datamodel/compbio/data/sequence/Score.java

   1 package compbio.data.sequence;\r
   2 \r
   3 import java.io.IOException;\r
   4 import java.io.Writer;\r
   5 import java.text.NumberFormat;\r
   6 import java.util.ArrayList;\r
   7 import java.util.Locale;\r
   8 import java.util.TreeSet;\r
   9 \r
  10 import javax.xml.bind.annotation.XmlAccessType;\r
  11 import javax.xml.bind.annotation.XmlAccessorType;\r
  12 \r
  13 import compbio.util.annotation.Immutable;\r
  14 \r
  15 /**\r
  16  * A value class for AACon annotation results storage. The objects of this type\r
  17  * are immutable\r
  18  * \r
  19  * @author pvtroshin\r
  20  * \r
  21  */\r
  22 @XmlAccessorType(XmlAccessType.FIELD)\r
  23 @Immutable\r
  24 public class Score implements Comparable<Score> {\r
  25 \r
  26         static final NumberFormat NUMBER_FORMAT = NumberFormat\r
  27                         .getNumberInstance(Locale.UK);\r
  28         static {\r
  29                 NUMBER_FORMAT.setGroupingUsed(false);\r
  30                 NUMBER_FORMAT.setMaximumFractionDigits(3);\r
  31         }\r
  32         // This should be Enum<?> but JAXB cannot serialize it.\r
  33         private final String method;\r
  34 \r
  35         private TreeSet<Range> ranges = new TreeSet<Range>();\r
  36 \r
  37         private ArrayList<Float> scores = new ArrayList<Float>(0);\r
  38 \r
  39         private Score() {\r
  40                 // JaXB default constructor\r
  41                 method = "";\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(Enum<?> method, ArrayList<Float> scores) {\r
  55                 this.method = method.toString();\r
  56                 this.scores = new ArrayList<Float>(scores);\r
  57         }\r
  58 \r
  59         /**\r
  60          * @param method\r
  61          *            the ConservationMethod with which {@code scores} were\r
  62          *            calculated\r
  63          * @param scores\r
  64          *            the actual conservation values for each column of the\r
  65          *            alignment\r
  66          * @param ranges\r
  67          *            The set of ranges i.e. parts of the sequence with specific\r
  68          *            function, usually can be calculated based on scores\r
  69          */\r
  70         public Score(Enum<?> method, ArrayList<Float> scores, TreeSet<Range> ranges) {\r
  71                 this.method = method.toString();\r
  72                 this.ranges = ranges;\r
  73                 this.scores = scores;\r
  74         }\r
  75 \r
  76         public Score(Enum<?> method, TreeSet<Range> ranges) {\r
  77                 this.method = method.toString();\r
  78                 this.ranges = ranges;\r
  79         }\r
  80 \r
  81         public Score(Enum<?> method, float[] scores) {\r
  82                 this.method = method.toString();\r
  83                 this.scores = toList(scores);\r
  84         }\r
  85 \r
  86         private ArrayList<Float> toList(float[] values) {\r
  87                 ArrayList<Float> vlist = new ArrayList<Float>();\r
  88                 for (float v : values) {\r
  89                         vlist.add(new Float(v));\r
  90                 }\r
  91                 return vlist;\r
  92         }\r
  93         /**\r
  94          * Returns the ConservationMethod\r
  95          * \r
  96          * @return the ConservationMethod\r
  97          */\r
  98         public String getMethod() {\r
  99                 return method;\r
 100         }\r
 101 \r
 102         /**\r
 103          * The column scores for the alignment\r
 104          * \r
 105          * @return the column scores for the alignment\r
 106          */\r
 107         public ArrayList<Float> getScores() {\r
 108                 return scores;\r
 109         }\r
 110 \r
 111         /**\r
 112          * Return Ranges if any Collections.EMPTY_SET otherwise\r
 113          * \r
 114          * @return\r
 115          */\r
 116         public TreeSet<Range> getRanges() {\r
 117                 return ranges;\r
 118         }\r
 119 \r
 120         public void setRanges(TreeSet<Range> ranges) {\r
 121                 this.ranges = ranges;\r
 122         }\r
 123 \r
 124         @Override\r
 125         public String toString() {\r
 126                 return "Score [method=" + method + ", ranges=" + ranges + ", scores="\r
 127                                 + scores + "]";\r
 128         }\r
 129 \r
 130         @Override\r
 131         public int hashCode() {\r
 132                 final int prime = 7;\r
 133                 int result = 1;\r
 134                 result = prime * result + ((method == null) ? 0 : method.hashCode());\r
 135                 result = prime * result + ((ranges == null) ? 0 : ranges.hashCode());\r
 136                 result = prime * result + ((scores == null) ? 0 : scores.hashCode());\r
 137                 return result;\r
 138         }\r
 139 \r
 140         @Override\r
 141         public boolean equals(Object obj) {\r
 142                 if (this == obj)\r
 143                         return true;\r
 144                 if (obj == null)\r
 145                         return false;\r
 146                 if (getClass() != obj.getClass())\r
 147                         return false;\r
 148                 Score other = (Score) obj;\r
 149                 if (method == null) {\r
 150                         if (other.method != null)\r
 151                                 return false;\r
 152                 } else if (!method.equals(other.method))\r
 153                         return false;\r
 154                 if (ranges == null) {\r
 155                         if (other.ranges != null)\r
 156                                 return false;\r
 157                 } else if (!ranges.equals(other.ranges))\r
 158                         return false;\r
 159                 if (scores == null) {\r
 160                         if (other.scores != null)\r
 161                                 return false;\r
 162                 } else if (!scores.equals(other.scores))\r
 163                         return false;\r
 164                 return true;\r
 165         }\r
 166 \r
 167         /**\r
 168          * Outputs the List of Score objects into the Output stream. The output\r
 169          * format is as follows:\r
 170          * \r
 171          * <pre>\r
 172          * {@code\r
 173          * #MethodName <space separated list of values>\r
 174          *        \r
 175          * For example:\r
 176          *       \r
 177          * #KABAT 0.2 0.3 0.2 0 0.645 0.333 1 1 0 0\r
 178          * #SMERFS 0.645 0.333 1 1 0 0 0.2 0.3 0.2 0\r
 179          * }\r
 180          * </pre>\r
 181          * \r
 182          * The maximum precision for values is 3 digits, but can be less.\r
 183          * \r
 184          * @param scores\r
 185          *            the list of scores to output\r
 186          * @param output\r
 187          *            the stream to output the data to\r
 188          * @throws IOException\r
 189          *             if the OutputStream cannot be written into\r
 190          * @throws NullPointerException\r
 191          *             if the output stream is null\r
 192          */\r
 193         public static void write(TreeSet<Score> scores, Writer writer)\r
 194                         throws IOException {\r
 195                 if (writer == null) {\r
 196                         throw new NullPointerException("Writer must be provided!");\r
 197                 }\r
 198                 for (Score score : scores) {\r
 199                         writer.write("#" + score.method + " ");\r
 200                         int count = score.ranges.size();\r
 201                         for (Range range : score.ranges) {\r
 202                                 count--;\r
 203                                 writer.write(range.toString());\r
 204                                 if (count != 0) {\r
 205                                         writer.write(", ");\r
 206                                 }\r
 207                         }\r
 208                         for (Float scoreVal : score.scores) {\r
 209                                 writer.write(NUMBER_FORMAT.format(scoreVal) + " ");\r
 210                         }\r
 211                         writer.write("\n");\r
 212                         writer.flush();\r
 213                 }\r
 214                 writer.flush();\r
 215         }\r
 216 \r
 217         @Override\r
 218         public int compareTo(Score o) {\r
 219                 return this.method.compareTo(o.method);\r
 220         }\r
 221 }\r