+/* Copyright (c) 2011 Peter Troshin\r
+ * \r
+ * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 \r
+ * \r
+ * This library is free software; you can redistribute it and/or modify it under the terms of the\r
+ * Apache License version 2 as published by the Apache Software Foundation\r
+ * \r
+ * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
+ * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
+ * License for more details.\r
+ * \r
+ * A copy of the license is in apache_license.txt. It is also available here:\r
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
+ * \r
+ * Any republication or derived work distributed in source code form\r
+ * must include this copyright and license notice.\r
+ */\r
package compbio.data.sequence;\r
\r
-import java.util.Arrays;\r
-import java.util.List;\r
+import java.io.IOException;\r
+import java.io.Writer;\r
+import java.text.NumberFormat;\r
+import java.util.ArrayList;\r
+import java.util.Locale;\r
+import java.util.TreeSet;\r
\r
import javax.xml.bind.annotation.XmlAccessType;\r
import javax.xml.bind.annotation.XmlAccessorType;\r
\r
import compbio.util.annotation.Immutable;\r
\r
+/**\r
+ * A value class for AACon annotation results storage. The objects of this type\r
+ * are immutable\r
+ * \r
+ * @author pvtroshin\r
+ * \r
+ */\r
@XmlAccessorType(XmlAccessType.FIELD)\r
@Immutable\r
-public class Score {\r
+public class Score implements Comparable<Score> {\r
\r
- private Method method;\r
+ static final NumberFormat NUMBER_FORMAT = NumberFormat\r
+ .getNumberInstance(Locale.UK);\r
+ static {\r
+ NUMBER_FORMAT.setGroupingUsed(false);\r
+ NUMBER_FORMAT.setMaximumFractionDigits(3);\r
+ }\r
+ // This should be Enum<?> but JAXB cannot serialize it.\r
+ private final String method;\r
+\r
+ private TreeSet<Range> ranges = new TreeSet<Range>();\r
\r
- private List<Float> scores;\r
+ private ArrayList<Float> scores = new ArrayList<Float>(0);\r
\r
private Score() {\r
// JaXB default constructor\r
+ method = "";\r
+ }\r
+\r
+ /**\r
+ * Instantiate the Score\r
+ * \r
+ * @param method\r
+ * the ConservationMethod with which {@code scores} were\r
+ * calculated\r
+ * @param scores\r
+ * the actual conservation values for each column of the\r
+ * alignment\r
+ */\r
+ public Score(Enum<?> method, ArrayList<Float> scores) {\r
+ this.method = method.toString();\r
+ this.scores = new ArrayList<Float>(scores);\r
}\r
\r
- public Score(Method method, List<Float> scores) {\r
- this.method = method;\r
+ /**\r
+ * @param method\r
+ * the ConservationMethod with which {@code scores} were\r
+ * calculated\r
+ * @param scores\r
+ * the actual conservation values for each column of the\r
+ * alignment\r
+ * @param ranges\r
+ * The set of ranges i.e. parts of the sequence with specific\r
+ * function, usually can be calculated based on scores\r
+ */\r
+ public Score(Enum<?> method, ArrayList<Float> scores, TreeSet<Range> ranges) {\r
+ this.method = method.toString();\r
+ this.ranges = ranges;\r
this.scores = scores;\r
}\r
\r
- public Method getMethod() {\r
+ public Score(Enum<?> method, TreeSet<Range> ranges) {\r
+ this.method = method.toString();\r
+ this.ranges = ranges;\r
+ }\r
+\r
+ public Score(Enum<?> method, float[] scores) {\r
+ this.method = method.toString();\r
+ this.scores = toList(scores);\r
+ }\r
+\r
+ private ArrayList<Float> toList(float[] values) {\r
+ ArrayList<Float> vlist = new ArrayList<Float>();\r
+ for (float v : values) {\r
+ vlist.add(new Float(v));\r
+ }\r
+ return vlist;\r
+ }\r
+ /**\r
+ * Returns the ConservationMethod\r
+ * \r
+ * @return the ConservationMethod\r
+ */\r
+ public String getMethod() {\r
return method;\r
}\r
\r
- public List<Float> getScores() {\r
+ /**\r
+ * The column scores for the alignment\r
+ * \r
+ * @return the column scores for the alignment\r
+ */\r
+ public ArrayList<Float> getScores() {\r
return scores;\r
}\r
\r
+ /**\r
+ * Return Ranges if any Collections.EMPTY_SET otherwise\r
+ * \r
+ * @return\r
+ */\r
+ public TreeSet<Range> getRanges() {\r
+ return ranges;\r
+ }\r
+\r
+ public void setRanges(TreeSet<Range> ranges) {\r
+ this.ranges = ranges;\r
+ }\r
+\r
@Override\r
public String toString() {\r
- return "Score [method=" + method + ", scores=" + scores + "]";\r
+ return "Score [method=" + method + ", ranges=" + ranges + ", scores="\r
+ + scores + "]";\r
}\r
\r
@Override\r
public int hashCode() {\r
- final int prime = 31;\r
+ final int prime = 7;\r
int result = 1;\r
result = prime * result + ((method == null) ? 0 : method.hashCode());\r
+ result = prime * result + ((ranges == null) ? 0 : ranges.hashCode());\r
result = prime * result + ((scores == null) ? 0 : scores.hashCode());\r
return result;\r
}\r
\r
- /*\r
- * TODO test ! (non-Javadoc)\r
- * \r
- * @see java.lang.Object#equals(java.lang.Object)\r
- */\r
@Override\r
public boolean equals(Object obj) {\r
if (this == obj)\r
if (getClass() != obj.getClass())\r
return false;\r
Score other = (Score) obj;\r
- if (method != other.method)\r
+ if (method == null) {\r
+ if (other.method != null)\r
+ return false;\r
+ } else if (!method.equals(other.method))\r
return false;\r
- if (scores == other.scores) {\r
- return true;\r
- }\r
- if (scores == null) {\r
+ if (ranges == null) {\r
+ if (other.ranges != null)\r
+ return false;\r
+ } else if (!ranges.equals(other.ranges))\r
return false;\r
- }\r
- if (!Arrays.deepEquals(scores.toArray(), other.scores.toArray()))\r
+ if (scores == null) {\r
+ if (other.scores != null)\r
+ return false;\r
+ } else if (!scores.equals(other.scores))\r
return false;\r
return true;\r
}\r
+\r
+ /**\r
+ * Outputs the List of Score objects into the Output stream. The output\r
+ * format is as follows:\r
+ * \r
+ * <pre>\r
+ * {@code\r
+ * #MethodName <space separated list of values>\r
+ * \r
+ * For example:\r
+ * \r
+ * #KABAT 0.2 0.3 0.2 0 0.645 0.333 1 1 0 0\r
+ * #SMERFS 0.645 0.333 1 1 0 0 0.2 0.3 0.2 0\r
+ * }\r
+ * </pre>\r
+ * \r
+ * The maximum precision for values is 3 digits, but can be less.\r
+ * \r
+ * @param scores\r
+ * the list of scores to output\r
+ * @param output\r
+ * the stream to output the data to\r
+ * @throws IOException\r
+ * if the OutputStream cannot be written into\r
+ * @throws NullPointerException\r
+ * if the output stream is null\r
+ */\r
+ public static void write(TreeSet<Score> scores, Writer writer)\r
+ throws IOException {\r
+ if (writer == null) {\r
+ throw new NullPointerException("Writer must be provided!");\r
+ }\r
+ for (Score score : scores) {\r
+ writer.write("#" + score.method + " ");\r
+ int count = score.ranges.size();\r
+ for (Range range : score.ranges) {\r
+ count--;\r
+ writer.write(range.toString());\r
+ if (count != 0) {\r
+ writer.write(", ");\r
+ }\r
+ }\r
+ for (Float scoreVal : score.scores) {\r
+ writer.write(NUMBER_FORMAT.format(scoreVal) + " ");\r
+ }\r
+ writer.write("\n");\r
+ writer.flush();\r
+ }\r
+ writer.flush();\r
+ }\r
+\r
+ @Override\r
+ public int compareTo(Score o) {\r
+ return this.method.compareTo(o.method);\r
+ }\r
}\r
git://source.jalview.org / jabaws.git / blobdiff