From d58eb8f688b1f04262d55866d74d5e8d67eb0d00 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 6 Feb 2009 14:54:03 +0000
Subject: [PATCH] showUnconserved IO

---
 src/jalview/io/AnnotationFile.java |    7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 1872f60..101fe2e 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -261,6 +261,7 @@ public class AnnotationFile
         String key = en.nextElement().toString();
         text.append("\t" + key + "=" + properties.get(key));
       }
+      // TODO: output alignment visualization settings here if required
 
     }
 
@@ -318,7 +319,7 @@ public class AnnotationFile
       text.append("displayBoxes=" + sg.getDisplayBoxes() + "\t");
       text.append("displayText=" + sg.getDisplayText() + "\t");
       text.append("colourText=" + sg.getColourText() + "\t");
-
+      text.append("showUnconserved="+sg.getShowunconserved()+"\t");
       if (sg.textColour != java.awt.Color.black)
       {
         text.append("textCol1="
@@ -937,6 +938,10 @@ public class AnnotationFile
         {
           sg.setDisplayBoxes(Boolean.valueOf(value).booleanValue());
         }
+        else if (key.equalsIgnoreCase("showUnconserved"))
+        {
+          sg.setShowunconserved(Boolean.valueOf(value).booleanValue());
+        }
         else if (key.equalsIgnoreCase("displayText"))
         {
           sg.setDisplayText(Boolean.valueOf(value).booleanValue());
-- 
1.7.10.2