patch for bug #36198 - more to follow on Monday.

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index a3328b3..a821066 100755 (executable)
--- 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 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -125,7 +125,7 @@ public class AnnotationFile
           refSeq = row.sequenceRef;\r
           text.append("\nSEQUENCE_REF\t" + refSeq.getName() + "\n");\r
         }\r
-        boolean hasGlyphs = false, hasLabels = false, hasValues = false, hasText = false;\r
+        boolean hasGlyphs = row.hasIcons, hasLabels = row.hasText, hasValues = row.hasScore, hasText = false;\r
         // lookahead to check what the annotation row object actually contains.\r
         for (int j = 0; row.annotations != null\r
                 && j < row.annotations.length\r
@@ -210,7 +210,7 @@ public class AnnotationFile
           if (row.annotations[j] != null)\r
           {\r
             comma = "";\r
-            if (hasGlyphs && row.annotations[j].secondaryStructure != ' ')\r
+            if (row.annotations[j].secondaryStructure != ' ') // could be also hasGlyphs || ... \r
             {\r
 \r
               text.append(comma + row.annotations[j].secondaryStructure);\r
@@ -748,7 +748,7 @@ public class AnnotationFile
         }\r
       }\r
 \r
-      if (hasSymbols && (token.equals("H") || token.equals("E")))\r
+      if (hasSymbols && (token.equals("H") || token.equals("E") || token.equals(" ")))\r
       {\r
         // Either this character represents a helix or sheet\r
         // or an integer which can be displayed\r