X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datamodel%2Fcompbio%2Fdata%2Fsequence%2FScore.java;h=f28bd0d6a34934551efb015baaa8290939a63e28;hb=aca9c5503b812c9c96aebb408748dc15728f9ad7;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..f28bd0d 100644
--- a/datamodel/compbio/data/sequence/Score.java
+++ b/datamodel/compbio/data/sequence/Score.java
@@ -12,8 +12,6 @@ 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;
 
@@ -28,25 +26,22 @@ import compbio.util.annotation.Immutable;
 @Immutable
 public class 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 = null;
 	}
 
 	/**
@@ -60,7 +55,7 @@ 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 +71,18 @@ 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 +98,7 @@ public class Score {
 	 * 
 	 * @return the ConservationMethod
 	 */
-	public Enum<?> getMethod() {
+	public String getMethod() {
 		return method;
 	}