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         public static ScoreManager newInstance(Map<String, Set<Score>> data) {\r
  60                 return new ScoreManager(data);\r
  61         }\r
  62 \r
  63         public static ScoreManager newInstanceSingleScore(\r
  64                         Map<String, Score> seqScoresMap) {\r
  65                 Map<String, Set<Score>> multipleScoresMap = new TreeMap<String, Set<Score>>();\r
  66                 for (Map.Entry<String, Score> seqScore : seqScoresMap.entrySet()) {\r
  67                         Set<Score> scores = new TreeSet<Score>();\r
  68                         scores.add(seqScore.getValue());\r
  69                         multipleScoresMap.put(seqScore.getKey(), scores);\r
  70                 }\r
  71                 return new ScoreManager(multipleScoresMap);\r
  72         }\r
  73 \r
  74         public static ScoreManager newInstanceSingleSequence(Set<Score> data) {\r
  75                 return new ScoreManager(ScoreManager.SINGLE_ENTRY_KEY,\r
  76                                 new TreeSet(data));\r
  77         }\r
  78 \r
  79         public Map<String, TreeSet<Score>> asMap() {\r
  80                 Map<String, TreeSet<Score>> seqScoresMap = new TreeMap<String, TreeSet<Score>>();\r
  81                 for (ScoreHolder sch : this.seqScores) {\r
  82                         TreeSet<Score> oldValue = seqScoresMap.put(sch.id, new TreeSet(\r
  83                                         sch.scores));\r
  84                         if (oldValue != null) {\r
  85                                 throw new IllegalStateException(\r
  86                                                 "Cannot represent this ScoreManager instance "\r
  87                                                                 + "as a Map as it contains duplicated keys: "\r
  88                                                                 + sch.id);\r
  89                         }\r
  90                 }\r
  91                 return seqScoresMap;\r
  92         }\r
  93 \r
  94         public Set<Score> asSet() {\r
  95                 if (seqScores.size() == 0 || seqScores.size() > 1) {\r
  96                         throw new IllegalStateException(\r
  97                                         "This ScoreManager has no or multiple sequence entries and thus "\r
  98                                                         + "cannot be represented as a Set. Number of entries are: "\r
  99                                                         + seqScores.size());\r
 100                 }\r
 101                 ScoreHolder sch = seqScores.get(0);\r
 102                 return sch.scores;\r
 103         }\r
 104 \r
 105         public int getNumberOfSeq() {\r
 106                 return seqScores.size();\r
 107         }\r
 108 \r
 109         public ScoreHolder getAnnotationForSequence(String seqId) {\r
 110                 for (ScoreHolder sch : seqScores) {\r
 111                         if (sch.id.equals(seqId)) {\r
 112                                 return sch;\r
 113                         }\r
 114                 }\r
 115                 return null;\r
 116         }\r
 117 \r
 118         public void writeOut(Writer outStream) throws IOException {\r
 119                 for (ScoreHolder oneSeqScores : seqScores) {\r
 120                         oneSeqScores.writeOut(outStream);\r
 121                 }\r
 122         }\r
 123 \r
 124         @Override\r
 125         public int hashCode() {\r
 126                 final int prime = 31;\r
 127                 int result = 1;\r
 128                 result = prime * result\r
 129                                 + ((seqScores == null) ? 0 : seqScores.hashCode());\r
 130                 return result;\r
 131         }\r
 132 \r
 133         @Override\r
 134         public boolean equals(Object obj) {\r
 135                 if (this == obj)\r
 136                         return true;\r
 137                 if (obj == null)\r
 138                         return false;\r
 139                 if (getClass() != obj.getClass())\r
 140                         return false;\r
 141                 ScoreManager other = (ScoreManager) obj;\r
 142                 if (seqScores == null) {\r
 143                         if (other.seqScores != null)\r
 144                                 return false;\r
 145                 } else if (!seqScores.equals(other.seqScores))\r
 146                         return false;\r
 147                 return true;\r
 148         }\r
 149 \r
 150         @XmlAccessorType(XmlAccessType.FIELD)\r
 151         public static class ScoreHolder {\r
 152 \r
 153                 public String id;\r
 154                 public TreeSet<Score> scores;\r
 155 \r
 156                 private ScoreHolder() {\r
 157                         // JAXB Default constructor should not be used otherwise\r
 158                 }\r
 159 \r
 160                 ScoreHolder(String id, Set<Score> scores) {\r
 161                         this.id = id;\r
 162                         this.scores = new TreeSet<Score>(scores);\r
 163                 }\r
 164 \r
 165                 public void writeOut(Writer writer) throws IOException {\r
 166                         writer.write(">" + id + "\n");\r
 167                         Score.write(scores, writer);\r
 168                 }\r
 169 \r
 170                 public Score getScoreByMethod(Enum<?> method) {\r
 171                         for (Score sc : scores) {\r
 172                                 if (method.toString().equals(sc.getMethod())) {\r
 173                                         return sc;\r
 174                                 }\r
 175                         }\r
 176                         return null;\r
 177                 }\r
 178                 public Score getScoreByMethod(String method) {\r
 179                         for (Score sc : scores) {\r
 180                                 if (method.toString().equals(sc.getMethod())) {\r
 181                                         return sc;\r
 182                                 }\r
 183                         }\r
 184                         return null;\r
 185                 }\r
 186                 public int getNumberOfScores() {\r
 187                         return scores.size();\r
 188                 }\r
 189 \r
 190                 @Override\r
 191                 public int hashCode() {\r
 192                         final int prime = 17;\r
 193                         int result = 1;\r
 194                         result = prime * result + ((id == null) ? 0 : id.hashCode());\r
 195                         result = prime * result\r
 196                                         + ((scores == null) ? 0 : scores.hashCode());\r
 197                         return result;\r
 198                 }\r
 199 \r
 200                 @Override\r
 201                 public boolean equals(Object obj) {\r
 202                         if (this == obj)\r
 203                                 return true;\r
 204                         if (obj == null)\r
 205                                 return false;\r
 206                         if (getClass() != obj.getClass())\r
 207                                 return false;\r
 208                         ScoreHolder other = (ScoreHolder) obj;\r
 209                         if (id == null) {\r
 210                                 if (other.id != null)\r
 211                                         return false;\r
 212                         } else if (!id.equals(other.id))\r
 213                                 return false;\r
 214                         if (scores == null) {\r
 215                                 if (other.scores != null)\r
 216                                         return false;\r
 217                         } else if (!scores.equals(other.scores))\r
 218                                 return false;\r
 219                         return true;\r
 220                 }\r
 221 \r
 222         }\r
 223 }\r