new services are registered in wsbuild

[jabaws.git] / datamodel / compbio / data / sequence / Score.java

diff --git a/datamodel/compbio/data/sequence/Score.java b/datamodel/compbio/data/sequence/Score.java
index 39bb398..b61c74e 100644 (file)
--- a/datamodel/compbio/data/sequence/Score.java
+++ b/datamodel/compbio/data/sequence/Score.java
@@ -6,15 +6,14 @@ import java.io.OutputStream;
 import java.io.OutputStreamWriter;\r
 import java.text.NumberFormat;\r
 import java.util.ArrayList;\r
-import java.util.Collections;\r
-import java.util.List;\r
 import java.util.Locale;\r
 import java.util.Set;\r
-import java.util.SortedSet;\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.XmlElement;\r
+import javax.xml.bind.annotation.XmlTransient;\r
 \r
 import compbio.util.annotation.Immutable;\r
 \r
@@ -29,6 +28,7 @@ import compbio.util.annotation.Immutable;
 @Immutable\r
 public class Score {\r
 \r
+       @XmlTransient\r
        static final NumberFormat NUMBER_FORMAT = NumberFormat\r
                        .getNumberInstance(Locale.UK);\r
        static {\r
@@ -37,10 +37,13 @@ public class Score {
        }\r
 \r
        private Enum<?> method;\r
+       // private String method;\r
 \r
-       private SortedSet<Range> ranges = new TreeSet<Range>();\r
+       @XmlElement\r
+       private TreeSet<Range> ranges = new TreeSet<Range>();\r
 \r
-       private List<Float> scores = Collections.emptyList();\r
+       @XmlElement\r
+       private ArrayList<Float> scores = new ArrayList<Float>(0);\r
 \r
        private Score() {\r
                // JaXB default constructor\r
@@ -56,7 +59,7 @@ public class Score {
         *            the actual conservation values for each column of the\r
         *            alignment\r
         */\r
-       public Score(Enum<?> method, List<Float> scores) {\r
+       public Score(Enum<?> method, ArrayList<Float> scores) {\r
                this.method = method;\r
                this.scores = new ArrayList<Float>(scores);\r
        }\r
@@ -72,13 +75,13 @@ public class Score {
         *            The set of ranges i.e. parts of the sequence with specific\r
         *            function, usually can be calculated based on scores\r
         */\r
-       public Score(Enum<?> method, List<Float> scores, SortedSet<Range> ranges) {\r
+       public Score(Enum<?> method, ArrayList<Float> scores, TreeSet<Range> ranges) {\r
                this.method = method;\r
                this.ranges = ranges;\r
                this.scores = scores;\r
        }\r
 \r
-       public Score(Enum<?> method, SortedSet<Range> ranges) {\r
+       public Score(Enum<?> method, TreeSet<Range> ranges) {\r
                this.method = method;\r
                this.ranges = ranges;\r
        }\r
@@ -88,8 +91,8 @@ public class Score {
                this.scores = toList(scores);\r
        }\r
 \r
-       private List<Float> toList(float[] values) {\r
-               List<Float> vlist = new ArrayList<Float>();\r
+       private ArrayList<Float> toList(float[] values) {\r
+               ArrayList<Float> vlist = new ArrayList<Float>();\r
                for (float v : values) {\r
                        vlist.add(new Float(v));\r
                }\r
@@ -109,7 +112,7 @@ public class Score {
         * \r
         * @return the column scores for the alignment\r
         */\r
-       public List<Float> getScores() {\r
+       public ArrayList<Float> getScores() {\r
                return scores;\r
        }\r
 \r
@@ -118,11 +121,11 @@ public class Score {
         * \r
         * @return\r
         */\r
-       public SortedSet<Range> getRanges() {\r
+       public TreeSet<Range> getRanges() {\r
                return ranges;\r
        }\r
 \r
-       public void setRanges(SortedSet<Range> ranges) {\r
+       public void setRanges(TreeSet<Range> ranges) {\r
                this.ranges = ranges;\r
        }\r
 \r