JAL-1355

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

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 989d62a..601339a 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -259,6 +259,7 @@ public class AlignmentAnnotation
       // Check for RNA secondary structure
       {
         // System.out.println(annotations[i].secondaryStructure);
+        // TODO: 2.8.2 should this ss symbol validation check be a function in RNA/ResidueProperties ?
         if (annotations[i].secondaryStructure == '('
                 || annotations[i].secondaryStructure == '['
                 || annotations[i].secondaryStructure == '<'
@@ -320,9 +321,7 @@ public class AlignmentAnnotation
                 // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
                 firstChar != ' '
                 && firstChar != '$'
-                && firstChar != '�' // JBPNote should explicitly express as
-                                    // unicode number to avoid source code
-                                    // translation problems
+                && firstChar != 0xCE
                 && firstChar != '('
                 && firstChar != '['
                 && firstChar != '>'
@@ -1113,4 +1112,9 @@ public class AlignmentAnnotation
   {
     this.calcId = calcId;
   }
+
+  public boolean isRNA()
+  {
+    return isrna;
+  }
 }