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