From 7a48562b8052a1ac9fb7c337d58b910f6f7fe0b5 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Wed, 22 May 2013 17:53:03 +0100
Subject: [PATCH] fix for JAL-1297: COMBINE output now follows specification
 and all additional annotation rows included in output (not
 just the first one which wasn't hidden)

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

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index a94bd3c..d15e7c5 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -132,6 +132,7 @@ public class AnnotationFile
       StringBuffer graphLine = new StringBuffer();
       StringBuffer rowprops = new StringBuffer();
       Hashtable graphGroup = new Hashtable();
+      BitSet graphGroupSeen = new BitSet();
 
       java.awt.Color color;
 
@@ -139,7 +140,7 @@ public class AnnotationFile
       {
         row = annotations[i];
 
-        if (!row.visible && !row.hasScore())
+        if (!row.visible && !row.hasScore() && !(row.graphGroup>-1 && graphGroupSeen.get(row.graphGroup)))
         {
           continue;
         }
@@ -251,6 +252,7 @@ public class AnnotationFile
 
           if (row.graphGroup > -1)
           {
+            graphGroupSeen.set(row.graphGroup);
             String key = String.valueOf(row.graphGroup);
             if (graphGroup.containsKey(key))
             {
@@ -382,10 +384,10 @@ public class AnnotationFile
       text.append(graphLine.toString());
       if (graphGroup.size() > 0)
       {
-        text.append("COMBINE\t");
         Enumeration en = graphGroup.elements();
         while (en.hasMoreElements())
         {
+          text.append("COMBINE\t");
           text.append(en.nextElement());
           text.append(newline);
         }
-- 
1.7.10.2