forester/java/src/org/forester/phylogeny/data/SequenceRelation.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 import java.util.LinkedHashMap;
  31 import java.util.Map;
  32
  33 public class SequenceRelation implements PhylogenyData {
  34
  35     //public final static Map<String, SEQUENCE_RELATION_TYPE> typesToNames = new LinkedHashMap<String, SEQUENCE_RELATION_TYPE>();
  36     public final static Map<SEQUENCE_RELATION_TYPE, String> typesToNames                                = new LinkedHashMap<SEQUENCE_RELATION_TYPE, String>();
  37     public final static String                              SEQUENCE_RELATION_TYPE_ORTHOLOGY            = "orthology";
  38     public final static String                              SEQUENCE_RELATION_TYPE_ONE_TO_ONE_ORTHOLOGY = "one_to_one_orthology";
  39     public final static String                              SEQUENCE_RELATION_TYPE_SUPER_ORTHOLOGY      = "super_orthology";
  40     public final static String                              SEQUENCE_RELATION_TYPE_PARALOGY             = "paralogy";
  41     public final static String                              SEQUENCE_RELATION_TYPE_ULTRA_PARALOGY       = "ultra_paralogy";
  42     public final static String                              SEQUENCE_RELATION_TYPE_XENOLOGY             = "xenology";
  43     public final static String                              SEQUENCE_RELATION_TYPE_UNKNOWN              = "unknown";
  44     public final static String                              SEQUENCE_RELATION_TYPE_OTHER                = "other";
  45     private Sequence                                        ref0;
  46     private Sequence                                        ref1;
  47     private SEQUENCE_RELATION_TYPE                          type;
  48     private Double                                          distance;
  49     private Confidence                                      confidence;
  50     static {
  51         typesToNames.put( SEQUENCE_RELATION_TYPE.orthology, SEQUENCE_RELATION_TYPE_ORTHOLOGY );
  52         typesToNames.put( SEQUENCE_RELATION_TYPE.one_to_one_orthology, SEQUENCE_RELATION_TYPE_ONE_TO_ONE_ORTHOLOGY );
  53         typesToNames.put( SEQUENCE_RELATION_TYPE.super_orthology, SEQUENCE_RELATION_TYPE_SUPER_ORTHOLOGY );
  54         typesToNames.put( SEQUENCE_RELATION_TYPE.paralogy, SEQUENCE_RELATION_TYPE_PARALOGY );
  55         typesToNames.put( SEQUENCE_RELATION_TYPE.ultra_paralogy, SEQUENCE_RELATION_TYPE_ULTRA_PARALOGY );
  56         typesToNames.put( SEQUENCE_RELATION_TYPE.xenology, SEQUENCE_RELATION_TYPE_XENOLOGY );
  57         typesToNames.put( SEQUENCE_RELATION_TYPE.unknown, SEQUENCE_RELATION_TYPE_UNKNOWN );
  58         typesToNames.put( SEQUENCE_RELATION_TYPE.other, SEQUENCE_RELATION_TYPE_OTHER );
  59     }
  60
  61     @Override
  62     public StringBuffer asSimpleText() {
  63         // TODO Auto-generated method stub
  64         return null;
  65     }
  66
  67     @Override
  68     public StringBuffer asText() {
  69         // TODO Auto-generated method stub
  70         return null;
  71     }
  72
  73     @Override
  74     public PhylogenyData copy() {
  75         // TODO Auto-generated method stub
  76         return null;
  77     }
  78
  79     public Confidence getConfidence() {
  80         return confidence;
  81     }
  82
  83     public Double getDistance() {
  84         return distance;
  85     }
  86
  87     public Sequence getRef0() {
  88         return ref0;
  89     }
  90
  91     public Sequence getRef1() {
  92         return ref1;
  93     }
  94
  95     public SEQUENCE_RELATION_TYPE getType() {
  96         return type;
  97     }
  98
  99     @Override
 100     public boolean isEqual( final PhylogenyData data ) {
 101         // TODO Auto-generated method stub
 102         return false;
 103     }
 104
 105     public void setConfidence( final Confidence confidence ) {
 106         this.confidence = confidence;
 107     }
 108
 109     public void setDistance( final Double distance ) {
 110         this.distance = distance;
 111     }
 112
 113     public void setRef0( final Sequence ref0 ) {
 114         this.ref0 = ref0;
 115     }
 116
 117     public void setRef1( final Sequence ref1 ) {
 118         this.ref1 = ref1;
 119     }
 120
 121     public void setType( final SEQUENCE_RELATION_TYPE type ) {
 122         this.type = type;
 123     }
 124
 125     @Override
 126     public StringBuffer toNHX() {
 127         throw new UnsupportedOperationException();
 128     }
 129
 130     @Override
 131     public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
 132         // TODO Auto-generated method stub
 133     }
 134
 135     public static String getPrintableNameByType( final SEQUENCE_RELATION_TYPE type ) {
 136         String s = typesToNames.get( type );
 137         if ( s != null ) {
 138             s = s.replace( '_', ' ' );
 139             if ( ( s.length() > 15 ) && s.toLowerCase().endsWith( "ology" ) ) {
 140                 s = s.substring( 0, s.length() - 5 ) + ".";
 141             }
 142         }
 143         return s;
 144     }
 145
 146     public static enum SEQUENCE_RELATION_TYPE {
 147         orthology, one_to_one_orthology, super_orthology, paralogy, ultra_paralogy, xenology, unknown, other;
 148     }
 149 }