back out duplicate jfree classpath entry

[jalview.git] / src / jalview / datamodel / AlignmentAnnotation.java

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 8a44535..e137225 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -75,9 +75,10 @@ public class AlignmentAnnotation
   public SequenceFeature[] _rnasecstr = null;
 
   /**
-   * position of annotation resulting in invalid WUSS parsing or -1
+   * position of annotation resulting in invalid WUSS parsing or -1. -2 means
+   * there was no RNA structure in this annotation
    */
-  private long invalidrnastruc = -1;
+  private long invalidrnastruc = -2;
 
   /**
    * Updates the _rnasecstr field Determines the positions that base pair and
@@ -118,6 +119,7 @@ public class AlignmentAnnotation
 
   private void _markRnaHelices()
   {
+    int mxval = 0;
     // Figure out number of helices
     // Length of rnasecstr is the number of pairs of positions that base pair
     // with each other in the secondary structure
@@ -133,6 +135,10 @@ public class AlignmentAnnotation
       try
       {
         val = Integer.valueOf(_rnasecstr[x].getFeatureGroup());
+        if (mxval < val)
+        {
+          mxval = val;
+        }
       } catch (NumberFormatException q)
       {
       }
@@ -141,9 +147,10 @@ public class AlignmentAnnotation
       annotations[_rnasecstr[x].getBegin()].value = val;
       annotations[_rnasecstr[x].getEnd()].value = val;
 
-      annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
-      annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
+      // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
+      // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
     }
+    setScore(mxval);
   }
   /**
    * map of positions in the associated annotation