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