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