Clean-up, refactoring, commenting. Parameters file containts only options since Jalvi...

[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 1cac69c..0ca5152 100644 (file)
--- a/datamodel/compbio/data/sequence/Score.java
+++ b/datamodel/compbio/data/sequence/Score.java
@@ -232,25 +232,26 @@ public class Score implements Comparable<Score> {
                writer.flush();\r
        }\r
 \r
+       // Old compareTo method\r
 //     @Override\r
 //     public int compareTo(Score o) {\r
 //             return this.method.compareTo(o.method);\r
 //     }\r
        \r
-       /* daniel wants to mess with this method and, while preserving the \r
-        * ordering when the method Enumerations are different, add additional\r
-        * constraints on how equal Score objects must be to be considered equal\r
+       /* daniel messed with this method. While preserving the original\r
+        * ordering when the method Enumerations are different, additional\r
+        * constraints have been added on how equal Score objects must be \r
+        * to be considered equal.\r
         * \r
         * It is necessary to distinguish Score objects by their ranges in order\r
         * to use a Set of Score objects to represent the alifold.out information\r
         * \r
-        * It is necessary to distinguish Score objects by their scores in order\r
-        * to return Stochastic Backtrack information reliably\r
+        * Distinguishing score objects by their Scores has the result of ordering\r
+        * the base pair contacts so into descending probability.\r
+        * \r
+        * Should this be in a new extended Score class?\r
         */\r
        \r
-       \r
-\r
-       \r
        @Override\r
        public int compareTo(Score o) {\r
                if (this.method.compareTo(o.method) != 0) {\r