X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2Fjabaws2%2FJws2Instance.java;h=36a42ab5309899f558cefdb3e6153338d13d45d6;hb=7b9f93ca2c7f5e5d9347f00be309522f76e3e778;hp=3bff20bbef5a05f132fbccf47fd2e9aa136a57f3;hpb=1da7e0f4efb175c55ded1b68e14bc4a9f955ec29;p=jalview.git

diff --git a/src/jalview/ws/jws2/jabaws2/Jws2Instance.java b/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
index 3bff20b..36a42ab 100644
--- a/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
+++ b/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
@@ -20,19 +20,16 @@
  */
 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 javax.swing.JMenu;
+import java.net.URL;
 
 import compbio.data.msa.JABAService;
 import compbio.data.msa.MsaWS;
@@ -41,12 +38,11 @@ import compbio.metadata.PresetManager;
 import compbio.metadata.RunnerConfig;
 
 public class Jws2Instance extends ServiceWithParameters
+        implements AutoCloseable
 {
 
   public JABAService service;
 
-  public String docUrl;
-
   /**
    * 
    * @param hosturl
@@ -66,14 +62,38 @@ 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)
     {
-      docUrl = description.substring(description.indexOf("http", p)).trim();
+      String docUrl = description.substring(description.indexOf("http", p))
+              .trim();
       if (docUrl.indexOf('\n') > -1)
       {
         docUrl = docUrl.substring(0, docUrl.indexOf("\n")).trim();
       }
+      if (docUrl.length() > 0)
+      {
+        try
+        {
+          URL url = new URL(docUrl);
+          if (url != null)
+          {
+            setDocumentationUrl(docUrl);
+          }
+        } catch (Exception x)
+        {
+
+        }
+      }
 
     }
   }
@@ -135,7 +155,7 @@ public class Jws2Instance extends ServiceWithParameters
   }
 
   @Override
-  protected void finalize() throws Throwable
+  public void close()
   {
     if (service != null)
     {
@@ -147,7 +167,7 @@ public class Jws2Instance extends ServiceWithParameters
         // ignore
       }
     }
-    super.finalize();
+    // super.finalize();
   }
 
   @Override
@@ -158,7 +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)
       {
@@ -170,20 +190,9 @@ 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
   public boolean hasParameters()
   {
     if (!lookedForParams)
@@ -200,31 +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
    * 
@@ -239,4 +223,48 @@ public class Jws2Instance extends ServiceWithParameters
       paramStore = new JabaParamStore(this, userParameterStore);
     }
   }
+
+  /**
+   * an object that implements one or more interfaces in jalview.ws.api
+   * 
+   * @return
+   */
+  @Override
+  public Object getEndpoint()
+  {
+    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)
+      {
+        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;
+    }
+  }
 }