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