X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datamodel%2Fcompbio%2Fdata%2Fsequence%2FScoreManager.java;h=d16a059ca7486311016c1ef2e0baf7a235554a20;hb=8ce6db56df6c0a1c2baca2fc2d33bcb10067c6cd;hp=f3843086f185a521358a708fde13f335902abdd9;hpb=3644426ec0e9e9ceb798bd426085d8d9dd8dbb56;p=jabaws.git

diff --git a/datamodel/compbio/data/sequence/ScoreManager.java b/datamodel/compbio/data/sequence/ScoreManager.java
index f384308..d16a059 100644
--- a/datamodel/compbio/data/sequence/ScoreManager.java
+++ b/datamodel/compbio/data/sequence/ScoreManager.java
@@ -1,22 +1,39 @@
+/* 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.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.TreeMap;
+import java.util.TreeSet;
 
 import javax.xml.bind.annotation.XmlAccessType;
 import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlTransient;
 
 @XmlAccessorType(XmlAccessType.FIELD)
 public class ScoreManager {
 
+	@XmlTransient
 	public static final String SINGLE_ENTRY_KEY = "Alignment";
 
 	private List<ScoreHolder> seqScores;
@@ -45,9 +62,9 @@ public class ScoreManager {
 
 	public static ScoreManager newInstanceSingleScore(
 			Map<String, Score> seqScoresMap) {
-		Map<String, Set<Score>> multipleScoresMap = new HashMap<String, Set<Score>>();
+		Map<String, Set<Score>> multipleScoresMap = new TreeMap<String, Set<Score>>();
 		for (Map.Entry<String, Score> seqScore : seqScoresMap.entrySet()) {
-			Set<Score> scores = new HashSet<Score>();
+			Set<Score> scores = new TreeSet<Score>();
 			scores.add(seqScore.getValue());
 			multipleScoresMap.put(seqScore.getKey(), scores);
 		}
@@ -55,13 +72,15 @@ public class ScoreManager {
 	}
 
 	public static ScoreManager newInstanceSingleSequence(Set<Score> data) {
-		return new ScoreManager(ScoreManager.SINGLE_ENTRY_KEY, data);
+		return new ScoreManager(ScoreManager.SINGLE_ENTRY_KEY,
+				new TreeSet(data));
 	}
 
-	public Map<String, Set<Score>> asMap() {
-		Map<String, Set<Score>> seqScoresMap = new HashMap<String, Set<Score>>();
+	public Map<String, TreeSet<Score>> asMap() {
+		Map<String, TreeSet<Score>> seqScoresMap = new TreeMap<String, TreeSet<Score>>();
 		for (ScoreHolder sch : this.seqScores) {
-			Set<Score> oldValue = seqScoresMap.put(sch.id, sch.scores);
+			TreeSet<Score> oldValue = seqScoresMap.put(sch.id, new TreeSet(
+					sch.scores));
 			if (oldValue != null) {
 				throw new IllegalStateException(
 						"Cannot represent this ScoreManager instance "
@@ -96,15 +115,17 @@ public class ScoreManager {
 		return null;
 	}
 
-	public void writeOut(OutputStream outStream) throws IOException {
-		BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(
-				outStream));
+	public void writeOut(Writer outStream) throws IOException {
+		assert outStream != null : "Output steam is not defined!";
+		if (seqScores == null) {
+			return;
+		}
 		for (ScoreHolder oneSeqScores : seqScores) {
+			if (oneSeqScores == null)
+				continue;
 			oneSeqScores.writeOut(outStream);
 		}
-		writer.flush();
 	}
-	
 
 	@Override
 	public int hashCode() {
@@ -132,13 +153,11 @@ public class ScoreManager {
 		return true;
 	}
 
-
-
 	@XmlAccessorType(XmlAccessType.FIELD)
 	public static class ScoreHolder {
 
 		public String id;
-		public Set<Score> scores;
+		public TreeSet<Score> scores;
 
 		private ScoreHolder() {
 			// JAXB Default constructor should not be used otherwise
@@ -146,25 +165,30 @@ public class ScoreManager {
 
 		ScoreHolder(String id, Set<Score> scores) {
 			this.id = id;
-			this.scores = scores;
+			this.scores = new TreeSet<Score>(scores);
 		}
 
-		public void writeOut(OutputStream outStream) throws IOException {
-			BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(
-					outStream));
+		public void writeOut(Writer writer) throws IOException {
 			writer.write(">" + id + "\n");
-			Score.write(scores, outStream);
+			Score.write(scores, writer);
 		}
 
 		public Score getScoreByMethod(Enum<?> method) {
 			for (Score sc : scores) {
-				if (method == sc.getMethod()) {
+				if (method.toString().equals(sc.getMethod())) {
+					return sc;
+				}
+			}
+			return null;
+		}
+		public Score getScoreByMethod(String method) {
+			for (Score sc : scores) {
+				if (method.toString().equals(sc.getMethod())) {
 					return sc;
 				}
 			}
 			return null;
 		}
-
 		public int getNumberOfScores() {
 			return scores.size();
 		}
@@ -200,7 +224,7 @@ public class ScoreManager {
 				return false;
 			return true;
 		}
-		
-		
+
 	}
+
 }