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("https://www.compbio.dundee.ac.uk/slivka");
  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   /**
  47    * TODO: tests needed for logic for determining type of each discovered
  48    * service. Then reimplement this routine !
  49    *
  50    * @return (MSA instances, one AAUI type instance, and the remaining all
  51    *         sequence analysis instances taking 1 sequence only)
  52    */
  53   List<ServiceWithParameters> getServiceInstances()
  54   {
  55     List<ServiceWithParameters> instances = new ArrayList<>();
  56     for (SlivkaService service : services)
  57     {
  58       ServiceWithParameters newinstance = null;
  59       for (String classifier : service.classifiers)
  60       {
  61         if (classifier.contains("Multiple sequence alignment"))
  62         {
  63           // MSA services always overwrite
  64           newinstance = new SlivkaMsaServiceInstance(slivkaClient, service);
  65         }
  66         if (classifier.contains("Protein sequence analysis"))
  67         {
  68           if (newinstance == null)
  69             {
  70               newinstance = (new SlivkaAnnotationServiceInstance(
  71                       slivkaClient,
  72
  73                       service, false));
  74             }
  75           }
  76
  77         if (classifier
  78                 .contains("Sequence alignment analysis (conservation)"))
  79         {
  80           // always overwrite other instances
  81           newinstance = new SlivkaAnnotationServiceInstance(slivkaClient,
  82                   service, true);
  83         }
  84       }
  85       if (newinstance != null)
  86       {
  87         instances.add(newinstance);
  88       }
  89     }
  90     return instances;
  91   }
  92
  93   private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
  94           this);
  95
  96   @Override
  97   public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
  98   {
  99     JMenu slivkaMenu = new JMenu("Slivka");
 100     wsmenu.add(slivkaMenu);
 101
 102     JMenu alignmentMenu = new JMenu("Sequence Alignment");
 103     slivkaMenu.add(alignmentMenu);
 104     JMenu disorderMenu = new JMenu("Protein sequence analysis");
 105     slivkaMenu.add(disorderMenu);
 106     JMenu conservationMenu = new JMenu("Conservation");
 107     slivkaMenu.add(conservationMenu);
 108     PreferredServiceRegistry.getRegistry().populateWSMenuEntry(
 109             getServiceInstances(),
 110               changeSupport, slivkaMenu, alignFrame, null);
 111
 112   }
 113
 114   List<SlivkaService>services=null;
 115
 116   volatile boolean started = false, finished = false;
 117
 118   Thread discoverer = null;
 119   @Override
 120   public void run()
 121   {
 122     discoverer = Thread.currentThread();
 123     started = true;
 124     try
 125     {
 126       services = slivkaClient.getServices();
 127     } catch (IOException e)
 128     {
 129       throw new IOError(e);
 130     }
 131     finished = true;
 132   }
 133
 134   public static List<ServiceWithParameters> getServices()
 135   {
 136     SlivkaWSDiscoverer us = getInstance();
 137     if (us.services == null)
 138     {
 139       us.run();
 140     }
 141     return us.getServiceInstances();
 142   }
 143
 144   public boolean hasServices()
 145   {
 146     return finished == true && services != null && services.size() > 0;
 147   }
 148
 149   public boolean isRunning()
 150   {
 151     return discoverer != null && discoverer.isAlive();
 152   }
 153 }