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(
  31               "gjb-www-1.cluster.lifesci.dundee.ac.uk", 3203);
  32     } catch (URISyntaxException e)
  33     {
  34       throw new RuntimeException(e);
  35     }
  36   }
  37
  38   public static SlivkaWSDiscoverer getInstance()
  39   {
  40     if (instance == null)
  41     {
  42       instance = new SlivkaWSDiscoverer();
  43     }
  44     return instance;
  45   }
  46
  47   /**
  48    * TODO: tests needed for logic for determining type of each discovered
  49    * service. Then reimplement this routine !
  50    *
  51    * @return (MSA instances, one AAUI type instance, and the remaining all
  52    *         sequence analysis instances taking 1 sequence only)
  53    */
  54   List<ServiceWithParameters> getServiceInstances()
  55   {
  56     List<ServiceWithParameters> instances = new ArrayList<>();
  57     for (SlivkaService service : services)
  58     {
  59       ServiceWithParameters newinstance = null;
  60       for (String classifier : service.classifiers)
  61       {
  62         if (classifier.contains("Multiple sequence alignment"))
  63         {
  64           // MSA services always overwrite
  65           newinstance = new SlivkaMsaServiceInstance(slivkaClient, service);
  66         }
  67         if (classifier.contains("Protein sequence analysis"))
  68         {
  69           if (newinstance == null)
  70             {
  71               newinstance = (new SlivkaAnnotationServiceInstance(
  72                       slivkaClient,
  73
  74                       service, false));
  75             }
  76           }
  77
  78         if (classifier
  79                 .contains("Sequence alignment analysis (conservation)"))
  80         {
  81           // always overwrite other instances
  82           newinstance = new SlivkaAnnotationServiceInstance(slivkaClient,
  83                   service, true);
  84         }
  85       }
  86       if (newinstance != null)
  87       {
  88         instances.add(newinstance);
  89       }
  90     }
  91     return instances;
  92   }
  93
  94   private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
  95           this);
  96
  97   @Override
  98   public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
  99   {
 100     JMenu slivkaMenu = new JMenu("Slivka");
 101     wsmenu.add(slivkaMenu);
 102
 103     JMenu alignmentMenu = new JMenu("Sequence Alignment");
 104     slivkaMenu.add(alignmentMenu);
 105     JMenu disorderMenu = new JMenu("Protein sequence analysis");
 106     slivkaMenu.add(disorderMenu);
 107     JMenu conservationMenu = new JMenu("Conservation");
 108     slivkaMenu.add(conservationMenu);
 109     PreferredServiceRegistry.getRegistry().populateWSMenuEntry(
 110             getServiceInstances(),
 111               changeSupport, slivkaMenu, alignFrame, null);
 112
 113   }
 114
 115   List<SlivkaService>services=null;
 116
 117   volatile boolean started = false, finished = false;
 118
 119   Thread discoverer = null;
 120   @Override
 121   public void run()
 122   {
 123     discoverer = Thread.currentThread();
 124     started = true;
 125     try
 126     {
 127       services = slivkaClient.getServices();
 128     } catch (IOException e)
 129     {
 130       throw new IOError(e);
 131     }
 132     finished = true;
 133   }
 134
 135   public static List<ServiceWithParameters> getServices()
 136   {
 137     SlivkaWSDiscoverer us = getInstance();
 138     if (us.services == null)
 139     {
 140       us.run();
 141     }
 142     return us.getServiceInstances();
 143   }
 144
 145   public boolean hasServices()
 146   {
 147     return finished == true && services != null && services.size() > 0;
 148   }
 149
 150   public boolean isRunning()
 151   {
 152     return discoverer != null && discoverer.isAlive();
 153   }
 154 }