From 9cad9986cac3bc401abae55d574ff64c51e96d5f Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 16 Apr 2010 16:43:38 +0000
Subject: [PATCH] patch for bug #36198 - more to follow on Monday.

---
 src/jalview/datamodel/AlignmentAnnotation.java |    7 ++++---
 src/jalview/io/AnnotationFile.java             |    6 +++---
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index a3328b3..a821066 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -179,7 +179,7 @@ public class AlignmentAnnotation
       if (annotations[i].secondaryStructure == 'H'
               || annotations[i].secondaryStructure == 'E')
       {
-        hasIcons = true;
+        hasIcons |= true;
       }
 
       if (annotations[i].displayCharacter == null)
@@ -191,14 +191,15 @@ public class AlignmentAnnotation
         firstChar = annotations[i].displayCharacter.charAt(0);
         // check to see if it looks like a sequence or is secondary structure
         // labelling.
-        if (
+        if (annotations[i].secondaryStructure!=' ' && !hasIcons &&
         // Uncomment to only catch case where displayCharacter==secondary
         // Structure
         // to correctly redisplay SS annotation imported from Stockholm,
         // exported to JalviewXML and read back in again.
         // &&
         // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
-        firstChar != 'H'
+        firstChar != ' '
+                && firstChar != 'H'
                 && firstChar != 'E'
                 && firstChar != '-'
                 && firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 00b7ead..ce1afc2 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -125,7 +125,7 @@ public class AnnotationFile
           refSeq = row.sequenceRef;
           text.append("\nSEQUENCE_REF\t" + refSeq.getName() + "\n");
         }
-        boolean hasGlyphs = false, hasLabels = false, hasValues = false, hasText = false;
+        boolean hasGlyphs = row.hasIcons, hasLabels = row.hasText, hasValues = row.hasScore, hasText = false;
         // lookahead to check what the annotation row object actually contains.
         for (int j = 0; row.annotations != null
                 && j < row.annotations.length
@@ -210,7 +210,7 @@ public class AnnotationFile
           if (row.annotations[j] != null)
           {
             comma = "";
-            if (hasGlyphs && row.annotations[j].secondaryStructure != ' ')
+            if (row.annotations[j].secondaryStructure != ' ') // could be also hasGlyphs || ... 
             {
 
               text.append(comma + row.annotations[j].secondaryStructure);
@@ -748,7 +748,7 @@ public class AnnotationFile
         }
       }
 
-      if (hasSymbols && (token.equals("H") || token.equals("E")))
+      if (hasSymbols && (token.equals("H") || token.equals("E") || token.equals(" ")))
       {
         // Either this character represents a helix or sheet
         // or an integer which can be displayed
-- 
1.7.10.2