datamodel/compbio/data/sequence/ScoreManager.java

   1 /* Copyright (c) 2011 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     \r
   4  * \r
   5  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
   6  *  Apache License version 2 as published by the Apache Software Foundation\r
   7  * \r
   8  *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
   9  *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
  10  *  License for more details.\r
  11  * \r
  12  *  A copy of the license is in apache_license.txt. It is also available here:\r
  13  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
  14  * \r
  15  * Any republication or derived work distributed in source code form\r
  16  * must include this copyright and license notice.\r
  17  */\r
  18 package compbio.data.sequence;\r
  19 \r
  20 import java.io.IOException;\r
  21 import java.io.Writer;\r
  22 import java.util.ArrayList;\r
  23 import java.util.List;\r
  24 import java.util.Map;\r
  25 import java.util.Set;\r
  26 import java.util.TreeMap;\r
  27 import java.util.TreeSet;\r
  28 \r
  29 import javax.xml.bind.annotation.XmlAccessType;\r
  30 import javax.xml.bind.annotation.XmlAccessorType;\r
  31 import javax.xml.bind.annotation.XmlTransient;\r
  32 \r
  33 @XmlAccessorType(XmlAccessType.FIELD)\r
  34 public class ScoreManager {\r
  35 \r
  36         @XmlTransient\r
  37         public static final String SINGLE_ENTRY_KEY = "Alignment";\r
  38 \r
  39         protected List<ScoreHolder> seqScores;\r
  40 \r
  41         // Do I have to change this to protected?\r
  42         protected ScoreManager() {\r
  43                 // Default JAXB constructor\r
  44         }\r
  45 \r
  46         private ScoreManager(String id, Set<Score> data) {\r
  47                 seqScores = new ArrayList<ScoreManager.ScoreHolder>();\r
  48                 seqScores.add(new ScoreHolder(id, data));\r
  49         }\r
  50 \r
  51         private ScoreManager(Map<String, Set<Score>> data) {\r
  52                 List<ScoreHolder> seqScores = new ArrayList<ScoreHolder>();\r
  53                 for (Map.Entry<String, Set<Score>> singleSeqScores : data.entrySet()) {\r
  54                         seqScores.add(new ScoreHolder(singleSeqScores.getKey(),\r
  55                                         singleSeqScores.getValue()));\r
  56                 }\r
  57                 this.seqScores = seqScores;\r
  58         }\r
  59 \r
  60         public static ScoreManager newInstance(Map<String, Set<Score>> data) {\r
  61                 return new ScoreManager(data);\r
  62         }\r
  63 \r
  64         public static ScoreManager newInstanceSingleScore(\r
  65                         Map<String, Score> seqScoresMap) {\r
  66                 Map<String, Set<Score>> multipleScoresMap = new TreeMap<String, Set<Score>>();\r
  67                 for (Map.Entry<String, Score> seqScore : seqScoresMap.entrySet()) {\r
  68                         Set<Score> scores = new TreeSet<Score>();\r
  69                         scores.add(seqScore.getValue());\r
  70                         multipleScoresMap.put(seqScore.getKey(), scores);\r
  71                 }\r
  72                 return new ScoreManager(multipleScoresMap);\r
  73         }\r
  74 \r
  75         public static ScoreManager newInstanceSingleSequence(Set<Score> data) {\r
  76                 return new ScoreManager(ScoreManager.SINGLE_ENTRY_KEY,\r
  77                                 new TreeSet(data));\r
  78         }\r
  79         \r
  80         public Map<String, TreeSet<Score>> asMap() {\r
  81                 Map<String, TreeSet<Score>> seqScoresMap = new TreeMap<String, TreeSet<Score>>();\r
  82                 for (ScoreHolder sch : this.seqScores) {\r
  83                         TreeSet<Score> oldValue = seqScoresMap.put(sch.id, new TreeSet(\r
  84                                         sch.scores));\r
  85                         if (oldValue != null) {\r
  86                                 throw new IllegalStateException(\r
  87                                                 "Cannot represent this ScoreManager instance "\r
  88                                                                 + "as a Map as it contains duplicated keys: "\r
  89                                                                 + sch.id);\r
  90                         }\r
  91                 }\r
  92                 return seqScoresMap;\r
  93         }\r
  94 \r
  95         public Set<Score> asSet() {\r
  96                 if (seqScores.size() == 0 || seqScores.size() > 1) {\r
  97                         throw new IllegalStateException(\r
  98                                         "This ScoreManager has no or multiple sequence entries and thus "\r
  99                                                         + "cannot be represented as a Set. Number of entries are: "\r
 100                                                         + seqScores.size());\r
 101                 }\r
 102                 ScoreHolder sch = seqScores.get(0);\r
 103                 return sch.scores;\r
 104         }\r
 105 \r
 106         public int getNumberOfSeq() {\r
 107                 return seqScores.size();\r
 108         }\r
 109 \r
 110         public ScoreHolder getAnnotationForSequence(String seqId) {\r
 111                 for (ScoreHolder sch : seqScores) {\r
 112                         if (sch.id.equals(seqId)) {\r
 113                                 return sch;\r
 114                         }\r
 115                 }\r
 116                 return null;\r
 117         }\r
 118 \r
 119         public void writeOut(Writer outStream) throws IOException {\r
 120                 assert outStream != null : "Output steam is not defined!";\r
 121                 if (seqScores == null) {\r
 122                         return;\r
 123                 }\r
 124                 for (ScoreHolder oneSeqScores : seqScores) {\r
 125                         if (oneSeqScores == null)\r
 126                                 continue;\r
 127                         oneSeqScores.writeOut(outStream);\r
 128                 }\r
 129         }\r
 130 \r
 131         @Override\r
 132         public int hashCode() {\r
 133                 final int prime = 31;\r
 134                 int result = 1;\r
 135                 result = prime * result\r
 136                                 + ((seqScores == null) ? 0 : seqScores.hashCode());\r
 137                 return result;\r
 138         }\r
 139 \r
 140         @Override\r
 141         public boolean equals(Object obj) {\r
 142                 if (this == obj)\r
 143                         return true;\r
 144                 if (obj == null)\r
 145                         return false;\r
 146                 if (getClass() != obj.getClass())\r
 147                         return false;\r
 148                 ScoreManager other = (ScoreManager) obj;\r
 149                 if (seqScores == null) {\r
 150                         if (other.seqScores != null)\r
 151                                 return false;\r
 152                 } else if (!seqScores.equals(other.seqScores))\r
 153                         return false;\r
 154                 return true;\r
 155         }\r
 156 \r
 157         @XmlAccessorType(XmlAccessType.FIELD)\r
 158         public static class ScoreHolder {\r
 159 \r
 160                 public String id;\r
 161                 public TreeSet<Score> scores;\r
 162 \r
 163                 private ScoreHolder() {\r
 164                         // JAXB Default constructor should not be used otherwise\r
 165                 }\r
 166 \r
 167                 ScoreHolder(String id, Set<Score> scores) {\r
 168                         this.id = id;\r
 169                         this.scores = new TreeSet<Score>(scores);               }\r
 170 \r
 171                 public void writeOut(Writer writer) throws IOException {\r
 172                         writer.write(">" + id + "\n");\r
 173                         Score.write(scores, writer);\r
 174                 }\r
 175 \r
 176                 public Score getScoreByMethod(Enum<?> method) {\r
 177                         for (Score sc : scores) {\r
 178                                 if (method.toString().equals(sc.getMethod())) {\r
 179                                         return sc;\r
 180                                 }\r
 181                         }\r
 182                         return null;\r
 183                 }\r
 184                 public Score getScoreByMethod(String method) {\r
 185                         for (Score sc : scores) {\r
 186                                 if (method.toString().equals(sc.getMethod())) {\r
 187                                         return sc;\r
 188                                 }\r
 189                         }\r
 190                         return null;\r
 191                 }\r
 192                 public int getNumberOfScores() {\r
 193                         return scores.size();\r
 194                 }\r
 195 \r
 196                 @Override\r
 197                 public int hashCode() {\r
 198                         final int prime = 17;\r
 199                         int result = 1;\r
 200                         result = prime * result + ((id == null) ? 0 : id.hashCode());\r
 201                         result = prime * result\r
 202                                         + ((scores == null) ? 0 : scores.hashCode());\r
 203                         return result;\r
 204                 }\r
 205 \r
 206                 @Override\r
 207                 public boolean equals(Object obj) {\r
 208                         if (this == obj)\r
 209                                 return true;\r
 210                         if (obj == null)\r
 211                                 return false;\r
 212                         if (getClass() != obj.getClass())\r
 213                                 return false;\r
 214                         ScoreHolder other = (ScoreHolder) obj;\r
 215                         if (id == null) {\r
 216                                 if (other.id != null)\r
 217                                         return false;\r
 218                         } else if (!id.equals(other.id))\r
 219                                 return false;\r
 220                         if (scores == null) {\r
 221                                 if (other.scores != null)\r
 222                                         return false;\r
 223                         } else if (!scores.equals(other.scores))\r
 224                                 return false;\r
 225                         return true;\r
 226                 }\r
 227 \r
 228         }\r
 229 \r
 230 }\r