forester/java/src/org/forester/phylogeny/data/ProteinDomain.java

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2008-2009 Christian M. Zmasek
   6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   7 // All rights reserved
   8 //
   9 // This library is free software; you can redistribute it and/or
  10 // modify it under the terms of the GNU Lesser General Public
  11 // License as published by the Free Software Foundation; either
  12 // version 2.1 of the License, or (at your option) any later version.
  13 //
  14 // This library is distributed in the hope that it will be useful,
  15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  17 // Lesser General Public License for more details.
  18 //
  19 // You should have received a copy of the GNU Lesser General Public
  20 // License along with this library; if not, write to the Free Software
  21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  22 //
  23 // Contact: phylosoft @ gmail . com
  24 // WWW: www.phylosoft.org/forester
  25
  26 package org.forester.phylogeny.data;
  27
  28 import java.io.IOException;
  29 import java.io.Writer;
  30
  31 import org.forester.io.parsers.phyloxml.PhyloXmlMapping;
  32 import org.forester.util.ForesterUtil;
  33
  34 public class ProteinDomain implements PhylogenyData {
  35
  36     final public static double CONFIDENCE_DEFAULT = 0.0;
  37     final public static String IDENTIFIER_DEFAULT = "";
  38     final private String       _name;
  39     final private int          _from;
  40     final private int          _to;
  41     final private String       _id;
  42     final private double       _confidence;
  43
  44     public ProteinDomain( final String name, final int from, final int to ) {
  45         this( name, from, to, ProteinDomain.IDENTIFIER_DEFAULT, ProteinDomain.CONFIDENCE_DEFAULT );
  46     }
  47
  48     public ProteinDomain( final String name, final int from, final int to, final double confidence ) {
  49         this( name, from, to, ProteinDomain.IDENTIFIER_DEFAULT, confidence );
  50     }
  51
  52     public ProteinDomain( final String name, final int from, final int to, final String id ) {
  53         this( name, from, to, id, ProteinDomain.CONFIDENCE_DEFAULT );
  54     }
  55
  56     public ProteinDomain( final String name, final int from, final int to, final String id, final double confidence ) {
  57         if ( ( from >= to ) || ( to < 0 ) ) {
  58             throw new IllegalArgumentException( "attempt to create protein domain from " + from + " to " + to );
  59         }
  60         _name = name;
  61         _from = from;
  62         _to = to;
  63         _id = id;
  64         _confidence = confidence;
  65     }
  66
  67     public StringBuffer asSimpleText() {
  68         return new StringBuffer( getName() );
  69     }
  70
  71     public StringBuffer asText() {
  72         final StringBuffer sb = new StringBuffer( getName() );
  73         sb.append( " [" );
  74         sb.append( getLength() );
  75         if ( !ForesterUtil.isEmpty( getId() ) ) {
  76             sb.append( " " );
  77             sb.append( getId() );
  78         }
  79         if ( getConfidence() != CONFIDENCE_DEFAULT ) {
  80             sb.append( " " );
  81             sb.append( getConfidence() );
  82         }
  83         sb.append( "]" );
  84         return sb;
  85     }
  86
  87     public PhylogenyData copy() {
  88         if ( getId() == null ) {
  89             return new ProteinDomain( getName(), getFrom(), getTo(), getConfidence() );
  90         }
  91         return new ProteinDomain( getName(), getFrom(), getTo(), getId(), getConfidence() );
  92     }
  93
  94     public double getConfidence() {
  95         return _confidence;
  96     }
  97
  98     public int getFrom() {
  99         return _from;
 100     }
 101
 102     public String getId() {
 103         return _id;
 104     }
 105
 106     public int getLength() {
 107         return ( getTo() - getFrom() + 1 );
 108     }
 109
 110     public String getName() {
 111         return _name;
 112     }
 113
 114     public int getTo() {
 115         return _to;
 116     }
 117
 118     public boolean isEqual( final PhylogenyData protein_domain ) {
 119         if ( protein_domain == null ) {
 120             return false;
 121         }
 122         if ( !( protein_domain instanceof ProteinDomain ) ) {
 123             return false;
 124         }
 125         else if ( ( ( ProteinDomain ) protein_domain ).getLength() != getLength() ) {
 126             return false;
 127         }
 128         else if ( !( ( ProteinDomain ) protein_domain ).getName().equals( getName() ) ) {
 129             return false;
 130         }
 131         return true;
 132     }
 133
 134     public StringBuffer toNHX() {
 135         throw new UnsupportedOperationException();
 136     }
 137
 138     public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
 139         writer.write( ForesterUtil.LINE_SEPARATOR );
 140         writer.write( indentation );
 141         if ( getId() != null ) {
 142             PhylogenyDataUtil.appendOpen( writer,
 143                                           PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_DOMAIN,
 144                                           PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_FROM,
 145                                           getFrom() + "",
 146                                           PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_TO,
 147                                           getTo() + "",
 148                                           PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_CONFIDENCE,
 149                                           getConfidence() + "",
 150                                           PhyloXmlMapping.IDENTIFIER,
 151                                           getId() );
 152         }
 153         else {
 154             PhylogenyDataUtil.appendOpen( writer,
 155                                           PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_DOMAIN,
 156                                           PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_FROM,
 157                                           getFrom() + "",
 158                                           PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_TO,
 159                                           getTo() + "",
 160                                           PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_CONFIDENCE,
 161                                           getConfidence() + "" );
 162         }
 163         writer.write( getName() );
 164         PhylogenyDataUtil.appendClose( writer, PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_DOMAIN );
 165     }
 166
 167     @Override
 168     public String toString() {
 169         return asText().toString();
 170     }
 171 }