Further work on statistics display

[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..f28bd0d 100644 (file)
--- 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;\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
@@ -35,15 +32,16 @@ public class Score {
                NUMBER_FORMAT.setGroupingUsed(false);\r
                NUMBER_FORMAT.setMaximumFractionDigits(3);\r
        }\r
+       // This should be Enum<?> but JAXB cannot serialize it.\r
+       private final String method;\r
 \r
-       private Enum<?> method;\r
+       private TreeSet<Range> ranges = new TreeSet<Range>();\r
 \r
-       private SortedSet<Range> ranges = new TreeSet<Range>();\r
-\r
-       private List<Float> scores = Collections.emptyList();\r
+       private ArrayList<Float> scores = new ArrayList<Float>(0);\r
 \r
        private Score() {\r
                // JaXB default constructor\r
+               method = null;\r
        }\r
 \r
        /**\r
@@ -56,8 +54,8 @@ public class Score {
         *            the actual conservation values for each column of the\r
         *            alignment\r
         */\r
-       public Score(Enum<?> method, List<Float> scores) {\r
-               this.method = method;\r
+       public Score(Enum<?> method, ArrayList<Float> scores) {\r
+               this.method = method.toString();\r
                this.scores = new ArrayList<Float>(scores);\r
        }\r
 \r
@@ -72,24 +70,24 @@ 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
-               this.method = method;\r
+       public Score(Enum<?> method, ArrayList<Float> scores, TreeSet<Range> ranges) {\r
+               this.method = method.toString();\r
                this.ranges = ranges;\r
                this.scores = scores;\r
        }\r
 \r
-       public Score(Enum<?> method, SortedSet<Range> ranges) {\r
-               this.method = method;\r
+       public Score(Enum<?> method, TreeSet<Range> ranges) {\r
+               this.method = method.toString();\r
                this.ranges = ranges;\r
        }\r
 \r
        public Score(Enum<?> method, float[] scores) {\r
-               this.method = method;\r
+               this.method = method.toString();\r
                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
@@ -100,7 +98,7 @@ public class Score {
         * \r
         * @return the ConservationMethod\r
         */\r
-       public Enum<?> getMethod() {\r
+       public String getMethod() {\r
                return method;\r
        }\r
 \r
@@ -109,7 +107,7 @@ 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 +116,11 @@ 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