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.PreferredServiceRegistry;
   7
   8 import java.beans.PropertyChangeSupport;
   9 import java.io.IOError;
  10 import java.io.IOException;
  11 import java.net.URISyntaxException;
  12 import java.util.ArrayList;
  13 import java.util.List;
  14
  15 import javax.swing.JMenu;
  16
  17 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  18 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  19
  20 public class SlivkaWSDiscoverer implements Runnable, WSMenuEntryProviderI
  21 {
  22   private static SlivkaWSDiscoverer instance = null;
  23
  24   private SlivkaClient slivkaClient;
  25
  26   private SlivkaWSDiscoverer()
  27   {
  28     try
  29     {
  30       slivkaClient = new SlivkaClient("localhost", 4954);
  31     } catch (URISyntaxException e)
  32     {
  33       throw new RuntimeException(e);
  34     }
  35   }
  36
  37   public static SlivkaWSDiscoverer getInstance()
  38   {
  39     if (instance == null)
  40     {
  41       instance = new SlivkaWSDiscoverer();
  42     }
  43     return instance;
  44   }
  45
  46   List<ServiceWithParameters> getServiceInstances()
  47   {
  48     List<ServiceWithParameters> instances = new ArrayList<>();
  49     for (SlivkaService service : services)
  50     {
  51       for (String classifier : service.classifiers)
  52       {
  53         if (classifier.contains("Multiple sequence alignment"))
  54         {
  55           instances
  56                   .add(new SlivkaMsaServiceInstance(slivkaClient, service));
  57         }
  58         else if (classifier.contains("Protein sequence analysis"))
  59         {
  60           instances.add(new SlivkaAnnotationServiceInstance(slivkaClient,
  61                   service, false));
  62         }
  63         else if (classifier
  64                 .contains("Sequence alignment analysis (conservation)"))
  65         {
  66           instances.add(new SlivkaAnnotationServiceInstance(slivkaClient,
  67                   service, true));
  68         }
  69
  70       }
  71     }
  72     return instances;
  73   }
  74
  75   private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
  76           this);
  77
  78   @Override
  79   public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
  80   {
  81     JMenu slivkaMenu = new JMenu("Slivka");
  82     wsmenu.add(slivkaMenu);
  83
  84     JMenu alignmentMenu = new JMenu("Sequence Alignment");
  85     slivkaMenu.add(alignmentMenu);
  86     JMenu disorderMenu = new JMenu("Protein sequence analysis");
  87     slivkaMenu.add(disorderMenu);
  88     JMenu conservationMenu = new JMenu("Conservation");
  89     slivkaMenu.add(conservationMenu);
  90     PreferredServiceRegistry.getRegistry().populateWSMenuEntry(
  91             getServiceInstances(),
  92               changeSupport, slivkaMenu, alignFrame, null);
  93
  94   }
  95
  96   List<SlivkaService>services=null;
  97
  98   volatile boolean started = false, finished = false;
  99
 100   Thread discoverer = null;
 101   @Override
 102   public void run()
 103   {
 104     discoverer = Thread.currentThread();
 105     started = true;
 106     try
 107     {
 108       services = slivkaClient.getServices();
 109     } catch (IOException e)
 110     {
 111       throw new IOError(e);
 112     }
 113     finished = true;
 114   }
 115
 116   public static List<ServiceWithParameters> getServices()
 117   {
 118     SlivkaWSDiscoverer us = getInstance();
 119     if (us.services == null)
 120     {
 121       us.run();
 122     }
 123     return us.getServiceInstances();
 124   }
 125
 126   public boolean hasServices()
 127   {
 128     return finished == true && services != null && services.size() > 0;
 129   }
 130
 131   public boolean isRunning()
 132   {
 133     return discoverer != null && discoverer.isAlive();
 134   }
 135 }