Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

[jalview.git] / src / jalview / ws / jws2 / MsaWSClient.java

diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java
index 23c6949..130dd12 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSClient.java
+++ b/src/jalview/ws/jws2/MsaWSClient.java
@@ -27,7 +27,12 @@ import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
 import jalview.gui.JvSwingUtils;
 import jalview.util.MessageManager;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
+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.params.ArgumentI;
 import jalview.ws.params.WsParamSetI;
 
 import java.awt.event.ActionEvent;
@@ -40,23 +45,28 @@ import javax.swing.JMenu;
 import javax.swing.JMenuItem;
 import javax.swing.ToolTipManager;
 
-import compbio.data.msa.MsaWS;
-import compbio.metadata.Argument;
-
 /**
- * DOCUMENT ME!
+ * MsaWSClient
+ * 
+ * Instantiates web service menu items for multiple alignment services, and
+ * holds logic for constructing a web service thread.
  * 
- * @author $author$
+ * 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 WSDL2Java generated stub for an archetypal MsaWSI service.
+   * server is a proxy class implementing the core methods for submitting,
+   * monitoring and retrieving results from a multiple sequence alignment
+   * service
    */
-  MsaWS server;
+  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)
@@ -66,7 +76,8 @@ 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)
@@ -92,8 +103,8 @@ public class MsaWSClient extends Jws2Client
    *          DOCUMENT ME!
    */
 
-  public MsaWSClient(Jws2Instance sh, WsParamSetI preset,
-          List<Argument> arguments, boolean editParams, String altitle,
+  public MsaWSClient(ServiceWithParameters sh, WsParamSetI preset,
+          List<ArgumentI> arguments, boolean editParams, String altitle,
           jalview.datamodel.AlignmentView msa, boolean submitGaps,
           boolean preserveOrder, AlignmentI seqdataset,
           AlignFrame _alignFrame)
@@ -104,25 +115,29 @@ public class MsaWSClient extends Jws2Client
       return;
     }
 
-    if (!(sh.service instanceof MsaWS))
+    if (!(sh instanceof JalviewServiceEndpointProviderI
+            && ((JalviewServiceEndpointProviderI) sh)
+                    .getEndpoint() instanceof MultipleSequenceAlignmentI))
     {
       // redundant at mo - but may change
       JvOptionPane.showMessageDialog(Desktop.desktop,
               MessageManager.formatMessage(
                       "label.service_called_is_not_msa_service",
                       new String[]
-                      { sh.serviceType }),
+                      { sh.getName() }),
               MessageManager.getString("label.internal_jalview_error"),
               JvOptionPane.WARNING_MESSAGE);
 
       return;
     }
-    server = (MsaWS) sh.service;
+    serviceHandle = sh;
+    server = (MultipleSequenceAlignmentI) ((JalviewServiceEndpointProviderI) sh)
+            .getEndpoint();
     if ((wsInfo = setWebService(sh, false)) == null)
     {
       JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
               .formatMessage("label.msa_service_is_unknown", new String[]
-              { sh.serviceType }),
+              { sh.getName() }),
               MessageManager.getString("label.internal_jalview_error"),
               JvOptionPane.WARNING_MESSAGE);
 
@@ -214,16 +229,28 @@ public class MsaWSClient extends Jws2Client
 
   @Override
   public void attachWSMenuEntry(JMenu rmsawsmenu,
-          final Jws2Instance service, final AlignFrame alignFrame)
+          final ServiceWithParameters service, final AlignFrame alignFrame)
   {
-    if (registerAAConWSInstance(rmsawsmenu, service, alignFrame))
+    if (Jws2ClientFactory.registerAAConWSInstance(rmsawsmenu,
+                    service, alignFrame))
     {
       // 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"))
     {
@@ -236,7 +263,8 @@ 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 ";