X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;fp=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=f84b18d0c5c0aec44cb5f01aeab751acf2c8cb21;hb=e191ef5205d9700ee33955ff89e0b3a4597d17d1;hp=0098d760eabbcc12a13f43d8c7ab947a899ea2b8;hpb=1253fe4ed610223c3c3b4e4983ec542e818efdfe;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 0098d76..f84b18d 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -294,6 +294,7 @@ public class AlignmentAnnotation
     char firstChar = 0;
     for (int i = 0; i < annotations.length; i++)
     {
+      // DEBUG System.out.println(i + ": " + annotations[i]);
       if (annotations[i] == null)
       {
         continue;
@@ -301,12 +302,15 @@ public class AlignmentAnnotation
       if (annotations[i].secondaryStructure == 'H'
               || annotations[i].secondaryStructure == 'E')
       {
+        // DEBUG System.out.println( "/H|E/ '" +
+        // annotations[i].secondaryStructure + "'");
         hasIcons |= true;
       }
       else
       // Check for RNA secondary structure
       {
-        // System.out.println(annotations[i].secondaryStructure);
+        // DEBUG System.out.println( "/else/ '" +
+        // annotations[i].secondaryStructure + "'");
         // TODO: 2.8.2 should this ss symbol validation check be a function in
         // RNA/ResidueProperties ?
         if (annotations[i].secondaryStructure == '('
@@ -317,10 +321,10 @@ public class AlignmentAnnotation
                 || annotations[i].secondaryStructure == 'B'
                 || annotations[i].secondaryStructure == 'C'
                 || annotations[i].secondaryStructure == 'D'
-                || annotations[i].secondaryStructure == 'E'
+                // || annotations[i].secondaryStructure == 'E'
                 || annotations[i].secondaryStructure == 'F'
                 || annotations[i].secondaryStructure == 'G'
-                || annotations[i].secondaryStructure == 'H'
+                // || annotations[i].secondaryStructure == 'H'
                 || annotations[i].secondaryStructure == 'I'
                 || annotations[i].secondaryStructure == 'J'
                 || annotations[i].secondaryStructure == 'K'
@@ -367,7 +371,7 @@ public class AlignmentAnnotation
         // &&
         // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
                 firstChar != ' ' && firstChar != '$' && firstChar != 0xCE
-                && firstChar != '(' && firstChar != '[' && firstChar != '>'
+                && firstChar != '(' && firstChar != '[' && firstChar != '<'
                 && firstChar != '{' && firstChar != 'A' && firstChar != 'B'
                 && firstChar != 'C' && firstChar != 'D' && firstChar != 'E'
                 && firstChar != 'F' && firstChar != 'G' && firstChar != 'H'