString() {
155 private String getAsStr() {
159 public static BinaryDomainCombination createInstance( final String ids ) {
160 if ( ids.indexOf( BinaryDomainCombination.SEPARATOR ) < 1 ) {
161 throw new IllegalArgumentException( "Unexpected format for binary domain combination [" + ids + "]" );
163 final String[] ids_ary = ids.split( BinaryDomainCombination.SEPARATOR );
164 if ( ids_ary.length != 2 ) {
165 throw new IllegalArgumentException( "Unexpected format for binary domain combination [" + ids + "]" );
167 return new BasicBinaryDomainCombination( ids_ary[ 0 ], ids_ary[ 1 ] );