From 75a1f7cee379a690c42b5ac2c5f58c4475f46564 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 22 Mar 2010 17:13:12 +0000
Subject: [PATCH] See note in Mantis bug #55537 : inconsistency between
 loading in exported histogram annotation and annotation row
 type dependent parsing of the column annotation fields.

---
 src/jalview/io/AnnotationFile.java |   45 +++++++++++++++++++++++++-----------
 1 file changed, 31 insertions(+), 14 deletions(-)

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 9381020..00b7ead 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -72,10 +72,18 @@ public class AnnotationFile
       this.hiddenRepSeqs = hiddenRepSeqs;
     }
   }
-
+  /**
+   * Prepare an annotation file given a set of annotations, groups, alignment properties and views. 
+   * @param annotations
+   * @param groups
+   * @param properties
+   * @param views
+   * @return annotation file
+   */
   public String printAnnotations(AlignmentAnnotation[] annotations,
           Vector groups, Hashtable properties, ViewDef[] views)
   {
+    // TODO: resolve views issue : annotationFile could contain visible region, or full data + hidden region specifications for a view.
     if (annotations != null)
     {
       boolean oneColour = true;
@@ -224,7 +232,6 @@ public class AnnotationFile
             if (hasLabels)
             {
               // TODO: labels are emitted after values for bar graphs.
-              text.append(comma);
               if // empty labels are allowed, so
               (row.annotations[j].displayCharacter != null
                       && row.annotations[j].displayCharacter.length() > 0
@@ -627,7 +634,7 @@ public class AnnotationFile
             }
             else
             {
-              annotations[index++] = parseAnnotation(token);
+              annotations[index++] = parseAnnotation(token, graphStyle);
               emptyColumn = false;
             }
           }
@@ -682,8 +689,9 @@ public class AnnotationFile
     return true;
   }
 
-  Annotation parseAnnotation(String string)
+  Annotation parseAnnotation(String string, int graphStyle)
   {
+    boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH); // don't do the glyph test if we don't want secondary structure
     String desc = null, displayChar = null;
     char ss = ' '; // secondaryStructure
     float value = 0;
@@ -698,31 +706,40 @@ public class AnnotationFile
       UserColourScheme ucs = new UserColourScheme();
 
       colour = ucs.getColourFromString(string.substring(i + 1, j));
-
+      if ( i>0 && string.charAt(i-1)==',')
+      {
+        // clip the preceding comma as well
+        i--;
+      }
       string = string.substring(0, i) + string.substring(j + 1);
     }
 
-    StringTokenizer st = new StringTokenizer(string, ",");
+    StringTokenizer st = new StringTokenizer(string, ",", true);
     String token;
+    boolean seenContent=false;
     while (st.hasMoreTokens())
     {
       token = st.nextToken().trim();
-      if (token.length() == 0)
+      if (token.equals(","))
       {
-        if (parsedValue && !dcset)
+        if (!seenContent && parsedValue && !dcset)
         {
           // allow the value below the bar/line to be empty
           dcset = true;
           displayChar = " ";
         }
+        seenContent = false;
         continue;
+      } else {
+        seenContent = true;
       }
 
       if (!parsedValue)
       {
         try
         {
-          displayChar = token;
+          displayChar = token; 
+          // foo
           value = new Float(token).floatValue();
           parsedValue = true;
           continue;
@@ -731,7 +748,7 @@ public class AnnotationFile
         }
       }
 
-      if (token.equals("H") || token.equals("E"))
+      if (hasSymbols && (token.equals("H") || token.equals("E")))
       {
         // Either this character represents a helix or sheet
         // or an integer which can be displayed
@@ -747,10 +764,10 @@ public class AnnotationFile
       }
 
     }
-    if (!dcset && string.charAt(string.length() - 1) == ',')
-    {
-      displayChar = " "; // empty display char symbol.
-    }
+//    if (!dcset && string.charAt(string.length() - 1) == ',')
+//    {
+//      displayChar = " "; // empty display char symbol.
+//    }
     if (displayChar != null && displayChar.length() > 1 && desc != null
             && desc.length() == 1)
     {
-- 
1.7.10.2