JAL-3807 JPred can now successfully submit and track the job.

[jalview.git] / src / jalview / ws / jws2 / jabaws2 / Jws2Instance.java

diff --git a/src/jalview/ws/jws2/jabaws2/Jws2Instance.java b/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
index 55799f0..36a42ab 100644 (file)
--- a/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
+++ b/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
@@ -20,22 +20,17 @@
  */
 package jalview.ws.jws2.jabaws2;
 
-import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.util.MessageManager;
 import jalview.ws.api.JalviewServiceEndpointProviderI;
 import jalview.ws.api.ServiceWithParameters;
 import jalview.ws.jws2.JabaParamStore;
-import jalview.ws.jws2.MsaWSClient;
-import jalview.ws.jws2.SequenceAnnotationWSClient;
 import jalview.ws.params.ParamDatastoreI;
 import jalview.ws.params.ParamManager;
 
 import java.io.Closeable;
 import java.net.URL;
 
-import javax.swing.JMenu;
-
 import compbio.data.msa.JABAService;
 import compbio.data.msa.MsaWS;
 import compbio.data.msa.SequenceAnnotation;
@@ -43,7 +38,7 @@ import compbio.metadata.PresetManager;
 import compbio.metadata.RunnerConfig;
 
 public class Jws2Instance extends ServiceWithParameters
-        implements JalviewServiceEndpointProviderI, AutoCloseable
+        implements AutoCloseable
 {
 
   public JABAService service;
@@ -67,6 +62,15 @@ public class Jws2Instance extends ServiceWithParameters
   {
     super(action, action, serviceType, description, hosturl);
     this.service = service;
+    if (service instanceof MsaWS<?>)
+    {
+      style = ServiceClient.MSAWSCLIENT;
+    }
+    else if (service instanceof SequenceAnnotation<?>)
+    {
+      style = ServiceClient.SEQUENCEANNOTATIONWSCLIENT;
+    }
+
     int p = description.indexOf("MORE INFORMATION:");
     if (p > -1)
     {
@@ -174,7 +178,7 @@ public class Jws2Instance extends ServiceWithParameters
       try
       {
         paramStore = new JabaParamStore(this,
-                (Desktop.instance != null ? Desktop.getUserParameterStore()
+                (Desktop.getInstance() != null ? Desktop.getUserParameterStore()
                         : null));
       } catch (Exception ex)
       {
@@ -186,18 +190,6 @@ public class Jws2Instance extends ServiceWithParameters
     return paramStore;
   }
 
-  public String getUri()
-  {
-    // TODO verify that service parameter sets in projects are consistent with
-    // Jalview 2.10.4
-    // this is only valid for Jaba 1.0 - this formula might have to change!
-    return getHostURL()
-            + (getHostURL().lastIndexOf("/") == (getHostURL().length() - 1)
-                    ? ""
-                    : "/")
-            + getName();
-  }
-
   private boolean hasParams = false, lookedForParams = false;
 
   @Override
@@ -217,31 +209,6 @@ public class Jws2Instance extends ServiceWithParameters
     return hasParams;
   }
 
-  public void attachWSMenuEntry(JMenu atpoint, AlignFrame alignFrame)
-  {
-    if (service instanceof MsaWS<?>)
-    {
-      new MsaWSClient().attachWSMenuEntry(atpoint, this, alignFrame);
-    }
-    else if (service instanceof SequenceAnnotation<?>)
-    {
-      new SequenceAnnotationWSClient().attachWSMenuEntry(atpoint, this,
-              alignFrame);
-    }
-  }
-
-  public String getNameURI()
-  {
-    return "java:" + getName();
-  }
-
-  jalview.ws.uimodel.AlignAnalysisUIText aaui;
-
-  public jalview.ws.uimodel.AlignAnalysisUIText getAlignAnalysisUI()
-  {
-    return aaui;
-  }
-
   /**
    * initialise a parameter store for this service
    * 
@@ -265,18 +232,39 @@ public class Jws2Instance extends ServiceWithParameters
   @Override
   public Object getEndpoint()
   {
-    if (aaui!=null) {
-      // TODO complete
-      return null;
-    } else {
-      if (service instanceof MsaWS<?>)
+    if (service instanceof MsaWS<?>)
+    {
+      if (aaui != null)
+      {
+        throw new Error(
+                "JABAWS MsaWS based instant calculation not implemented.");
+
+      }
+      else
+      {
+        return new JabawsMsaInstance(this);
+      }
+    }
+    else
+    {
+      if (service instanceof compbio.data.msa.SequenceAnnotation)
       {
-      return new JabawsMsaInstance(this);
-    } else {
-        // TODO complete
-        // service is for sequence analysis
-        return null;
+        if (aaui != null)
+        {
+          try
+          {
+            // probably a factory would be nicer but..
+            return aaui.getClient().getConstructor(getClass())
+                    .newInstance(this);
+          } catch (Throwable t)
+          {
+            throw new Error("Implementation Error in web service framework",
+                    t);
+          }
+        }
+        return new AADisorderClient(this);
+      }
+      return null;
     }
   }
 }
-}