datamodel/compbio/data/sequence/ScoreManager.java

   1 package compbio.data.sequence;\r
   2 \r
   3 import java.io.IOException;\r
   4 import java.io.Writer;\r
   5 import java.util.ArrayList;\r
   6 import java.util.List;\r
   7 import java.util.Map;\r
   8 import java.util.Set;\r
   9 import java.util.TreeMap;\r
  10 import java.util.TreeSet;\r
  11 \r
  12 import javax.xml.bind.annotation.XmlAccessType;\r
  13 import javax.xml.bind.annotation.XmlAccessorType;\r
  14 import javax.xml.bind.annotation.XmlTransient;\r
  15 \r
  16 @XmlAccessorType(XmlAccessType.FIELD)\r
  17 public class ScoreManager {\r
  18 \r
  19         @XmlTransient\r
  20         public static final String SINGLE_ENTRY_KEY = "Alignment";\r
  21 \r
  22         private List<ScoreHolder> seqScores;\r
  23 \r
  24         private ScoreManager() {\r
  25                 // Default JAXB constructor\r
  26         }\r
  27 \r
  28         private ScoreManager(String id, Set<Score> data) {\r
  29                 seqScores = new ArrayList<ScoreManager.ScoreHolder>();\r
  30                 seqScores.add(new ScoreHolder(id, data));\r
  31         }\r
  32 \r
  33         private ScoreManager(Map<String, Set<Score>> data) {\r
  34                 List<ScoreHolder> seqScores = new ArrayList<ScoreHolder>();\r
  35                 for (Map.Entry<String, Set<Score>> singleSeqScores : data.entrySet()) {\r
  36                         seqScores.add(new ScoreHolder(singleSeqScores.getKey(),\r
  37                                         singleSeqScores.getValue()));\r
  38                 }\r
  39                 this.seqScores = seqScores;\r
  40         }\r
  41 \r
  42         public static ScoreManager newInstance(Map<String, Set<Score>> data) {\r
  43                 return new ScoreManager(data);\r
  44         }\r
  45 \r
  46         public static ScoreManager newInstanceSingleScore(\r
  47                         Map<String, Score> seqScoresMap) {\r
  48                 Map<String, Set<Score>> multipleScoresMap = new TreeMap<String, Set<Score>>();\r
  49                 for (Map.Entry<String, Score> seqScore : seqScoresMap.entrySet()) {\r
  50                         Set<Score> scores = new TreeSet<Score>();\r
  51                         scores.add(seqScore.getValue());\r
  52                         multipleScoresMap.put(seqScore.getKey(), scores);\r
  53                 }\r
  54                 return new ScoreManager(multipleScoresMap);\r
  55         }\r
  56 \r
  57         public static ScoreManager newInstanceSingleSequence(Set<Score> data) {\r
  58                 return new ScoreManager(ScoreManager.SINGLE_ENTRY_KEY,\r
  59                                 new TreeSet(data));\r
  60         }\r
  61 \r
  62         public Map<String, TreeSet<Score>> asMap() {\r
  63                 Map<String, TreeSet<Score>> seqScoresMap = new TreeMap<String, TreeSet<Score>>();\r
  64                 for (ScoreHolder sch : this.seqScores) {\r
  65                         TreeSet<Score> oldValue = seqScoresMap.put(sch.id, new TreeSet(\r
  66                                         sch.scores));\r
  67                         if (oldValue != null) {\r
  68                                 throw new IllegalStateException(\r
  69                                                 "Cannot represent this ScoreManager instance "\r
  70                                                                 + "as a Map as it contains duplicated keys: "\r
  71                                                                 + sch.id);\r
  72                         }\r
  73                 }\r
  74                 return seqScoresMap;\r
  75         }\r
  76 \r
  77         public Set<Score> asSet() {\r
  78                 if (seqScores.size() == 0 || seqScores.size() > 1) {\r
  79                         throw new IllegalStateException(\r
  80                                         "This ScoreManager has no or multiple sequence entries and thus "\r
  81                                                         + "cannot be represented as a Set. Number of entries are: "\r
  82                                                         + seqScores.size());\r
  83                 }\r
  84                 ScoreHolder sch = seqScores.get(0);\r
  85                 return sch.scores;\r
  86         }\r
  87 \r
  88         public int getNumberOfSeq() {\r
  89                 return seqScores.size();\r
  90         }\r
  91 \r
  92         public ScoreHolder getAnnotationForSequence(String seqId) {\r
  93                 for (ScoreHolder sch : seqScores) {\r
  94                         if (sch.id.equals(seqId)) {\r
  95                                 return sch;\r
  96                         }\r
  97                 }\r
  98                 return null;\r
  99         }\r
 100 \r
 101         public void writeOut(Writer outStream) throws IOException {\r
 102                 for (ScoreHolder oneSeqScores : seqScores) {\r
 103                         oneSeqScores.writeOut(outStream);\r
 104                 }\r
 105         }\r
 106 \r
 107         @Override\r
 108         public int hashCode() {\r
 109                 final int prime = 31;\r
 110                 int result = 1;\r
 111                 result = prime * result\r
 112                                 + ((seqScores == null) ? 0 : seqScores.hashCode());\r
 113                 return result;\r
 114         }\r
 115 \r
 116         @Override\r
 117         public boolean equals(Object obj) {\r
 118                 if (this == obj)\r
 119                         return true;\r
 120                 if (obj == null)\r
 121                         return false;\r
 122                 if (getClass() != obj.getClass())\r
 123                         return false;\r
 124                 ScoreManager other = (ScoreManager) obj;\r
 125                 if (seqScores == null) {\r
 126                         if (other.seqScores != null)\r
 127                                 return false;\r
 128                 } else if (!seqScores.equals(other.seqScores))\r
 129                         return false;\r
 130                 return true;\r
 131         }\r
 132 \r
 133         @XmlAccessorType(XmlAccessType.FIELD)\r
 134         public static class ScoreHolder {\r
 135 \r
 136                 public String id;\r
 137                 public TreeSet<Score> scores;\r
 138 \r
 139                 private ScoreHolder() {\r
 140                         // JAXB Default constructor should not be used otherwise\r
 141                 }\r
 142 \r
 143                 ScoreHolder(String id, Set<Score> scores) {\r
 144                         this.id = id;\r
 145                         this.scores = new TreeSet<Score>(scores);\r
 146                 }\r
 147 \r
 148                 public void writeOut(Writer writer) throws IOException {\r
 149                         writer.write(">" + id + "\n");\r
 150                         Score.write(scores, writer);\r
 151                 }\r
 152 \r
 153                 public Score getScoreByMethod(Enum<?> method) {\r
 154                         for (Score sc : scores) {\r
 155                                 if (method.toString().equals(sc.getMethod())) {\r
 156                                         return sc;\r
 157                                 }\r
 158                         }\r
 159                         return null;\r
 160                 }\r
 161                 public Score getScoreByMethod(String method) {\r
 162                         for (Score sc : scores) {\r
 163                                 if (method.toString().equals(sc.getMethod())) {\r
 164                                         return sc;\r
 165                                 }\r
 166                         }\r
 167                         return null;\r
 168                 }\r
 169                 public int getNumberOfScores() {\r
 170                         return scores.size();\r
 171                 }\r
 172 \r
 173                 @Override\r
 174                 public int hashCode() {\r
 175                         final int prime = 17;\r
 176                         int result = 1;\r
 177                         result = prime * result + ((id == null) ? 0 : id.hashCode());\r
 178                         result = prime * result\r
 179                                         + ((scores == null) ? 0 : scores.hashCode());\r
 180                         return result;\r
 181                 }\r
 182 \r
 183                 @Override\r
 184                 public boolean equals(Object obj) {\r
 185                         if (this == obj)\r
 186                                 return true;\r
 187                         if (obj == null)\r
 188                                 return false;\r
 189                         if (getClass() != obj.getClass())\r
 190                                 return false;\r
 191                         ScoreHolder other = (ScoreHolder) obj;\r
 192                         if (id == null) {\r
 193                                 if (other.id != null)\r
 194                                         return false;\r
 195                         } else if (!id.equals(other.id))\r
 196                                 return false;\r
 197                         if (scores == null) {\r
 198                                 if (other.scores != null)\r
 199                                         return false;\r
 200                         } else if (!scores.equals(other.scores))\r
 201                                 return false;\r
 202                         return true;\r
 203                 }\r
 204 \r
 205         }\r
 206 }\r