forester/java/src/org/forester/phylogeny/data/Accession.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
  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.nhx.NHXtags;
  32 import org.forester.io.parsers.phyloxml.PhyloXmlMapping;
  33 import org.forester.util.ForesterUtil;
  34
  35 public final class Accession implements PhylogenyData, Comparable<Accession> {
  36
  37     final private String _comment;
  38     final private String _source;
  39     final private String _source_value;
  40     final private String _value;
  41
  42     public Accession( final String value, final String source ) {
  43         _value = value;
  44         _source = source;
  45         _comment = "";
  46         if ( source != null ) {
  47             _source_value = source + value;
  48         }
  49         else {
  50             _source_value = value;
  51         }
  52     }
  53
  54     public Accession( final String value, final String source, final String comment ) {
  55         _value = value;
  56         _source = source;
  57         _comment = comment;
  58         if ( source != null ) {
  59             _source_value = source + value;
  60         }
  61         else {
  62             _source_value = value;
  63         }
  64     }
  65
  66     @Override
  67     public StringBuffer asSimpleText() {
  68         return new StringBuffer( getValue() );
  69     }
  70
  71     @Override
  72     public StringBuffer asText() {
  73         final StringBuffer sb = new StringBuffer();
  74         if ( !ForesterUtil.isEmpty( getSource() ) ) {
  75             sb.append( getSource() );
  76             sb.append( ": " );
  77         }
  78         sb.append( getValue() );
  79         if ( !ForesterUtil.isEmpty( getComment() ) ) {
  80             sb.append( " (" );
  81             sb.append( getComment() );
  82             sb.append( ")" );
  83         }
  84         return sb;
  85     }
  86
  87     @Override
  88     public int compareTo( final Accession o ) {
  89         if ( equals( o ) ) {
  90             return 0;
  91         }
  92         return _source_value.compareTo( o._source_value );
  93     }
  94
  95     @Override
  96     public PhylogenyData copy() {
  97         return new Accession( getValue(), getSource() );
  98     }
  99
 100     @Override
 101     public boolean equals( final Object o ) {
 102         if ( this == o ) {
 103             return true;
 104         }
 105         else if ( o == null ) {
 106             return false;
 107         }
 108         else if ( o.getClass() != this.getClass() ) {
 109             throw new IllegalArgumentException( "attempt to check [" + this.getClass() + "] equality to " + o + " ["
 110                     + o.getClass() + "]" );
 111         }
 112         else {
 113             return isEqual( ( Accession ) o );
 114         }
 115     }
 116
 117     public String getComment() {
 118         return _comment;
 119     }
 120
 121     public String getSource() {
 122         return _source;
 123     }
 124
 125     public String getValue() {
 126         return _value;
 127     }
 128
 129     @Override
 130     public int hashCode() {
 131         return _source_value.hashCode();
 132     }
 133
 134     @Override
 135     public boolean isEqual( final PhylogenyData data ) {
 136         if ( this == data ) {
 137             return true;
 138         }
 139         if ( ( data == null ) || ( getValue() == null ) ) {
 140             return false;
 141         }
 142         final Accession a = ( Accession ) data;
 143         if ( ( getSource() != null ) && ( a.getSource() != null ) ) {
 144             return ( a.getValue().equals( getValue() ) && a.getSource().equals( getSource() ) );
 145         }
 146         return ( a.getValue().equals( getValue() ) );
 147     }
 148
 149     @Override
 150     public StringBuffer toNHX() {
 151         final StringBuffer sb = new StringBuffer();
 152         sb.append( ":" );
 153         sb.append( NHXtags.SEQUENCE_ACCESSION );
 154         sb.append( ForesterUtil.replaceIllegalNhxCharacters( getValue() ) );
 155         return sb;
 156     }
 157
 158     @Override
 159     public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
 160         if ( ForesterUtil.isEmpty( getSource() ) ) {
 161             if ( ForesterUtil.isEmpty( getComment() ) ) {
 162                 PhylogenyDataUtil.appendElement( writer,
 163                                                  PhyloXmlMapping.ACCESSION,
 164                                                  getValue(),
 165                                                  PhyloXmlMapping.ACCESSION_SOURCE_ATTR,
 166                                                  "unknown",
 167                                                  indentation );
 168             }
 169             else {
 170                 PhylogenyDataUtil.appendElement( writer,
 171                                                  PhyloXmlMapping.ACCESSION,
 172                                                  getValue(),
 173                                                  PhyloXmlMapping.ACCESSION_SOURCE_ATTR,
 174                                                  "unknown",
 175                                                  PhyloXmlMapping.ACCESSION_COMMENT_ATTR,
 176                                                  getComment(),
 177                                                  indentation );
 178             }
 179         }
 180         else {
 181             if ( ForesterUtil.isEmpty( getComment() ) ) {
 182                 PhylogenyDataUtil.appendElement( writer,
 183                                                  PhyloXmlMapping.ACCESSION,
 184                                                  getValue(),
 185                                                  PhyloXmlMapping.ACCESSION_SOURCE_ATTR,
 186                                                  getSource(),
 187                                                  indentation );
 188             }
 189             else {
 190                 PhylogenyDataUtil.appendElement( writer,
 191                                                  PhyloXmlMapping.ACCESSION,
 192                                                  getValue(),
 193                                                  PhyloXmlMapping.ACCESSION_SOURCE_ATTR,
 194                                                  getSource(),
 195                                                  PhyloXmlMapping.ACCESSION_COMMENT_ATTR,
 196                                                  getComment(),
 197                                                  indentation );
 198             }
 199         }
 200     }
 201
 202     @Override
 203     public String toString() {
 204         return asText().toString();
 205     }
 206 }