From 7db575b815f21c6e023f6482fe258c39e84b436e Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 15 Feb 2006 15:17:29 +0000
Subject: [PATCH] Features file has startgroup, endgroup

---
 src/jalview/appletgui/AlignFrame.java |   20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 96dc64b..6d70bf7 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -153,6 +153,7 @@ public class AlignFrame extends Frame implements ActionListener,
       SequenceFeature sf;
       FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
       int lineNo = 0;
+      String featureGroup = null;
       while ( (line = in.readLine()) != null)
       {
         lineNo++;
@@ -160,8 +161,22 @@ public class AlignFrame extends Frame implements ActionListener,
         if (st.countTokens() == 2)
         {
           type = st.nextToken();
-          UserColourScheme ucs = new UserColourScheme(st.nextToken());
-          fr.setColour(type, ucs.findColour("A"));
+          if(type.equalsIgnoreCase("startgroup"))
+          {
+            featureGroup = st.nextToken();
+          }
+          else if(type.equalsIgnoreCase("endgroup"))
+          {
+            //We should check whether this is the current group,
+            //but at present theres no way of showing more than 1 group
+            st.nextToken();
+            featureGroup = null;
+          }
+          else
+          {
+            UserColourScheme ucs = new UserColourScheme(st.nextToken());
+            fr.setColour(type, ucs.findColour("A"));
+          }
           continue;
         }
 
@@ -195,6 +210,7 @@ public class AlignFrame extends Frame implements ActionListener,
           }
 
           sf = new SequenceFeature(type, desc, "", start, end);
+          sf.setFeatureGroup(featureGroup);
 
           seq.addSequenceFeature(sf);
         }
-- 
1.7.10.2