X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=04861a265c7e22625966afe2a9f7c304f69a892d;hb=2e699d341f8e64868e3c279f9c02af617c4e9b44;hp=801a9ab3db5f528b1f75fb3d6b8025bd1026e5fc;hpb=37479c92b982f22da98bb5a8d2eb404fa804bc7d;p=jalview.git

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 801a9ab..04861a2 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -287,7 +287,7 @@ public class AnnotationFile
 
        if(refSeq!=null)
        {
-         annotation.createSequenceMapping(refSeq, refSeqIndex);
+         annotation.createSequenceMapping(refSeq, refSeqIndex, false);
          refSeq.addAlignmentAnnotation(annotation);
        }
 
@@ -333,7 +333,8 @@ public class AnnotationFile
         // Either this character represents a helix or sheet
         // or an integer which can be displayed
         ss = token.charAt(0);
-        displayChar = "";
+        if(displayChar.equals(token.substring(0,1)))
+          displayChar = "";
       }
       else if(desc.length()<1)
         desc = token;
@@ -355,7 +356,7 @@ public class AnnotationFile
         for(int j=0; j<annotations.length; j++)
         {
           if(annotations[j]!=null)
-            annotations[j].colour = ucs.findColour("A");
+            annotations[j].colour = ucs.findColour('A');
         }
       }
     }
@@ -413,7 +414,7 @@ public class AnnotationFile
     if(st.hasMoreTokens())
     {
       UserColourScheme ucs = new UserColourScheme(st.nextToken());
-      colour = ucs.findColour("A");
+      colour = ucs.findColour('A');
     }
 
     annotation.setThreshold(new GraphLine(value, label, colour));