datamodel/compbio/data/sequence/Score.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.text.NumberFormat;\r
   8 import java.util.ArrayList;\r
   9 import java.util.Arrays;\r
  10 import java.util.List;\r
  11 import java.util.Locale;\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 import compbio.util.annotation.Immutable;\r
  18 \r
  19 /**\r
  20  * A value class for AACon annotation results storage\r
  21  * \r
  22  * @author pvtroshin\r
  23  * \r
  24  */\r
  25 @XmlAccessorType(XmlAccessType.FIELD)\r
  26 @Immutable\r
  27 public class Score {\r
  28 \r
  29         static final NumberFormat NUMBER_FORMAT = NumberFormat\r
  30                         .getNumberInstance(Locale.UK);\r
  31         static {\r
  32                 NUMBER_FORMAT.setGroupingUsed(false);\r
  33                 NUMBER_FORMAT.setMaximumFractionDigits(3);\r
  34         }\r
  35 \r
  36         private ConservationMethod method;\r
  37 \r
  38         private List<Float> scores;\r
  39 \r
  40         private Score() {\r
  41                 // JaXB default constructor\r
  42         }\r
  43 \r
  44         /**\r
  45          * Instantiate the Score\r
  46          * \r
  47          * @param method\r
  48          *            the ConservationMethod with which {@code scores} were\r
  49          *            calculated\r
  50          * @param scores\r
  51          *            the actual conservation values for each column of the\r
  52          *            alignment\r
  53          */\r
  54         public Score(ConservationMethod method, List<Float> scores) {\r
  55                 this.method = method;\r
  56                 this.scores = new ArrayList<Float>(scores);\r
  57         }\r
  58 \r
  59         /**\r
  60          * Returns the ConservationMethod\r
  61          * \r
  62          * @return the ConservationMethod\r
  63          */\r
  64         public ConservationMethod getMethod() {\r
  65                 return method;\r
  66         }\r
  67 \r
  68         /**\r
  69          * The column scores for the alignment\r
  70          * \r
  71          * @return the column scores for the alignment\r
  72          */\r
  73         public List<Float> getScores() {\r
  74                 return scores;\r
  75         }\r
  76 \r
  77         @Override\r
  78         public String toString() {\r
  79                 return "Score [method=" + method + ", scores=" + scores + "]";\r
  80         }\r
  81 \r
  82         @Override\r
  83         public int hashCode() {\r
  84                 final int prime = 31;\r
  85                 int result = 1;\r
  86                 result = prime * result + ((method == null) ? 0 : method.hashCode());\r
  87                 result = prime * result + ((scores == null) ? 0 : scores.hashCode());\r
  88                 return result;\r
  89         }\r
  90 \r
  91         /*\r
  92          * TODO test ! (non-Javadoc)\r
  93          * \r
  94          * @see java.lang.Object#equals(java.lang.Object)\r
  95          */\r
  96         @Override\r
  97         public boolean equals(Object obj) {\r
  98                 if (this == obj)\r
  99                         return true;\r
 100                 if (obj == null)\r
 101                         return false;\r
 102                 if (getClass() != obj.getClass())\r
 103                         return false;\r
 104                 Score other = (Score) obj;\r
 105                 if (method != other.method)\r
 106                         return false;\r
 107                 if (scores == other.scores) {\r
 108                         return true;\r
 109                 }\r
 110                 if (scores == null) {\r
 111                         return false;\r
 112                 }\r
 113                 if (!Arrays.deepEquals(scores.toArray(), other.scores.toArray()))\r
 114                         return false;\r
 115                 return true;\r
 116         }\r
 117 \r
 118         /**\r
 119          * Outputs the List of Score objects into the Output stream. The output\r
 120          * format is as follows:\r
 121          * \r
 122          * <pre>\r
 123          *        #MethodName <space separated list of values>\r
 124          *        \r
 125          * For example:\r
 126          *       \r
 127          *        #KABAT 0.2 0.3 0.2 0 0.645 0.333 1 1 0 0\r
 128          *    #SMERFS 0.645 0.333 1 1 0 0 0.2 0.3 0.2 0\r
 129          * </pre>\r
 130          * \r
 131          * The maximum precision for values is 3 digits, but can be less.\r
 132          * \r
 133          * @param scores\r
 134          *            the list of scores to output\r
 135          * @param output\r
 136          *            the stream to output the data to\r
 137          * @throws IOException\r
 138          *             if the OutputStream cannot be written into\r
 139          * @throws NullPointerException\r
 140          *             if the output stream is null\r
 141          */\r
 142         public static void write(Set<Score> scores, OutputStream output)\r
 143                         throws IOException {\r
 144                 if (output == null) {\r
 145                         throw new NullPointerException("OutputStream must be provided!");\r
 146                 }\r
 147                 BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(\r
 148                                 output));\r
 149                 for (Score score : scores) {\r
 150                         writer.write("#" + score.method + " ");\r
 151                         for (Float scoreVal : score.getScores()) {\r
 152                                 writer.write(NUMBER_FORMAT.format(scoreVal) + " ");\r
 153                         }\r
 154                         writer.write("\n");\r
 155                 }\r
 156                 writer.flush();\r
 157         }\r
 158 }\r