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         return null;
  64     }
  65
  66     @Override
  67     public StringBuffer asText() {
  68         return null;
  69     }
  70
  71     @Override
  72     public PhylogenyData copy() {
  73         // TODO Auto-generated method stub
  74         return null;
  75     }
  76
  77     public Confidence getConfidence() {
  78         return confidence;
  79     }
  80
  81     public Double getDistance() {
  82         return distance;
  83     }
  84
  85     public Sequence getRef0() {
  86         return ref0;
  87     }
  88
  89     public Sequence getRef1() {
  90         return ref1;
  91     }
  92
  93     public SEQUENCE_RELATION_TYPE getType() {
  94         return type;
  95     }
  96
  97     @Override
  98     public boolean isEqual( final PhylogenyData data ) {
  99         // TODO Auto-generated method stub
 100         return false;
 101     }
 102
 103     public void setConfidence( final Confidence confidence ) {
 104         this.confidence = confidence;
 105     }
 106
 107     public void setDistance( final Double distance ) {
 108         this.distance = distance;
 109     }
 110
 111     public void setRef0( final Sequence ref0 ) {
 112         this.ref0 = ref0;
 113     }
 114
 115     public void setRef1( final Sequence ref1 ) {
 116         this.ref1 = ref1;
 117     }
 118
 119     public void setType( final SEQUENCE_RELATION_TYPE type ) {
 120         this.type = type;
 121     }
 122
 123     @Override
 124     public StringBuffer toNHX() {
 125         throw new UnsupportedOperationException();
 126     }
 127
 128     @Override
 129     public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
 130         // TODO Auto-generated method stub
 131     }
 132
 133     public static String getPrintableNameByType( final SEQUENCE_RELATION_TYPE type ) {
 134         String s = typesToNames.get( type );
 135         if ( s != null ) {
 136             s = s.replace( '_', ' ' );
 137             if ( ( s.length() > 15 ) && s.toLowerCase().endsWith( "ology" ) ) {
 138                 s = s.substring( 0, s.length() - 5 ) + ".";
 139             }
 140         }
 141         return s;
 142     }
 143
 144     public static enum SEQUENCE_RELATION_TYPE {
 145         orthology, one_to_one_orthology, super_orthology, paralogy, ultra_paralogy, xenology, unknown, other;
 146     }
 147 }