JAL-3066 JAL-3070 pull up non-jabaws specific service descriptor components for annot...

[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 143bc1c..9f2d4ae 100644 (file)
--- a/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
+++ b/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
@@ -32,6 +32,7 @@ import jalview.ws.params.ParamDatastoreI;
 import jalview.ws.params.ParamManager;
 
 import java.io.Closeable;
+import java.net.URL;
 
 import javax.swing.JMenu;
 
@@ -47,8 +48,6 @@ public class Jws2Instance extends ServiceWithParameters
 
   public JABAService service;
 
-  public String docUrl;
-
   /**
    * 
    * @param hosturl
@@ -71,11 +70,26 @@ public class Jws2Instance extends ServiceWithParameters
     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)
+        {
+
+        }
+      }
 
     }
   }
@@ -172,18 +186,6 @@ 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
@@ -216,18 +218,6 @@ public class Jws2Instance extends ServiceWithParameters
     }
   }
 
-  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
    * 
@@ -251,18 +241,39 @@ 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;
     }
   }
 }
-}