From 35a5186a5d49868d70138aab55dfd284119914f4 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 20 Aug 2008 15:54:22 +0000
Subject: [PATCH] Use 0f rather than NaN to specify non-valued annotation
 elements.

---
 src/jalview/io/AnnotationFile.java |    2 +-
 src/jalview/io/StockholmFile.java  |    6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 13cfc38..288ce2f 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -190,7 +190,7 @@ public class AnnotationFile
               }
 
               color = row.annotations[j].colour;
-              if (row.annotations[j].value != 0f)
+              if (row.annotations[j].value != 0f && row.annotations[j].value!=Float.NaN) 
               {
                 text.append(comma + row.annotations[j].value);
               }
diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index d5f3cc2..ccbe818 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -480,18 +480,18 @@ public class StockholmFile extends AlignFile
     {
       String pos = annots.substring(i, i + 1);
       Annotation ann;
-      ann = new Annotation(pos, "", ' ', Float.NaN);
+      ann = new Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not be written out 
       if (ss)
       {
         ann.secondaryStructure = jalview.schemes.ResidueProperties
                 .getDssp3state(pos).charAt(0);
         if (ann.secondaryStructure == pos.charAt(0) || pos.charAt(0) == 'C')
         {
-          ann.displayCharacter = "";
+          ann.displayCharacter = ""; // null; // " ";
         }
         else
         {
-          ann.displayCharacter += " ";
+          ann.displayCharacter = " "+ann.displayCharacter;
         }
       }
 
-- 
1.7.10.2