X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datamodel%2Fcompbio%2Fdata%2Fsequence%2FScore.java;h=ec4cadc4a5e2a8650e1376bd4f681aad1b5f64d8;hb=ba2d4e920e433bd080f448248e7dacade69a27a0;hp=b61c74e4f17703a680c4279149a58ec34c3dc531;hpb=7e625752237ee07e815bfb28048bb0b1193b45c5;p=jabaws.git

diff --git a/datamodel/compbio/data/sequence/Score.java b/datamodel/compbio/data/sequence/Score.java
index b61c74e..ec4cadc 100644
--- a/datamodel/compbio/data/sequence/Score.java
+++ b/datamodel/compbio/data/sequence/Score.java
@@ -1,19 +1,31 @@
+/* Copyright (c) 2011 Peter Troshin
+ *  
+ *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     
+ * 
+ *  This library is free software; you can redistribute it and/or modify it under the terms of the
+ *  Apache License version 2 as published by the Apache Software Foundation
+ * 
+ *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
+ *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache 
+ *  License for more details.
+ * 
+ *  A copy of the license is in apache_license.txt. It is also available here:
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
+ * 
+ * Any republication or derived work distributed in source code form
+ * must include this copyright and license notice.
+ */
 package compbio.data.sequence;
 
-import java.io.BufferedWriter;
 import java.io.IOException;
-import java.io.OutputStream;
-import java.io.OutputStreamWriter;
+import java.io.Writer;
 import java.text.NumberFormat;
 import java.util.ArrayList;
 import java.util.Locale;
-import java.util.Set;
 import java.util.TreeSet;
 
 import javax.xml.bind.annotation.XmlAccessType;
 import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlTransient;
 
 import compbio.util.annotation.Immutable;
 
@@ -26,27 +38,24 @@ import compbio.util.annotation.Immutable;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @Immutable
-public class Score {
+public class Score implements Comparable<Score> {
 
-	@XmlTransient
 	static final NumberFormat NUMBER_FORMAT = NumberFormat
 			.getNumberInstance(Locale.UK);
 	static {
 		NUMBER_FORMAT.setGroupingUsed(false);
 		NUMBER_FORMAT.setMaximumFractionDigits(3);
 	}
+	// This should be Enum<?> but JAXB cannot serialize it.
+	private final String method;
 
-	private Enum<?> method;
-	// private String method;
-
-	@XmlElement
 	private TreeSet<Range> ranges = new TreeSet<Range>();
 
-	@XmlElement
 	private ArrayList<Float> scores = new ArrayList<Float>(0);
 
 	private Score() {
 		// JaXB default constructor
+		method = "";
 	}
 
 	/**
@@ -60,7 +69,7 @@ public class Score {
 	 *            alignment
 	 */
 	public Score(Enum<?> method, ArrayList<Float> scores) {
-		this.method = method;
+		this.method = method.toString();
 		this.scores = new ArrayList<Float>(scores);
 	}
 
@@ -76,18 +85,18 @@ public class Score {
 	 *            function, usually can be calculated based on scores
 	 */
 	public Score(Enum<?> method, ArrayList<Float> scores, TreeSet<Range> ranges) {
-		this.method = method;
+		this.method = method.toString();
 		this.ranges = ranges;
 		this.scores = scores;
 	}
 
 	public Score(Enum<?> method, TreeSet<Range> ranges) {
-		this.method = method;
+		this.method = method.toString();
 		this.ranges = ranges;
 	}
 
 	public Score(Enum<?> method, float[] scores) {
-		this.method = method;
+		this.method = method.toString();
 		this.scores = toList(scores);
 	}
 
@@ -103,7 +112,7 @@ public class Score {
 	 * 
 	 * @return the ConservationMethod
 	 */
-	public Enum<?> getMethod() {
+	public String getMethod() {
 		return method;
 	}
 
@@ -119,7 +128,7 @@ public class Score {
 	/**
 	 * Return Ranges if any Collections.EMPTY_SET otherwise
 	 * 
-	 * @return
+	 * @return ordered set of Range
 	 */
 	public TreeSet<Range> getRanges() {
 		return ranges;
@@ -191,27 +200,38 @@ public class Score {
 	 * 
 	 * @param scores
 	 *            the list of scores to output
-	 * @param output
-	 *            the stream to output the data to
+	 * @param writer
 	 * @throws IOException
 	 *             if the OutputStream cannot be written into
 	 * @throws NullPointerException
 	 *             if the output stream is null
 	 */
-	public static void write(Set<Score> scores, OutputStream output)
+	public static void write(TreeSet<Score> scores, Writer writer)
 			throws IOException {
-		if (output == null) {
-			throw new NullPointerException("OutputStream must be provided!");
+		if (writer == null) {
+			throw new NullPointerException("Writer must be provided!");
 		}
-		BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(
-				output));
 		for (Score score : scores) {
 			writer.write("#" + score.method + " ");
-			for (Float scoreVal : score.getScores()) {
+			int count = score.ranges.size();
+			for (Range range : score.ranges) {
+				count--;
+				writer.write(range.toString());
+				if (count != 0) {
+					writer.write(", ");
+				}
+			}
+			for (Float scoreVal : score.scores) {
 				writer.write(NUMBER_FORMAT.format(scoreVal) + " ");
 			}
 			writer.write("\n");
+			writer.flush();
 		}
 		writer.flush();
 	}
+
+	@Override
+	public int compareTo(Score o) {
+		return this.method.compareTo(o.method);
+	}
 }