+/* 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.io.BufferedWriter;\r
import java.io.IOException;\r
-import java.io.OutputStream;\r
-import java.io.OutputStreamWriter;\r
+import java.io.Writer;\r
import java.util.ArrayList;\r
-import java.util.HashMap;\r
-import java.util.HashSet;\r
import java.util.List;\r
import java.util.Map;\r
import java.util.Set;\r
+import java.util.TreeMap;\r
+import java.util.TreeSet;\r
\r
import javax.xml.bind.annotation.XmlAccessType;\r
import javax.xml.bind.annotation.XmlAccessorType;\r
+import javax.xml.bind.annotation.XmlTransient;\r
\r
@XmlAccessorType(XmlAccessType.FIELD)\r
public class ScoreManager {\r
\r
+ @XmlTransient\r
public static final String SINGLE_ENTRY_KEY = "Alignment";\r
\r
private List<ScoreHolder> seqScores;\r
\r
public static ScoreManager newInstanceSingleScore(\r
Map<String, Score> seqScoresMap) {\r
- Map<String, Set<Score>> multipleScoresMap = new HashMap<String, Set<Score>>();\r
+ Map<String, Set<Score>> multipleScoresMap = new TreeMap<String, Set<Score>>();\r
for (Map.Entry<String, Score> seqScore : seqScoresMap.entrySet()) {\r
- Set<Score> scores = new HashSet<Score>();\r
+ Set<Score> scores = new TreeSet<Score>();\r
scores.add(seqScore.getValue());\r
multipleScoresMap.put(seqScore.getKey(), scores);\r
}\r
}\r
\r
public static ScoreManager newInstanceSingleSequence(Set<Score> data) {\r
- return new ScoreManager(ScoreManager.SINGLE_ENTRY_KEY, data);\r
+ return new ScoreManager(ScoreManager.SINGLE_ENTRY_KEY,\r
+ new TreeSet(data));\r
}\r
\r
- public Map<String, Set<Score>> asMap() {\r
- Map<String, Set<Score>> seqScoresMap = new HashMap<String, Set<Score>>();\r
+ public Map<String, TreeSet<Score>> asMap() {\r
+ Map<String, TreeSet<Score>> seqScoresMap = new TreeMap<String, TreeSet<Score>>();\r
for (ScoreHolder sch : this.seqScores) {\r
- Set<Score> oldValue = seqScoresMap.put(sch.id, sch.scores);\r
+ TreeSet<Score> oldValue = seqScoresMap.put(sch.id, new TreeSet(\r
+ sch.scores));\r
if (oldValue != null) {\r
throw new IllegalStateException(\r
"Cannot represent this ScoreManager instance "\r
return null;\r
}\r
\r
- public void writeOut(OutputStream outStream) throws IOException {\r
- BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(\r
- outStream));\r
+ public void writeOut(Writer outStream) throws IOException {\r
+ assert outStream != null : "Output steam is not defined!";\r
+ if (seqScores == null) {\r
+ return;\r
+ }\r
for (ScoreHolder oneSeqScores : seqScores) {\r
+ if (oneSeqScores == null)\r
+ continue;\r
oneSeqScores.writeOut(outStream);\r
}\r
- writer.flush();\r
}\r
- \r
\r
@Override\r
public int hashCode() {\r
return true;\r
}\r
\r
-\r
-\r
@XmlAccessorType(XmlAccessType.FIELD)\r
public static class ScoreHolder {\r
\r
public String id;\r
- public Set<Score> scores;\r
+ public TreeSet<Score> scores;\r
\r
private ScoreHolder() {\r
// JAXB Default constructor should not be used otherwise\r
\r
ScoreHolder(String id, Set<Score> scores) {\r
this.id = id;\r
- this.scores = scores;\r
+ this.scores = new TreeSet<Score>(scores);\r
}\r
\r
- public void writeOut(OutputStream outStream) throws IOException {\r
- BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(\r
- outStream));\r
+ public void writeOut(Writer writer) throws IOException {\r
writer.write(">" + id + "\n");\r
- Score.write(scores, outStream);\r
+ Score.write(scores, writer);\r
}\r
\r
public Score getScoreByMethod(Enum<?> method) {\r
for (Score sc : scores) {\r
- if (method == sc.getMethod()) {\r
+ if (method.toString().equals(sc.getMethod())) {\r
+ return sc;\r
+ }\r
+ }\r
+ return null;\r
+ }\r
+ public Score getScoreByMethod(String method) {\r
+ for (Score sc : scores) {\r
+ if (method.toString().equals(sc.getMethod())) {\r
return sc;\r
}\r
}\r
return null;\r
}\r
-\r
public int getNumberOfScores() {\r
return scores.size();\r
}\r
return false;\r
return true;\r
}\r
- \r
- \r
+\r
}\r
+\r
}\r
git://source.jalview.org / jabaws.git / blobdiff