JAL-3070 reinstate the internal test service URL for Slivka-bio

[jalview.git] / src / jalview / ws / slivkaws / SlivkaWSDiscoverer.java

diff --git a/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java b/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
index dfa3d89..7720b11 100644 (file)
--- a/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
+++ b/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
@@ -1,89 +1,136 @@
 package jalview.ws.slivkaws;
 
-import jalview.datamodel.AlignmentView;
 import jalview.gui.AlignFrame;
 import jalview.ws.WSMenuEntryProviderI;
-import jalview.ws.jws2.MsaWSClient;
+import jalview.ws.api.ServiceWithParameters;
+import jalview.ws.jws2.PreferredServiceRegistry;
 
-import java.awt.event.ActionEvent;
+import java.beans.PropertyChangeSupport;
+import java.io.IOError;
 import java.io.IOException;
 import java.net.URISyntaxException;
+import java.util.ArrayList;
+import java.util.List;
 
 import javax.swing.JMenu;
-import javax.swing.JMenuItem;
 
 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
+import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
 
-public class SlivkaWSDiscoverer
-  implements Runnable, WSMenuEntryProviderI
+public class SlivkaWSDiscoverer implements Runnable, WSMenuEntryProviderI
 {
   private static SlivkaWSDiscoverer instance = null;
-  private SlivkaClient client;
-  private ClustaloWS clustalo;
 
-  private SlivkaWSDiscoverer() {
+  private SlivkaClient slivkaClient;
+
+  private SlivkaWSDiscoverer()
+  {
     try
     {
-      client = new SlivkaClient("gjb-www-1.cluster.lifesci.dundee.ac.uk", 3203);
+      slivkaClient = new SlivkaClient(
+              "gjb-www-1.cluster.lifesci.dundee.ac.uk", 3203);
     } catch (URISyntaxException e)
     {
       throw new RuntimeException(e);
     }
-    clustalo = new ClustaloWS(client);
   }
 
   public static SlivkaWSDiscoverer getInstance()
   {
-    if (instance == null) {
-               instance = new SlivkaWSDiscoverer();
-       }
+    if (instance == null)
+    {
+      instance = new SlivkaWSDiscoverer();
+    }
     return instance;
   }
 
-  @Override
-  public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
+  List<ServiceWithParameters> getServiceInstances()
   {
-    JMenu submenu = new JMenu("Slivka");
-
-    JMenuItem noParamMenuItem = new JMenuItem("ClustalO with defaults");
-    noParamMenuItem.addActionListener((ActionEvent e) -> {
-      AlignmentView msa = alignFrame.gatherSequencesForAlignment();
-      if (msa != null)
-      {
-        new MsaWSClient(
-            clustalo, alignFrame.getTitle(), msa, false, true,
-            alignFrame.getViewport().getAlignment().getDataset(),
-            alignFrame);
-      }
-    });
-    submenu.add(noParamMenuItem);
-
-    JMenuItem parametrisedMenuItem = new JMenuItem("ClustalO with custom parameters");
-    parametrisedMenuItem.addActionListener((ActionEvent evt) -> {
-      AlignmentView msa = alignFrame.gatherSequencesForAlignment();
-      if (msa != null)
+    List<ServiceWithParameters> instances = new ArrayList<>();
+    for (SlivkaService service : services)
+    {
+      for (String classifier : service.classifiers)
       {
-        try
+        if (classifier.contains("Multiple sequence alignment"))
         {
-          SlivkaParamSet paramSet = new SlivkaParamSet(clustalo.getService());
-          new MsaWSClient(
-              clustalo, paramSet, null, true, alignFrame.getTitle(), msa, false, true,
-              alignFrame.getViewport().getAlignment().getDataset(), alignFrame
-          );
-        } catch (IOException e)
+          instances
+                  .add(new SlivkaMsaServiceInstance(slivkaClient, service));
+        }
+        else if (classifier.contains("Protein sequence analysis"))
         {
-          e.printStackTrace();
+          instances.add(new SlivkaAnnotationServiceInstance(slivkaClient,
+                  service, false));
         }
+        else if (classifier
+                .contains("Sequence alignment analysis (conservation)"))
+        {
+          instances.add(new SlivkaAnnotationServiceInstance(slivkaClient,
+                  service, true));
+        }
+
       }
-    });
-    submenu.add(parametrisedMenuItem);
+    }
+    return instances;
+  }
+
+  private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
+          this);
+
+  @Override
+  public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
+  {
+    JMenu slivkaMenu = new JMenu("Slivka");
+    wsmenu.add(slivkaMenu);
 
-    wsmenu.add(submenu);
+    JMenu alignmentMenu = new JMenu("Sequence Alignment");
+    slivkaMenu.add(alignmentMenu);
+    JMenu disorderMenu = new JMenu("Protein sequence analysis");
+    slivkaMenu.add(disorderMenu);
+    JMenu conservationMenu = new JMenu("Conservation");
+    slivkaMenu.add(conservationMenu);
+    PreferredServiceRegistry.getRegistry().populateWSMenuEntry(
+            getServiceInstances(),
+              changeSupport, slivkaMenu, alignFrame, null);
+    
   }
 
+  List<SlivkaService>services=null;
+
+  volatile boolean started = false, finished = false;
+
+  Thread discoverer = null;
   @Override
   public void run()
   {
+    discoverer = Thread.currentThread();
+    started = true;
+    try
+    {
+      services = slivkaClient.getServices();
+    } catch (IOException e)
+    {
+      throw new IOError(e);
+    }
+    finished = true;
+  }
 
+  public static List<ServiceWithParameters> getServices()
+  {
+    SlivkaWSDiscoverer us = getInstance();
+    if (us.services == null)
+    {
+      us.run();
+    }
+    return us.getServiceInstances();
+  }
+
+  public boolean hasServices()
+  {
+    return finished == true && services != null && services.size() > 0;
+  }
+
+  public boolean isRunning()
+  {
+    return discoverer != null && discoverer.isAlive();
   }
 }