ensure lastSeq is refreshed if new feature added

[jalview.git] / src / jalview / io / AnnotationFile.java

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index d004c1a..04861a2 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -287,7 +287,7 @@ public class AnnotationFile
 \r
        if(refSeq!=null)\r
        {\r
-         annotation.createSequenceMapping(refSeq, refSeqIndex);\r
+         annotation.createSequenceMapping(refSeq, refSeqIndex, false);\r
          refSeq.addAlignmentAnnotation(annotation);\r
        }\r
 \r
@@ -356,7 +356,7 @@ public class AnnotationFile
         for(int j=0; j<annotations.length; j++)\r
         {\r
           if(annotations[j]!=null)\r
-            annotations[j].colour = ucs.findColour("A");\r
+            annotations[j].colour = ucs.findColour('A');\r
         }\r
       }\r
     }\r
@@ -414,7 +414,7 @@ public class AnnotationFile
     if(st.hasMoreTokens())\r
     {\r
       UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
-      colour = ucs.findColour("A");\r
+      colour = ucs.findColour('A');\r
     }\r
 \r
     annotation.setThreshold(new GraphLine(value, label, colour));\r