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