src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java

   1 package jalview.ws.slivkaws;
   2
   3 import jalview.gui.AlignFrame;
   4 import jalview.ws.WSMenuEntryProviderI;
   5 import jalview.ws.api.ServiceWithParameters;
   6 import jalview.ws.jws2.MsaWSClient;
   7 import jalview.ws.jws2.PreferredServiceRegistry;
   8 import jalview.ws.jws2.SequenceAnnotationWSClient;
   9
  10 import java.beans.PropertyChangeSupport;
  11 import java.io.IOError;
  12 import java.io.IOException;
  13 import java.net.URISyntaxException;
  14 import java.util.ArrayList;
  15 import java.util.List;
  16
  17 import javax.swing.JMenu;
  18
  19 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  20 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  21
  22 public class SlivkaWSDiscoverer implements Runnable, WSMenuEntryProviderI
  23 {
  24   private static SlivkaWSDiscoverer instance = null;
  25
  26   private SlivkaClient slivkaClient;
  27
  28   private SlivkaWSDiscoverer()
  29   {
  30     try
  31     {
  32       slivkaClient = new SlivkaClient("localhost", 4954);
  33     } catch (URISyntaxException e)
  34     {
  35       throw new RuntimeException(e);
  36     }
  37   }
  38
  39   public static SlivkaWSDiscoverer getInstance()
  40   {
  41     if (instance == null)
  42     {
  43       instance = new SlivkaWSDiscoverer();
  44     }
  45     return instance;
  46   }
  47
  48   private void addMsaServiceClient(JMenu alignmentMenu,
  49           SlivkaService service, AlignFrame alignFrame)
  50   {
  51     SlivkaMsaServiceInstance instance = new SlivkaMsaServiceInstance(
  52             slivkaClient, service);
  53     MsaWSClient client = new MsaWSClient();
  54     client.attachWSMenuEntry(alignmentMenu, instance, alignFrame);
  55     alignmentMenu.addSeparator();
  56   }
  57
  58   private void addDisorderServiceClient(JMenu disorderMenu,
  59           SlivkaService service, AlignFrame alignFrame)
  60   {
  61     SlivkaAnnotationServiceInstance serviceInstance = new SlivkaAnnotationServiceInstance(
  62             slivkaClient, service, false);
  63
  64     SequenceAnnotationWSClient client = new SequenceAnnotationWSClient();
  65     client.attachWSMenuEntry(disorderMenu, serviceInstance, alignFrame);
  66     disorderMenu.addSeparator();
  67   }
  68
  69   private void addConservationServiceClient(JMenu conservationMenu,
  70           SlivkaService service, AlignFrame alignFrame)
  71   {
  72     SlivkaAnnotationServiceInstance serviceInstance = new SlivkaAnnotationServiceInstance(
  73             slivkaClient, service, true);
  74     SequenceAnnotationWSClient client = new SequenceAnnotationWSClient();
  75     client.attachWSMenuEntry(conservationMenu, serviceInstance, alignFrame);
  76     conservationMenu.addSeparator();
  77   }
  78
  79   private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
  80           this);
  81
  82   @Override
  83   public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
  84   {
  85     JMenu slivkaMenu = new JMenu("Slivka");
  86     wsmenu.add(slivkaMenu);
  87
  88     JMenu alignmentMenu = new JMenu("Sequence Alignment");
  89     slivkaMenu.add(alignmentMenu);
  90     JMenu disorderMenu = new JMenu("Protein sequence analysis");
  91     slivkaMenu.add(disorderMenu);
  92     JMenu conservationMenu = new JMenu("Conservation");
  93     slivkaMenu.add(conservationMenu);
  94     try
  95     {
  96       List<ServiceWithParameters> instances = new ArrayList<>();
  97       for (SlivkaService service : slivkaClient.getServices())
  98       {
  99         for (String classifier : service.classifiers)
 100         {
 101           if (classifier.contains("Multiple sequence alignment"))
 102           {
 103             instances.add(
 104                     new SlivkaMsaServiceInstance(slivkaClient, service));
 105             // addMsaServiceClient(alignmentMenu, service, alignFrame);
 106           }
 107           else if (classifier.contains("Protein sequence analysis"))
 108           {
 109             instances.add(new SlivkaAnnotationServiceInstance(slivkaClient,
 110                     service, false));
 111             // addDisorderServiceClient(disorderMenu, service, alignFrame);
 112           }
 113           else if (classifier
 114                   .contains("Sequence alignment analysis (conservation)"))
 115           {
 116             instances.add(new SlivkaAnnotationServiceInstance(slivkaClient,
 117                     service, true));
 118             // addConservationServiceClient(conservationMenu, service,
 119             // alignFrame);
 120           }
 121
 122         }
 123       }
 124       PreferredServiceRegistry.getRegistry().populateWSMenuEntry(instances,
 125               changeSupport, slivkaMenu, alignFrame, null);
 126     } catch (IOException e)
 127     {
 128       throw new IOError(e);
 129     }
 130   }
 131
 132   @Override
 133   public void run()
 134   {
 135
 136   }
 137 }