revised renderer and annotation model to support different pair-patterns - needs...

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

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 8115af4..1433f73 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -263,10 +263,10 @@ public class AlignmentAnnotation
                        || annotations[i].secondaryStructure == 'B'
                        || annotations[i].secondaryStructure == 'C'
                        || annotations[i].secondaryStructure == 'D'
-                       || annotations[i].secondaryStructure == '1'
+                       || annotations[i].secondaryStructure == 'E'
                        || annotations[i].secondaryStructure == 'F'
                        || annotations[i].secondaryStructure == 'G'
-                       || annotations[i].secondaryStructure == '2'
+                       || annotations[i].secondaryStructure == 'H'
                        || annotations[i].secondaryStructure == 'I'
                        || annotations[i].secondaryStructure == 'J'
                        || annotations[i].secondaryStructure == 'K'
@@ -315,8 +315,8 @@ public class AlignmentAnnotation
                 // &&
                 // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
                 firstChar != ' '
-                && firstChar != 'H'
-                && firstChar != 'E'
+                && firstChar != '$'
+                && firstChar != 'µ' // JBPNote should explicitly express as unicode number to avoid source code translation problems
                 && firstChar != '('
                 && firstChar != '['
                 && firstChar != '>'
@@ -325,10 +325,10 @@ public class AlignmentAnnotation
                 && firstChar != 'B'
                 && firstChar != 'C'
                 && firstChar != 'D'
-                && firstChar != '1'
+                && firstChar != 'E'
                 && firstChar != 'F'
                 && firstChar != 'G'
-                && firstChar != '2'
+                && firstChar != 'H'
                 && firstChar != 'I'
                 && firstChar != 'J'
                 && firstChar != 'K'