From 95d74892773dede6aeb3a4791340f022d2df8903 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 23 Apr 2010 15:11:10 +0000
Subject: [PATCH] next attempt for Bug #36198 - appears to work reproducibly

---
 src/jalview/io/AnnotationFile.java |   43 +++++++++++++++++++++++-------------
 1 file changed, 28 insertions(+), 15 deletions(-)

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index ce1afc2..87b21d3 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -210,10 +210,15 @@ public class AnnotationFile
           if (row.annotations[j] != null)
           {
             comma = "";
-            if (row.annotations[j].secondaryStructure != ' ') // could be also hasGlyphs || ... 
+            if (hasGlyphs) // could be also hasGlyphs || ... 
             {
 
-              text.append(comma + row.annotations[j].secondaryStructure);
+              text.append(comma);
+              if (row.annotations[j].secondaryStructure != ' ')
+              {
+                // only write out the field if its not whitespace.
+                text.append(row.annotations[j].secondaryStructure);
+              }
               comma = ",";
             }
             if (hasValues)
@@ -717,8 +722,10 @@ public class AnnotationFile
     StringTokenizer st = new StringTokenizer(string, ",", true);
     String token;
     boolean seenContent=false;
+    int pass=0;
     while (st.hasMoreTokens())
     {
+      pass++;
       token = st.nextToken().trim();
       if (token.equals(","))
       {
@@ -746,8 +753,12 @@ public class AnnotationFile
         } catch (NumberFormatException ex)
         {
         }
+      } else {
+        if (token.length()==1)
+        {
+          displayChar = token;
+        }
       }
-
       if (hasSymbols && (token.equals("H") || token.equals("E") || token.equals(" ")))
       {
         // Either this character represents a helix or sheet
@@ -758,7 +769,7 @@ public class AnnotationFile
           displayChar = "";
         }
       }
-      else if (desc == null)
+      else if (desc == null || (parsedValue && pass>2))
       {
         desc = token;
       }
@@ -768,19 +779,21 @@ public class AnnotationFile
 //    {
 //      displayChar = " "; // empty display char symbol.
 //    }
-    if (displayChar != null && displayChar.length() > 1 && desc != null
-            && desc.length() == 1)
+    if (displayChar != null && desc!=null && desc.length()==1) 
     {
-      String tmp = displayChar;
-      displayChar = desc;
-      desc = tmp;
+      if (displayChar.length() > 1)
+      {
+        // switch desc and displayChar - legacy support  
+        String tmp = displayChar;
+        displayChar = desc;
+        desc = tmp;
+      } else {
+        if (displayChar.equals(desc)) {
+          // duplicate label - hangover from the 'robust parser' above
+          desc = null;
+        }
+      }
     }
-    /*
-     * In principle, this code will ensure that the Annotation element generated
-     * is renderable by any of the applet or application rendering code but
-     * instead we check for null strings when the display character is rendered.
-     * if (displayChar==null) { displayChar=""; }
-     */
     Annotation anot = new Annotation(displayChar, desc, ss, value);
 
     anot.colour = colour;
-- 
1.7.10.2