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.XmlSeeAlso;\r
  32 import javax.xml.bind.annotation.XmlTransient;\r
  33 \r
  34 @XmlSeeAlso({RNAStructScoreManager.class})\r
  35 @XmlAccessorType(XmlAccessType.FIELD)\r
  36 public class ScoreManager {\r
  37 \r
  38         @XmlTransient\r
  39         public static final String SINGLE_ENTRY_KEY = "Alignment";\r
  40 \r
  41         protected List<ScoreHolder> seqScores;\r
  42 \r
  43         // Do I have to change this to protected?\r
  44         protected ScoreManager() {\r
  45                 // Default JAXB constructor\r
  46         }\r
  47 \r
  48         private ScoreManager(String id, Set<Score> data) {\r
  49                 seqScores = new ArrayList<ScoreManager.ScoreHolder>();\r
  50                 seqScores.add(new ScoreHolder(id, data));\r
  51         }\r
  52 \r
  53         private ScoreManager(Map<String, Set<Score>> data) {\r
  54                 System.out.println("A ScoreManager was created!!");\r
  55 \r
  56                 \r
  57                 List<ScoreHolder> seqScores = new ArrayList<ScoreHolder>();\r
  58                 for (Map.Entry<String, Set<Score>> singleSeqScores : data.entrySet()) {\r
  59                         seqScores.add(new ScoreHolder(singleSeqScores.getKey(),\r
  60                                         singleSeqScores.getValue()));\r
  61                 }\r
  62                 this.seqScores = seqScores;\r
  63         }\r
  64 \r
  65         public static ScoreManager newInstance(Map<String, Set<Score>> data) {\r
  66                 System.out.println("A ScoreManager was created!!");\r
  67 \r
  68                 \r
  69                 return new ScoreManager(data);\r
  70         }\r
  71 \r
  72         public static ScoreManager newInstanceSingleScore(\r
  73                         Map<String, Score> seqScoresMap) {\r
  74                 \r
  75                 System.out.println("A ScoreManager was created!!");\r
  76 \r
  77                 \r
  78                 Map<String, Set<Score>> multipleScoresMap = new TreeMap<String, Set<Score>>();\r
  79                 for (Map.Entry<String, Score> seqScore : seqScoresMap.entrySet()) {\r
  80                         Set<Score> scores = new TreeSet<Score>();\r
  81                         scores.add(seqScore.getValue());\r
  82                         multipleScoresMap.put(seqScore.getKey(), scores);\r
  83                 }\r
  84                 return new ScoreManager(multipleScoresMap);\r
  85         }\r
  86 \r
  87         public static ScoreManager newInstanceSingleSequence(Set<Score> data) {\r
  88                 System.out.println("A ScoreManager was created!!");\r
  89 \r
  90                 \r
  91                 return new ScoreManager(ScoreManager.SINGLE_ENTRY_KEY,\r
  92                                 new TreeSet(data));\r
  93         }\r
  94         \r
  95         public Map<String, TreeSet<Score>> asMap() {\r
  96                 Map<String, TreeSet<Score>> seqScoresMap = new TreeMap<String, TreeSet<Score>>();\r
  97                 for (ScoreHolder sch : this.seqScores) {\r
  98                         TreeSet<Score> oldValue = seqScoresMap.put(sch.id, new TreeSet(\r
  99                                         sch.scores));\r
 100                         if (oldValue != null) {\r
 101                                 throw new IllegalStateException(\r
 102                                                 "Cannot represent this ScoreManager instance "\r
 103                                                                 + "as a Map as it contains duplicated keys: "\r
 104                                                                 + sch.id);\r
 105                         }\r
 106                 }\r
 107                 return seqScoresMap;\r
 108         }\r
 109 \r
 110         public Set<Score> asSet() {\r
 111                 if (seqScores.size() == 0 || seqScores.size() > 1) {\r
 112                         throw new IllegalStateException(\r
 113                                         "This ScoreManager has no or multiple sequence entries and thus "\r
 114                                                         + "cannot be represented as a Set. Number of entries are: "\r
 115                                                         + seqScores.size());\r
 116                 }\r
 117                 ScoreHolder sch = seqScores.get(0);\r
 118                 return sch.scores;\r
 119         }\r
 120 \r
 121         public int getNumberOfSeq() {\r
 122                 return seqScores.size();\r
 123         }\r
 124 \r
 125         public ScoreHolder getAnnotationForSequence(String seqId) {\r
 126                 for (ScoreHolder sch : seqScores) {\r
 127                         if (sch.id.equals(seqId)) {\r
 128                                 return sch;\r
 129                         }\r
 130                 }\r
 131                 return null;\r
 132         }\r
 133 \r
 134         public void writeOut(Writer outStream) throws IOException {\r
 135                 assert outStream != null : "Output steam is not defined!";\r
 136                 if (seqScores == null) {\r
 137                         return;\r
 138                 }\r
 139                 for (ScoreHolder oneSeqScores : seqScores) {\r
 140                         if (oneSeqScores == null)\r
 141                                 continue;\r
 142                         oneSeqScores.writeOut(outStream);\r
 143                 }\r
 144         }\r
 145 \r
 146         @Override\r
 147         public int hashCode() {\r
 148                 final int prime = 31;\r
 149                 int result = 1;\r
 150                 result = prime * result\r
 151                                 + ((seqScores == null) ? 0 : seqScores.hashCode());\r
 152                 return result;\r
 153         }\r
 154 \r
 155         @Override\r
 156         public boolean equals(Object obj) {\r
 157                 if (this == obj)\r
 158                         return true;\r
 159                 if (obj == null)\r
 160                         return false;\r
 161                 if (getClass() != obj.getClass())\r
 162                         return false;\r
 163                 ScoreManager other = (ScoreManager) obj;\r
 164                 if (seqScores == null) {\r
 165                         if (other.seqScores != null)\r
 166                                 return false;\r
 167                 } else if (!seqScores.equals(other.seqScores))\r
 168                         return false;\r
 169                 return true;\r
 170         }\r
 171 \r
 172         @XmlAccessorType(XmlAccessType.FIELD)\r
 173         public static class ScoreHolder {\r
 174 \r
 175                 public String id;\r
 176                 public TreeSet<Score> scores;\r
 177 \r
 178                 private ScoreHolder() {\r
 179                         // JAXB Default constructor should not be used otherwise\r
 180                 }\r
 181 \r
 182                 ScoreHolder(String id, Set<Score> scores) {\r
 183                         this.id = id;\r
 184                         this.scores = new TreeSet<Score>(scores);               }\r
 185 \r
 186                 public void writeOut(Writer writer) throws IOException {\r
 187                         writer.write(">" + id + "\n");\r
 188                         Score.write(scores, writer);\r
 189                 }\r
 190 \r
 191                 public Score getScoreByMethod(Enum<?> method) {\r
 192                         for (Score sc : scores) {\r
 193                                 if (method.toString().equals(sc.getMethod())) {\r
 194                                         return sc;\r
 195                                 }\r
 196                         }\r
 197                         return null;\r
 198                 }\r
 199                 public Score getScoreByMethod(String method) {\r
 200                         for (Score sc : scores) {\r
 201                                 if (method.toString().equals(sc.getMethod())) {\r
 202                                         return sc;\r
 203                                 }\r
 204                         }\r
 205                         return null;\r
 206                 }\r
 207                 public int getNumberOfScores() {\r
 208                         return scores.size();\r
 209                 }\r
 210 \r
 211                 @Override\r
 212                 public int hashCode() {\r
 213                         final int prime = 17;\r
 214                         int result = 1;\r
 215                         result = prime * result + ((id == null) ? 0 : id.hashCode());\r
 216                         result = prime * result\r
 217                                         + ((scores == null) ? 0 : scores.hashCode());\r
 218                         return result;\r
 219                 }\r
 220 \r
 221                 @Override\r
 222                 public boolean equals(Object obj) {\r
 223                         if (this == obj)\r
 224                                 return true;\r
 225                         if (obj == null)\r
 226                                 return false;\r
 227                         if (getClass() != obj.getClass())\r
 228                                 return false;\r
 229                         ScoreHolder other = (ScoreHolder) obj;\r
 230                         if (id == null) {\r
 231                                 if (other.id != null)\r
 232                                         return false;\r
 233                         } else if (!id.equals(other.id))\r
 234                                 return false;\r
 235                         if (scores == null) {\r
 236                                 if (other.scores != null)\r
 237                                         return false;\r
 238                         } else if (!scores.equals(other.scores))\r
 239                                 return false;\r
 240                         return true;\r
 241                 }\r
 242 \r
 243         }\r
 244 \r
 245 }\r