next attempt for Bug #36198 - appears to work reproducibly

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index ce1afc2..87b21d3 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -210,10 +210,15 @@ public class AnnotationFile
           if (row.annotations[j] != null)\r
           {\r
             comma = "";\r
-            if (row.annotations[j].secondaryStructure != ' ') // could be also hasGlyphs || ... \r
+            if (hasGlyphs) // could be also hasGlyphs || ... \r
             {\r
 \r
-              text.append(comma + row.annotations[j].secondaryStructure);\r
+              text.append(comma);\r
+              if (row.annotations[j].secondaryStructure != ' ')\r
+              {\r
+                // only write out the field if its not whitespace.\r
+                text.append(row.annotations[j].secondaryStructure);\r
+              }\r
               comma = ",";\r
             }\r
             if (hasValues)\r
@@ -717,8 +722,10 @@ public class AnnotationFile
     StringTokenizer st = new StringTokenizer(string, ",", true);\r
     String token;\r
     boolean seenContent=false;\r
+    int pass=0;\r
     while (st.hasMoreTokens())\r
     {\r
+      pass++;\r
       token = st.nextToken().trim();\r
       if (token.equals(","))\r
       {\r
@@ -746,8 +753,12 @@ public class AnnotationFile
         } catch (NumberFormatException ex)\r
         {\r
         }\r
+      } else {\r
+        if (token.length()==1)\r
+        {\r
+          displayChar = token;\r
+        }\r
       }\r
-\r
       if (hasSymbols && (token.equals("H") || token.equals("E") || token.equals(" ")))\r
       {\r
         // Either this character represents a helix or sheet\r
@@ -758,7 +769,7 @@ public class AnnotationFile
           displayChar = "";\r
         }\r
       }\r
-      else if (desc == null)\r
+      else if (desc == null || (parsedValue && pass>2))\r
       {\r
         desc = token;\r
       }\r
@@ -768,19 +779,21 @@ public class AnnotationFile
 //    {\r
 //      displayChar = " "; // empty display char symbol.\r
 //    }\r
-    if (displayChar != null && displayChar.length() > 1 && desc != null\r
-            && desc.length() == 1)\r
+    if (displayChar != null && desc!=null && desc.length()==1) \r
     {\r
-      String tmp = displayChar;\r
-      displayChar = desc;\r
-      desc = tmp;\r
+      if (displayChar.length() > 1)\r
+      {\r
+        // switch desc and displayChar - legacy support  \r
+        String tmp = displayChar;\r
+        displayChar = desc;\r
+        desc = tmp;\r
+      } else {\r
+        if (displayChar.equals(desc)) {\r
+          // duplicate label - hangover from the 'robust parser' above\r
+          desc = null;\r
+        }\r
+      }\r
     }\r
-    /*\r
-     * In principle, this code will ensure that the Annotation element generated\r
-     * is renderable by any of the applet or application rendering code but\r
-     * instead we check for null strings when the display character is rendered.\r
-     * if (displayChar==null) { displayChar=""; }\r
-     */\r
     Annotation anot = new Annotation(displayChar, desc, ss, value);\r
 \r
     anot.colour = colour;\r