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.HashSet;\r
   8 import java.util.List;\r
   9 \r
  10 public class ScoreManager {\r
  11 \r
  12         private List<ScoreHolder> seqScores;\r
  13 \r
  14         private ScoreManager() {\r
  15                 // Default JAXB constructor\r
  16         }\r
  17 \r
  18         public int getNumberOfSeq() {\r
  19                 return seqScores.size();\r
  20         }\r
  21 \r
  22         public ScoreHolder getFirstSequenceScores() {\r
  23                 if (seqScores.isEmpty())\r
  24                         return null;\r
  25                 return seqScores.get(0);\r
  26         }\r
  27 \r
  28         public ScoreHolder getAnnotationForSequence(String seqId) {\r
  29                 for (ScoreHolder sch : seqScores) {\r
  30                         if (sch.id.equals(seqId)) {\r
  31                                 return sch;\r
  32                         }\r
  33                 }\r
  34                 return null;\r
  35         }\r
  36 \r
  37         public void writeOut(OutputStream outStream) throws IOException {\r
  38                 BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(\r
  39                                 outStream));\r
  40                 for (ScoreHolder oneSeqScores : seqScores) {\r
  41                         oneSeqScores.writeOut(outStream);\r
  42                 }\r
  43                 writer.flush();\r
  44         }\r
  45 \r
  46         public static class ScoreHolder {\r
  47 \r
  48                 public String id;\r
  49                 public HashSet<Score> scores;\r
  50 \r
  51                 public void writeOut(OutputStream outStream) throws IOException {\r
  52                         BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(\r
  53                                         outStream));\r
  54                         writer.write(">" + id + "\n");\r
  55                         Score.write(scores, outStream);\r
  56                 }\r
  57 \r
  58                 public Score getFirstScore() {\r
  59                         if (scores.isEmpty())\r
  60                                 return null;\r
  61                         return scores.iterator().next();\r
  62                 }\r
  63 \r
  64                 public Score getScoreByMethod(Enum<?> method) {\r
  65                         for (Score sc : scores) {\r
  66                                 if (method == sc.getMethod()) {\r
  67                                         return sc;\r
  68                                 }\r
  69                         }\r
  70                         return null;\r
  71                 }\r
  72 \r
  73                 public int getNumberOfScores() {\r
  74                         return scores.size();\r
  75                 }\r
  76         }\r
  77 }\r