From 348802fdd7804327b447a17eac6f3df11181220a Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 27 Apr 2007 09:53:27 +0000
Subject: [PATCH] one colour flag in annotation export

---
 src/jalview/io/AnnotationFile.java |   12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 463e922..e54ae71 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -40,6 +40,7 @@ public class AnnotationFile
   {
     if (annotations != null)
     {
+      boolean oneColour = true;
       AlignmentAnnotation row;
       String comma;
       SequenceI refSeq = null;
@@ -61,6 +62,7 @@ public class AnnotationFile
         }
 
         color = null;
+        oneColour = true;
 
         if (row.sequenceRef == null)
         {
@@ -151,6 +153,11 @@ public class AnnotationFile
 
             if (row.annotations[j] != null)
             {
+              if(color!=null && !color.equals(row.annotations[j].colour))
+              {
+                oneColour = false;
+              }
+
               color = row.annotations[j].colour;
               if (row.annotations[j].value != 0f)
               {
@@ -174,7 +181,7 @@ public class AnnotationFile
 
         text.append("\n");
 
-        if (color != null && color != java.awt.Color.black)
+        if (color != null && color != java.awt.Color.black && oneColour)
         {
           colours.append("COLOUR\t"
                          + row.label + "\t"
@@ -578,7 +585,8 @@ public class AnnotationFile
 
     }
 
-    if (displayChar.length() > 1
+    if (displayChar!=null
+        && displayChar.length() > 1
         &&  desc!=null
         && desc.length() == 1)
     {
-- 
1.7.10.2