From 688f6f0151570be3f3aa3b161963a0532d4bf775 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 6 Apr 2006 09:24:42 +0000
Subject: [PATCH] Must copy feature settings from one frame to another as they
 are not attached ot the dataset

---
 src/jalview/gui/AlignFrame.java |   15 +++++++++++----
 src/jalview/ws/MsaWSClient.java |   13 +++++++++++--
 2 files changed, 22 insertions(+), 6 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index ccf7303..0167b39 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -195,6 +195,11 @@ public class AlignFrame
     return  jalview.bin.Cache.getProperty("VERSION");
   }
 
+  public FeatureRenderer getFeatureRenderer()
+  {
+    return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
+  }
+
 
   public void fetchSequence_actionPerformed(ActionEvent e)
   {
@@ -707,8 +712,9 @@ public class AlignFrame
         String newtitle = new String("Copied sequences");
 
         //>>>This is a fix for the moment, until a better solution is found!!<<<
-        FeatureRenderer fr = af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
-        fr.featureColours = alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
+        af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
+            alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+
 
         if (title.startsWith("Copied sequences"))
         {
@@ -2355,6 +2361,7 @@ public class AlignFrame
       {
         // Add any Multiple Sequence Alignment Services
         final JMenu msawsmenu = new JMenu("Alignment");
+        final AlignFrame af = this;
         for (int i = 0, j = msaws.size(); i < j; i++)
         {
           final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
@@ -2366,7 +2373,7 @@ public class AlignFrame
             {
               SequenceI[] msa = gatherSequencesForAlignment();
               new jalview.ws.MsaWSClient(sh, title, msa,
-                  false, true, viewport.getAlignment().getDataset());
+                  false, true, viewport.getAlignment().getDataset(), af);
 
             }
 
@@ -2383,7 +2390,7 @@ public class AlignFrame
               {
                 SequenceI[] msa = gatherSequencesForAlignment();
                 new jalview.ws.MsaWSClient(sh, title, msa,
-                    true, true, viewport.getAlignment().getDataset());
+                    true, true, viewport.getAlignment().getDataset(), af);
 
               }
 
diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java
index 479f22f..59a858e 100755
--- a/src/jalview/ws/MsaWSClient.java
+++ b/src/jalview/ws/MsaWSClient.java
@@ -43,6 +43,7 @@ public class MsaWSClient
    * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
    */
   ext.vamsas.MuscleWS server;
+  AlignFrame alignFrame;
 
 
   /**
@@ -56,10 +57,14 @@ public class MsaWSClient
    * @param preserveOrder DOCUMENT ME!
    */
 
-  public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle, SequenceI[] msa,
-                     boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
+  public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle,
+                     SequenceI[] msa,
+                     boolean submitGaps, boolean preserveOrder,
+                     Alignment seqdataset,
+                     AlignFrame _alignFrame)
   {
 
+    alignFrame = _alignFrame;
     if (!sh.getAbstractName().equals("MsaWS"))
     {
       JOptionPane.showMessageDialog(Desktop.desktop,
@@ -474,6 +479,10 @@ public class MsaWSClient
           }
           // TODO: JBPNote Should also rename the query sequence sometime...
           AlignFrame af = new AlignFrame(al);
+
+          //>>>This is a fix for the moment, until a better solution is found!!<<<
+          alignFrame.getFeatureRenderer().transferSettings(af.getFeatureRenderer());
+
           af.addSortByOrderMenuItem(ServiceName + " Ordering",
                                     msaorder);
 
-- 
1.7.10.2