doco writing.

[jalview.git] / src / jalview / ws / MsaWSClient.java

diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java
index 479f22f..7d65ceb 100755 (executable)
--- 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.\r
    */\r
   ext.vamsas.MuscleWS server;\r
+  AlignFrame alignFrame;\r
 \r
 \r
   /**\r
@@ -56,10 +57,14 @@ public class MsaWSClient
    * @param preserveOrder DOCUMENT ME!\r
    */\r
 \r
-  public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle, SequenceI[] msa,\r
-                     boolean submitGaps, boolean preserveOrder, Alignment seqdataset)\r
+  public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle,\r
+                     SequenceI[] msa,\r
+                     boolean submitGaps, boolean preserveOrder,\r
+                     Alignment seqdataset,\r
+                     AlignFrame _alignFrame)\r
   {\r
 \r
+    alignFrame = _alignFrame;\r
     if (!sh.getAbstractName().equals("MsaWS"))\r
     {\r
       JOptionPane.showMessageDialog(Desktop.desktop,\r
@@ -474,6 +479,10 @@ public class MsaWSClient
           }\r
           // TODO: JBPNote Should also rename the query sequence sometime...\r
           AlignFrame af = new AlignFrame(al);\r
+\r
+          //>>>This is a fix for the moment, until a better solution is found!!<<<\r
+          af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());\r
+\r
           af.addSortByOrderMenuItem(ServiceName + " Ordering",\r
                                     msaorder);\r
 \r