From 2d552096087f757e4a3fcb4df97cf549b2ff8155 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 3 Aug 2018 15:15:02 +0100
Subject: [PATCH] =?utf8?q?JAL-3070=20MsaWSClient=20doens=E2=80=99t=20depend=20?=
 =?utf8?q?on=20Jws2Instance=20-=20now=20need=20to=20remove=20dependency=20on?=
 =?utf8?q?=20Jws2Client=20!?=
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---
 src/jalview/ws/jws2/MsaWSClient.java |   45 ++++++++++++++++++++++++++--------
 1 file changed, 35 insertions(+), 10 deletions(-)

diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java
index a545d5d..7a3d9d3 100644
--- a/src/jalview/ws/jws2/MsaWSClient.java
+++ b/src/jalview/ws/jws2/MsaWSClient.java
@@ -27,7 +27,10 @@ import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
 import jalview.gui.JvSwingUtils;
 import jalview.util.MessageManager;
+import jalview.ws.WSMenuEntryProviderI;
+import jalview.ws.api.JalviewServiceEndpointProviderI;
 import jalview.ws.api.MultipleSequenceAlignmentI;
+import jalview.ws.api.ServiceWithParameters;
 import jalview.ws.gui.MsaWSThread;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.ArgumentI;
@@ -44,12 +47,18 @@ import javax.swing.JMenuItem;
 import javax.swing.ToolTipManager;
 
 /**
- * DOCUMENT ME!
+ * MsaWSClient
  * 
- * @author $author$
+ * Instantiates web service menu items for multiple alignment services, and
+ * holds logic for constructing a web service thread.
+ * 
+ * TODO remove dependency on Jws2Client methods for creating AACon service UI
+ * elements.
+ * 
+ * @author Jim Procter et al
  * @version $Revision$
  */
-public class MsaWSClient extends Jws2Client
+public class MsaWSClient extends Jws2Client implements WSMenuEntryProviderI
 {
   /**
    * server is a proxy class implementing the core methods for submitting,
@@ -58,7 +67,7 @@ public class MsaWSClient extends Jws2Client
    */
   MultipleSequenceAlignmentI server;
 
-  public MsaWSClient(Jws2Instance sh, String altitle,
+  public MsaWSClient(ServiceWithParameters sh, String altitle,
           jalview.datamodel.AlignmentView msa, boolean submitGaps,
           boolean preserveOrder, AlignmentI seqdataset,
           AlignFrame _alignFrame)
@@ -68,7 +77,8 @@ public class MsaWSClient extends Jws2Client
     // TODO Auto-generated constructor stub
   }
 
-  public MsaWSClient(Jws2Instance sh, WsParamSetI preset, String altitle,
+  public MsaWSClient(ServiceWithParameters sh, WsParamSetI preset,
+          String altitle,
           jalview.datamodel.AlignmentView msa, boolean submitGaps,
           boolean preserveOrder, AlignmentI seqdataset,
           AlignFrame _alignFrame)
@@ -94,7 +104,7 @@ public class MsaWSClient extends Jws2Client
    *          DOCUMENT ME!
    */
 
-  public MsaWSClient(Jws2Instance sh, WsParamSetI preset,
+  public MsaWSClient(ServiceWithParameters sh, WsParamSetI preset,
           List<ArgumentI> arguments, boolean editParams, String altitle,
           jalview.datamodel.AlignmentView msa, boolean submitGaps,
           boolean preserveOrder, AlignmentI seqdataset,
@@ -106,7 +116,9 @@ public class MsaWSClient extends Jws2Client
       return;
     }
 
-    if (!(sh.getEndpoint() instanceof MultipleSequenceAlignmentI))
+    if (!(sh instanceof JalviewServiceEndpointProviderI
+            && ((JalviewServiceEndpointProviderI) sh)
+                    .getEndpoint() instanceof MultipleSequenceAlignmentI))
     {
       // redundant at mo - but may change
       JvOptionPane.showMessageDialog(Desktop.desktop,
@@ -120,7 +132,8 @@ public class MsaWSClient extends Jws2Client
       return;
     }
     serviceHandle = sh;
-    server = (MultipleSequenceAlignmentI) sh.getEndpoint();
+    server = (MultipleSequenceAlignmentI) ((JalviewServiceEndpointProviderI) sh)
+            .getEndpoint();
     if ((wsInfo = setWebService(sh, false)) == null)
     {
       JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
@@ -229,9 +242,20 @@ public class MsaWSClient extends Jws2Client
       // Alignment dependent analysis calculation WS gui
       return;
     }
+    serviceHandle = service;
     setWebService(service, true); // headless
+    attachWSMenuEntry(rmsawsmenu, alignFrame);
+  }
+
+  @Override
+  public void attachWSMenuEntry(JMenu wsmenu, AlignFrame alignFrame)
+  {
     boolean finished = true, submitGaps = false;
-    JMenu msawsmenu = rmsawsmenu;
+    /**
+     * temp variables holding msa service submenu or root service menu
+     */
+    JMenu msawsmenu = wsmenu;
+    JMenu rmsawsmenu = wsmenu;
     String svcname = WebServiceName;
     if (svcname.endsWith("WS"))
     {
@@ -244,7 +268,8 @@ public class MsaWSClient extends Jws2Client
       rmsawsmenu.add(msawsmenu);
       calcName = "";
     }
-    boolean hasparams = service.hasParameters();
+    boolean hasparams = serviceHandle.hasParameters();
+    ServiceWithParameters service = (ServiceWithParameters) serviceHandle;
     do
     {
       String action = "Align ";
-- 
1.7.10.2