// $Id: // Exp $ // FORESTER -- software libraries and applications // for evolutionary biology research and applications. // // Copyright (C) 2008-2009 Christian M. Zmasek // Copyright (C) 2008-2009 Burnham Institute for Medical Research // All rights reserved // // This library is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public // License as published by the Free Software Foundation; either // version 2.1 of the License, or (at your option) any later version. // // This library is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU // Lesser General Public License for more details. // // You should have received a copy of the GNU Lesser General Public // License along with this library; if not, write to the Free Software // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com // WWW: www.phylosoft.org/forester package org.forester.surfacing; import org.forester.protein.BinaryDomainCombination; import org.forester.protein.DomainId; import org.forester.util.ForesterUtil; public class BasicBinaryDomainCombination implements BinaryDomainCombination { String _data; //String _id_0; // String _id_1; //DomainId _id_0; //DomainId _id_1; BasicBinaryDomainCombination() { //_id_0 = null; // _id_1 = null; _data = null; } public BasicBinaryDomainCombination( final String id_0, final String id_1 ) { if ( ( id_0 == null ) || ( id_1 == null ) ) { throw new IllegalArgumentException( "attempt to create binary domain combination using null" ); } final String my_id_0 = id_0.trim(); final String my_id_1 = id_1.trim(); if ( my_id_0.toLowerCase().compareTo( my_id_1.toLowerCase() ) < 0 ) { //_id_0 = my_id_0; //_id_1 = my_id_1; _data = my_id_0 + BinaryDomainCombination.SEPARATOR + my_id_1; } else { //_id_0 = my_id_1; // _id_1 = my_id_0; _data = my_id_1 + BinaryDomainCombination.SEPARATOR + my_id_0; } } public BasicBinaryDomainCombination( final DomainId id_0, final DomainId id_1 ) { this( id_0.getId(), id_1.getId() ); } @Override public int compareTo( final BinaryDomainCombination binary_domain_combination ) { if ( binary_domain_combination.getClass() != this.getClass() ) { throw new IllegalArgumentException( "attempt to compare [" + binary_domain_combination.getClass() + "] to " + "[" + this.getClass() + "]" ); } if ( equals( binary_domain_combination ) ) { return 0; } final int x = getId0().compareTo( binary_domain_combination.getId0() ); if ( x != 0 ) { return x; } else { return getId1().compareTo( binary_domain_combination.getId1() ); } } @Override public boolean equals( final Object o ) { if ( this == o ) { return true; } else if ( o == null ) { throw new IllegalArgumentException( "attempt to check [" + this.getClass() + "] equality to null" ); } else if ( o.getClass() != this.getClass() ) { throw new IllegalArgumentException( "attempt to check [" + this.getClass() + "] equality to [" + o.getClass() + "]" ); } else { return ( getId0().equals( ( ( BinaryDomainCombination ) o ).getId0() ) ) && ( getId1().equals( ( ( BinaryDomainCombination ) o ).getId1() ) ); } } @Override public DomainId getId0() { return new DomainId( _data.split( BinaryDomainCombination.SEPARATOR )[ 0 ] ); } @Override public DomainId getId1() { // return new DomainId( _id_1 ); return new DomainId( _data.split( BinaryDomainCombination.SEPARATOR )[ 1 ] ); } @Override public int hashCode() { // return getId0().hashCode() + ( 19 * getId1().hashCode() ); // return ( _id_0 + _id_1 ).hashCode(); return _data.hashCode(); } @Override public StringBuffer toGraphDescribingLanguage( final OutputFormat format, final String node_attribute, final String edge_attribute ) { final StringBuffer sb = new StringBuffer(); switch ( format ) { case DOT: if ( ForesterUtil.isEmpty( node_attribute ) ) { sb.append( getId0() ); sb.append( " -- " ); sb.append( getId1() ); if ( !ForesterUtil.isEmpty( edge_attribute ) ) { sb.append( " " ); sb.append( edge_attribute ); } sb.append( ";" ); } else { sb.append( getId0() ); sb.append( " " ); sb.append( node_attribute ); sb.append( ";" ); sb.append( ForesterUtil.LINE_SEPARATOR ); sb.append( getId1() ); sb.append( " " ); sb.append( node_attribute ); sb.append( ";" ); sb.append( ForesterUtil.LINE_SEPARATOR ); sb.append( getId0() ); sb.append( " -- " ); sb.append( getId1() ); if ( !ForesterUtil.isEmpty( edge_attribute ) ) { sb.append( " " ); sb.append( edge_attribute ); } sb.append( ";" ); } break; default: throw new AssertionError( "unknown format:" + format ); } return sb; } @Override public String toString() { return _data; // final StringBuffer sb = new StringBuffer(); // sb.append( _id_0 ); // sb.append( BinaryDomainCombination.SEPARATOR ); // sb.append( _id_1 ); // return sb.toString(); } public static BinaryDomainCombination createInstance( final String ids ) { if ( ids.indexOf( BinaryDomainCombination.SEPARATOR ) < 1 ) { throw new IllegalArgumentException( "Unexpected format for binary domain combination [" + ids + "]" ); } final String[] ids_ary = ids.split( BinaryDomainCombination.SEPARATOR ); if ( ids_ary.length != 2 ) { throw new IllegalArgumentException( "Unexpected format for binary domain combination [" + ids + "]" ); } return new BasicBinaryDomainCombination( ids_ary[ 0 ], ids_ary[ 1 ] ); } }