X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datamodel%2Fcompbio%2Fdata%2Fsequence%2FScore.java;h=f28bd0d6a34934551efb015baaa8290939a63e28;hb=aca9c5503b812c9c96aebb408748dc15728f9ad7;hp=39bb39818bf5bb4f46dc82d612ede0750c4bb7b1;hpb=c1e5e6f8c46bee0a7db6a643222bec916b7178da;p=jabaws.git

diff --git a/datamodel/compbio/data/sequence/Score.java b/datamodel/compbio/data/sequence/Score.java
index 39bb398..f28bd0d 100644
--- a/datamodel/compbio/data/sequence/Score.java
+++ b/datamodel/compbio/data/sequence/Score.java
@@ -6,11 +6,8 @@ import java.io.OutputStream;
 import java.io.OutputStreamWriter;
 import java.text.NumberFormat;
 import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
 import java.util.Locale;
 import java.util.Set;
-import java.util.SortedSet;
 import java.util.TreeSet;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -35,15 +32,16 @@ public class Score {
 		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 TreeSet<Range> ranges = new TreeSet<Range>();
 
-	private SortedSet<Range> ranges = new TreeSet<Range>();
-
-	private List<Float> scores = Collections.emptyList();
+	private ArrayList<Float> scores = new ArrayList<Float>(0);
 
 	private Score() {
 		// JaXB default constructor
+		method = null;
 	}
 
 	/**
@@ -56,8 +54,8 @@ public class Score {
 	 *            the actual conservation values for each column of the
 	 *            alignment
 	 */
-	public Score(Enum<?> method, List<Float> scores) {
-		this.method = method;
+	public Score(Enum<?> method, ArrayList<Float> scores) {
+		this.method = method.toString();
 		this.scores = new ArrayList<Float>(scores);
 	}
 
@@ -72,24 +70,24 @@ public class Score {
 	 *            The set of ranges i.e. parts of the sequence with specific
 	 *            function, usually can be calculated based on scores
 	 */
-	public Score(Enum<?> method, List<Float> scores, SortedSet<Range> ranges) {
-		this.method = method;
+	public Score(Enum<?> method, ArrayList<Float> scores, TreeSet<Range> ranges) {
+		this.method = method.toString();
 		this.ranges = ranges;
 		this.scores = scores;
 	}
 
-	public Score(Enum<?> method, SortedSet<Range> ranges) {
-		this.method = method;
+	public Score(Enum<?> method, TreeSet<Range> ranges) {
+		this.method = method.toString();
 		this.ranges = ranges;
 	}
 
 	public Score(Enum<?> method, float[] scores) {
-		this.method = method;
+		this.method = method.toString();
 		this.scores = toList(scores);
 	}
 
-	private List<Float> toList(float[] values) {
-		List<Float> vlist = new ArrayList<Float>();
+	private ArrayList<Float> toList(float[] values) {
+		ArrayList<Float> vlist = new ArrayList<Float>();
 		for (float v : values) {
 			vlist.add(new Float(v));
 		}
@@ -100,7 +98,7 @@ public class Score {
 	 * 
 	 * @return the ConservationMethod
 	 */
-	public Enum<?> getMethod() {
+	public String getMethod() {
 		return method;
 	}
 
@@ -109,7 +107,7 @@ public class Score {
 	 * 
 	 * @return the column scores for the alignment
 	 */
-	public List<Float> getScores() {
+	public ArrayList<Float> getScores() {
 		return scores;
 	}
 
@@ -118,11 +116,11 @@ public class Score {
 	 * 
 	 * @return
 	 */
-	public SortedSet<Range> getRanges() {
+	public TreeSet<Range> getRanges() {
 		return ranges;
 	}
 
-	public void setRanges(SortedSet<Range> ranges) {
+	public void setRanges(TreeSet<Range> ranges) {
 		this.ranges = ranges;
 	}