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fix for JAL-701 - ensure '<' appears in tooltip in application and allow html tags...
[jalview.git] / src / jalview / datamodel / AlignmentAnnotation.java
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index bd5bfcf..483c821 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -380,7 +380,7 @@ public class AlignmentAnnotation
     {
       this.score = annotation.score;
     }
-    if (threshold != null)
+    if (annotation.threshold != null)
     {
       threshold = new GraphLine(annotation.threshold);
     }
@@ -813,6 +813,12 @@ public class AlignmentAnnotation
   {
     if (seqname && this.sequenceRef != null)
     {
+      int i=description.toLowerCase().indexOf("<html>");
+      if (i>-1)
+      {
+        // move the html tag to before the sequence reference.
+        return "<html>"+sequenceRef.getName()+" : "+description.substring(i+6);
+      }
       return sequenceRef.getName() + " : " + description;
     }
     return description;