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: https://sites.google.com/site/cmzmasek/home/software/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     @Override
  68     public StringBuffer asSimpleText() {
  69         return new StringBuffer( getName() );
  70     }
  71
  72     @Override
  73     public StringBuffer asText() {
  74         final StringBuffer sb = new StringBuffer( getName() );
  75         sb.append( " [" );
  76         sb.append( getLength() );
  77         if ( !ForesterUtil.isEmpty( getId() ) ) {
  78             sb.append( " " );
  79             sb.append( getId() );
  80         }
  81         if ( getConfidence() != CONFIDENCE_DEFAULT ) {
  82             sb.append( " " );
  83             sb.append( getConfidence() );
  84         }
  85         sb.append( "]" );
  86         return sb;
  87     }
  88
  89     @Override
  90     public PhylogenyData copy() {
  91         if ( getId() == null ) {
  92             return new ProteinDomain( getName(), getFrom(), getTo(), getConfidence() );
  93         }
  94         return new ProteinDomain( getName(), getFrom(), getTo(), getId(), getConfidence() );
  95     }
  96
  97     public double getConfidence() {
  98         return _confidence;
  99     }
 100
 101     public int getFrom() {
 102         return _from;
 103     }
 104
 105     public String getId() {
 106         return _id;
 107     }
 108
 109     public int getLength() {
 110         return ( ( getTo() - getFrom() ) + 1 );
 111     }
 112
 113     public String getName() {
 114         return _name;
 115     }
 116
 117     public int getTo() {
 118         return _to;
 119     }
 120
 121     @Override
 122     public boolean isEqual( final PhylogenyData protein_domain ) {
 123         if ( protein_domain == null ) {
 124             return false;
 125         }
 126         if ( !( protein_domain instanceof ProteinDomain ) ) {
 127             return false;
 128         }
 129         else if ( ( ( ProteinDomain ) protein_domain ).getLength() != getLength() ) {
 130             return false;
 131         }
 132         else if ( !( ( ProteinDomain ) protein_domain ).getName().equals( getName() ) ) {
 133             return false;
 134         }
 135         return true;
 136     }
 137
 138     @Override
 139     public StringBuffer toNHX() {
 140         throw new UnsupportedOperationException();
 141     }
 142
 143     @Override
 144     public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
 145         writer.write( ForesterUtil.LINE_SEPARATOR );
 146         writer.write( indentation );
 147         if ( getId() != null ) {
 148             PhylogenyDataUtil.appendOpen( writer,
 149                                           PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_DOMAIN,
 150                                           PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_FROM,
 151                                           getFrom() + "",
 152                                           PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_TO,
 153                                           getTo() + "",
 154                                           PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_CONFIDENCE,
 155                                           getConfidence() + "",
 156                                           PhyloXmlMapping.IDENTIFIER,
 157                                           getId() );
 158         }
 159         else {
 160             PhylogenyDataUtil.appendOpen( writer,
 161                                           PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_DOMAIN,
 162                                           PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_FROM,
 163                                           getFrom() + "",
 164                                           PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_TO,
 165                                           getTo() + "",
 166                                           PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_CONFIDENCE,
 167                                           getConfidence() + "" );
 168         }
 169         writer.write( getName() );
 170         PhylogenyDataUtil.appendClose( writer, PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_DOMAIN );
 171     }
 172
 173     @Override
 174     public String toString() {
 175         return asText().toString();
 176     }
 177 }