datamodel/compbio/data/sequence/ScoreManager.java

   1 package compbio.data.sequence;\r
   2 \r
   3 import java.io.BufferedWriter;\r
   4 import java.io.IOException;\r
   5 import java.io.OutputStream;\r
   6 import java.io.OutputStreamWriter;\r
   7 import java.util.ArrayList;\r
   8 import java.util.HashMap;\r
   9 import java.util.HashSet;\r
  10 import java.util.List;\r
  11 import java.util.Map;\r
  12 import java.util.Set;\r
  13 \r
  14 import javax.xml.bind.annotation.XmlAccessType;\r
  15 import javax.xml.bind.annotation.XmlAccessorType;\r
  16 import javax.xml.bind.annotation.XmlTransient;\r
  17 \r
  18 @XmlAccessorType(XmlAccessType.FIELD)\r
  19 public class ScoreManager {\r
  20 \r
  21         @XmlTransient\r
  22         public static final String SINGLE_ENTRY_KEY = "Alignment";\r
  23 \r
  24         private List<ScoreHolder> seqScores;\r
  25 \r
  26         private ScoreManager() {\r
  27                 // Default JAXB constructor\r
  28         }\r
  29 \r
  30         private ScoreManager(String id, Set<Score> data) {\r
  31                 seqScores = new ArrayList<ScoreManager.ScoreHolder>();\r
  32                 seqScores.add(new ScoreHolder(id, data));\r
  33         }\r
  34 \r
  35         private ScoreManager(Map<String, Set<Score>> data) {\r
  36                 List<ScoreHolder> seqScores = new ArrayList<ScoreHolder>();\r
  37                 for (Map.Entry<String, Set<Score>> singleSeqScores : data.entrySet()) {\r
  38                         seqScores.add(new ScoreHolder(singleSeqScores.getKey(),\r
  39                                         singleSeqScores.getValue()));\r
  40                 }\r
  41                 this.seqScores = seqScores;\r
  42         }\r
  43 \r
  44         public static ScoreManager newInstance(Map<String, Set<Score>> data) {\r
  45                 return new ScoreManager(data);\r
  46         }\r
  47 \r
  48         public static ScoreManager newInstanceSingleScore(\r
  49                         Map<String, Score> seqScoresMap) {\r
  50                 Map<String, Set<Score>> multipleScoresMap = new HashMap<String, Set<Score>>();\r
  51                 for (Map.Entry<String, Score> seqScore : seqScoresMap.entrySet()) {\r
  52                         Set<Score> scores = new HashSet<Score>();\r
  53                         scores.add(seqScore.getValue());\r
  54                         multipleScoresMap.put(seqScore.getKey(), scores);\r
  55                 }\r
  56                 return new ScoreManager(multipleScoresMap);\r
  57         }\r
  58 \r
  59         public static ScoreManager newInstanceSingleSequence(Set<Score> data) {\r
  60                 return new ScoreManager(ScoreManager.SINGLE_ENTRY_KEY, data);\r
  61         }\r
  62 \r
  63         public Map<String, Set<Score>> asMap() {\r
  64                 Map<String, Set<Score>> seqScoresMap = new HashMap<String, Set<Score>>();\r
  65                 for (ScoreHolder sch : this.seqScores) {\r
  66                         Set<Score> oldValue = seqScoresMap.put(sch.id, 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(OutputStream outStream) throws IOException {\r
 102                 BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(\r
 103                                 outStream));\r
 104                 for (ScoreHolder oneSeqScores : seqScores) {\r
 105                         oneSeqScores.writeOut(outStream);\r
 106                 }\r
 107                 writer.flush();\r
 108         }\r
 109 \r
 110         @Override\r
 111         public int hashCode() {\r
 112                 final int prime = 31;\r
 113                 int result = 1;\r
 114                 result = prime * result\r
 115                                 + ((seqScores == null) ? 0 : seqScores.hashCode());\r
 116                 return result;\r
 117         }\r
 118 \r
 119         @Override\r
 120         public boolean equals(Object obj) {\r
 121                 if (this == obj)\r
 122                         return true;\r
 123                 if (obj == null)\r
 124                         return false;\r
 125                 if (getClass() != obj.getClass())\r
 126                         return false;\r
 127                 ScoreManager other = (ScoreManager) obj;\r
 128                 if (seqScores == null) {\r
 129                         if (other.seqScores != null)\r
 130                                 return false;\r
 131                 } else if (!seqScores.equals(other.seqScores))\r
 132                         return false;\r
 133                 return true;\r
 134         }\r
 135 \r
 136         @XmlAccessorType(XmlAccessType.FIELD)\r
 137         public static class ScoreHolder {\r
 138 \r
 139                 public String id;\r
 140                 public HashSet<Score> scores;\r
 141 \r
 142                 private ScoreHolder() {\r
 143                         // JAXB Default constructor should not be used otherwise\r
 144                 }\r
 145 \r
 146                 ScoreHolder(String id, Set<Score> scores) {\r
 147                         this.id = id;\r
 148                         this.scores = new HashSet<Score>(scores);\r
 149                 }\r
 150 \r
 151                 public void writeOut(OutputStream outStream) throws IOException {\r
 152                         BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(\r
 153                                         outStream));\r
 154                         writer.write(">" + id + "\n");\r
 155                         Score.write(scores, outStream);\r
 156                 }\r
 157 \r
 158                 public Score getScoreByMethod(Enum<?> method) {\r
 159                         for (Score sc : scores) {\r
 160                                 if (method.toString().equals(sc.getMethod())) {\r
 161                                         return sc;\r
 162                                 }\r
 163                         }\r
 164                         return null;\r
 165                 }\r
 166                 public int getNumberOfScores() {\r
 167                         return scores.size();\r
 168                 }\r
 169 \r
 170                 @Override\r
 171                 public int hashCode() {\r
 172                         final int prime = 17;\r
 173                         int result = 1;\r
 174                         result = prime * result + ((id == null) ? 0 : id.hashCode());\r
 175                         result = prime * result\r
 176                                         + ((scores == null) ? 0 : scores.hashCode());\r
 177                         return result;\r
 178                 }\r
 179 \r
 180                 @Override\r
 181                 public boolean equals(Object obj) {\r
 182                         if (this == obj)\r
 183                                 return true;\r
 184                         if (obj == null)\r
 185                                 return false;\r
 186                         if (getClass() != obj.getClass())\r
 187                                 return false;\r
 188                         ScoreHolder other = (ScoreHolder) obj;\r
 189                         if (id == null) {\r
 190                                 if (other.id != null)\r
 191                                         return false;\r
 192                         } else if (!id.equals(other.id))\r
 193                                 return false;\r
 194                         if (scores == null) {\r
 195                                 if (other.scores != null)\r
 196                                         return false;\r
 197                         } else if (!scores.equals(other.scores))\r
 198                                 return false;\r
 199                         return true;\r
 200                 }\r
 201 \r
 202         }\r
 203 }\r