Merge branch 'develop' into features/JAL-2094_colourInterface

[jalview.git] / src / jalview / renderer / AnnotationRenderer.java

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 634b1e4..82f6ffb 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -220,7 +220,7 @@ public class AnnotationRenderer
             || !dc.equals(row_annotations[column].displayCharacter);
     // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
     // If a closing base pair half of the stem, display a backward arrow
-    if (column > 0 && Rna.isClosingParenthesis(dc.charAt(0)))
+    if (column > 0 && Rna.isClosingParenthesis(dc))
     {
 
       if (diffupstream)
@@ -751,7 +751,7 @@ public class AnnotationRenderer
                             validEnd);
                     break;
                   }
-
+                  // no break if isRNA - falls through to drawNotCanonicalAnnot!
                 case 'E':
                   if (!isRNA)
                   {
@@ -760,6 +760,7 @@ public class AnnotationRenderer
                             validEnd);
                     break;
                   }
+                  // no break if isRNA - fall through to drawNotCanonicalAnnot!
 
                 case '{':
                 case '}':
@@ -867,7 +868,6 @@ public class AnnotationRenderer
         {
           validRes = true;
         }
-
         // x ++;
 
         if (row.hasIcons)
@@ -882,6 +882,7 @@ public class AnnotationRenderer
                       startRes, column, validRes, validEnd);
               break;
             }
+            // no break if isRNA - fall through to drawNotCanonicalAnnot!
 
           case 'E':
             if (!isRNA)
@@ -890,6 +891,7 @@ public class AnnotationRenderer
                       startRes, column, validRes, validEnd);
               break;
             }
+            // no break if isRNA - fall through to drawNotCanonicalAnnot!
 
           case '(':
           case ')': // Stem case for RNA secondary structure