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