See note in Mantis bug #55537 : inconsistency between loading in exported histogram...

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 9381020..00b7ead 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -72,10 +72,18 @@ public class AnnotationFile
       this.hiddenRepSeqs = hiddenRepSeqs;\r
     }\r
   }\r
-\r
+  /**\r
+   * Prepare an annotation file given a set of annotations, groups, alignment properties and views. \r
+   * @param annotations\r
+   * @param groups\r
+   * @param properties\r
+   * @param views\r
+   * @return annotation file\r
+   */\r
   public String printAnnotations(AlignmentAnnotation[] annotations,\r
           Vector groups, Hashtable properties, ViewDef[] views)\r
   {\r
+    // TODO: resolve views issue : annotationFile could contain visible region, or full data + hidden region specifications for a view.\r
     if (annotations != null)\r
     {\r
       boolean oneColour = true;\r
@@ -224,7 +232,6 @@ public class AnnotationFile
             if (hasLabels)\r
             {\r
               // TODO: labels are emitted after values for bar graphs.\r
-              text.append(comma);\r
               if // empty labels are allowed, so\r
               (row.annotations[j].displayCharacter != null\r
                       && row.annotations[j].displayCharacter.length() > 0\r
@@ -627,7 +634,7 @@ public class AnnotationFile
             }\r
             else\r
             {\r
-              annotations[index++] = parseAnnotation(token);\r
+              annotations[index++] = parseAnnotation(token, graphStyle);\r
               emptyColumn = false;\r
             }\r
           }\r
@@ -682,8 +689,9 @@ public class AnnotationFile
     return true;\r
   }\r
 \r
-  Annotation parseAnnotation(String string)\r
+  Annotation parseAnnotation(String string, int graphStyle)\r
   {\r
+    boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH); // don't do the glyph test if we don't want secondary structure\r
     String desc = null, displayChar = null;\r
     char ss = ' '; // secondaryStructure\r
     float value = 0;\r
@@ -698,31 +706,40 @@ public class AnnotationFile
       UserColourScheme ucs = new UserColourScheme();\r
 \r
       colour = ucs.getColourFromString(string.substring(i + 1, j));\r
-\r
+      if ( i>0 && string.charAt(i-1)==',')\r
+      {\r
+        // clip the preceding comma as well\r
+        i--;\r
+      }\r
       string = string.substring(0, i) + string.substring(j + 1);\r
     }\r
 \r
-    StringTokenizer st = new StringTokenizer(string, ",");\r
+    StringTokenizer st = new StringTokenizer(string, ",", true);\r
     String token;\r
+    boolean seenContent=false;\r
     while (st.hasMoreTokens())\r
     {\r
       token = st.nextToken().trim();\r
-      if (token.length() == 0)\r
+      if (token.equals(","))\r
       {\r
-        if (parsedValue && !dcset)\r
+        if (!seenContent && parsedValue && !dcset)\r
         {\r
           // allow the value below the bar/line to be empty\r
           dcset = true;\r
           displayChar = " ";\r
         }\r
+        seenContent = false;\r
         continue;\r
+      } else {\r
+        seenContent = true;\r
       }\r
 \r
       if (!parsedValue)\r
       {\r
         try\r
         {\r
-          displayChar = token;\r
+          displayChar = token; \r
+          // foo\r
           value = new Float(token).floatValue();\r
           parsedValue = true;\r
           continue;\r
@@ -731,7 +748,7 @@ public class AnnotationFile
         }\r
       }\r
 \r
-      if (token.equals("H") || token.equals("E"))\r
+      if (hasSymbols && (token.equals("H") || token.equals("E")))\r
       {\r
         // Either this character represents a helix or sheet\r
         // or an integer which can be displayed\r
@@ -747,10 +764,10 @@ public class AnnotationFile
       }\r
 \r
     }\r
-    if (!dcset && string.charAt(string.length() - 1) == ',')\r
-    {\r
-      displayChar = " "; // empty display char symbol.\r
-    }\r
+//    if (!dcset && string.charAt(string.length() - 1) == ',')\r
+//    {\r
+//      displayChar = " "; // empty display char symbol.\r
+//    }\r
     if (displayChar != null && displayChar.length() > 1 && desc != null\r
             && desc.length() == 1)\r
     {\r