From e1138429961fa5e88f89b66ba9a413a003328e02 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 26 Apr 2007 17:15:13 +0000
Subject: [PATCH] use hasScore method to test presence of score in annotation.

---
 src/jalview/gui/AnnotationLabels.java |    2 +-
 src/jalview/gui/Jalview2XML.java      |    5 ++---
 src/jalview/io/AnnotationFile.java    |    2 +-
 3 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 0ea7730..54263aa 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -380,7 +380,7 @@ public class AnnotationLabels
       {
         desc.append(aa.description+"<br>");
       }
-      if(!Float.isNaN(aa.score))
+      if(aa.hasScore())
       {
         desc.append("Score: "+aa.score);
       }
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index b90f497..45c76ee 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -534,7 +534,7 @@ public class Jalview2XML
         }
 
         an.setLabel(aa[i].label);
-        if (!Float.isNaN(aa[i].score))
+        if (aa[i].hasScore())
         {
           an.setScore(aa[i].getScore());
         }
@@ -1338,12 +1338,11 @@ public class Jalview2XML
 
           for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
           {
-
             anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
 
                     ae[aa].getDisplayCharacter(),
                     ae[aa].getDescription(),
-                    ae[aa].getSecondaryStructure()==null ? ' ' :
+                    (ae[aa].getSecondaryStructure()==null || ae[aa].getSecondaryStructure().length() == 0) ? ' ' :
                       ae[aa].getSecondaryStructure().charAt(0),
                       ae[aa].getValue()
 
diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index a936dac..463e922 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -169,7 +169,7 @@ public class AnnotationFile
           text.append("|");
         }
 
-        if(!Float.isNaN(row.score))
+        if(row.hasScore())
           text.append("\t"+row.score);
 
         text.append("\n");
-- 
1.7.10.2