JAL-3066 hack to instantiate the correct client according to slivka service annotatio...

[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 b799c5a..f8ac60f 100644 (file)
--- a/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
+++ b/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
@@ -1,77 +1,154 @@
 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)
+  /**
+   * TODO: tests needed for logic for determining type of each discovered
+   * service. Then reimplement this routine !
+   * 
+   * @return (MSA instances, one AAUI type instance, and the remaining all
+   *         sequence analysis instances taking 1 sequence only)
+   */
+  List<ServiceWithParameters> getServiceInstances()
   {
-    JMenu submenu = new JMenu("Slivka");
-    JMenuItem menuItem = new JMenuItem("ClustalO with defaults");
-    menuItem.addActionListener((ActionEvent e) -> {
+    List<ServiceWithParameters> instances = new ArrayList<>();
+    for (SlivkaService service : services)
+    {
+      ServiceWithParameters newinstance = null;
+      for (String classifier : service.classifiers)
+      {
+        if (classifier.contains("Multiple sequence alignment"))
+        {
+          // MSA services always overwrite
+          newinstance = new SlivkaMsaServiceInstance(slivkaClient, service);
+        }
+        if (classifier.contains("Protein sequence analysis"))
+        {
+          if (newinstance == null)
+            {
+              newinstance = (new SlivkaAnnotationServiceInstance(
+                      slivkaClient,
 
-      AlignmentView msa = alignFrame.gatherSequencesForAlignment();
+                      service, false));
+            }
+          }
 
-      if (msa != null)
+        if (classifier
+                .contains("Sequence alignment analysis (conservation)"))
+        {
+          // always overwrite other instances
+          newinstance = new SlivkaAnnotationServiceInstance(slivkaClient,
+                  service, true);
+        }
+      }
+      if (newinstance != null)
       {
-        new MsaWSClient(clustalo, alignFrame.getTitle(), msa, false,
-            true,
-            alignFrame.getViewport().getAlignment().getDataset(),
-            alignFrame);
+        instances.add(newinstance);
       }
-//
-//      List<SequenceI> sequences = alignFrame.getViewport().getAlignment().getSequences();
-//      try
-//      {
-//        clustalo.align(sequences, null, null);
-//      } catch (FormValidationException | IOException exc)
-//      {
-//        throw new RuntimeException(exc);
-//      }
-    });
-    submenu.add(menuItem);
-    wsmenu.add(submenu);
+    }
+    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);
+
+    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();
   }
 }