fixed introduced bug (doh)

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

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 801a9ab..77f8810 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -101,17 +101,17 @@ public class AnnotationFile
         if(row.annotations[j]!=null)\r
         {\r
           comma = "";\r
-          if (row.annotations[j].displayCharacter.length() > 0\r
-              && !row.annotations[j].displayCharacter.equals(" "))\r
-          {\r
-            text.append(row.annotations[j].displayCharacter);\r
-            comma = ",";\r
-          }\r
           if (row.annotations[j].secondaryStructure!=' ')\r
           {\r
             text.append(comma + row.annotations[j].secondaryStructure);\r
             comma = ",";\r
           }\r
+          if (row.annotations[j].displayCharacter.length() > 0 \r
+                  && !row.annotations[j].displayCharacter.equals(" "))\r
+              {\r
+                text.append(comma + row.annotations[j].displayCharacter);\r
+                comma = ",";\r
+              }\r
           if (row.annotations[j].value!=0f)\r
           {\r
             color = row.annotations[j].colour;\r
@@ -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
@@ -333,7 +333,8 @@ public class AnnotationFile
         // Either this character represents a helix or sheet\r
         // or an integer which can be displayed\r
         ss = token.charAt(0);\r
-        displayChar = "";\r
+        if(displayChar.equals(token.substring(0,1)))\r
+          displayChar = "";\r
       }\r
       else if(desc.length()<1)\r
         desc = token;\r
@@ -355,7 +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
@@ -413,7 +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