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