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.jws2.MsaWSClient;
   6 import jalview.ws.jws2.SequenceAnnotationWSClient;
   7
   8 import java.io.IOError;
   9 import java.io.IOException;
  10 import java.net.URISyntaxException;
  11
  12 import javax.swing.JMenu;
  13
  14 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  15 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  16
  17 public class SlivkaWSDiscoverer implements Runnable, WSMenuEntryProviderI
  18 {
  19   private static SlivkaWSDiscoverer instance = null;
  20
  21   private SlivkaClient slivkaClient;
  22
  23   private SlivkaWSDiscoverer()
  24   {
  25     try
  26     {
  27       slivkaClient = new SlivkaClient("gjb-www-1.cluster.lifesci.dundee.ac.uk", 3203);
  28     } catch (URISyntaxException e)
  29     {
  30       throw new RuntimeException(e);
  31     }
  32   }
  33
  34   public static SlivkaWSDiscoverer getInstance()
  35   {
  36     if (instance == null)
  37     {
  38       instance = new SlivkaWSDiscoverer();
  39     }
  40     return instance;
  41   }
  42
  43   private void addMsaServiceClient(JMenu alignmentMenu,
  44           SlivkaService service, AlignFrame alignFrame)
  45   {
  46     SlivkaMsaServiceInstance instance = new SlivkaMsaServiceInstance(
  47             slivkaClient, service);
  48     MsaWSClient client = new MsaWSClient();
  49     client.attachWSMenuEntry(alignmentMenu, instance, alignFrame);
  50     alignmentMenu.addSeparator();
  51   }
  52
  53   private void addDisorderServiceClient(JMenu disorderMenu,
  54           SlivkaService service, AlignFrame alignFrame)
  55   {
  56     SlivkaAnnotationServiceInstance serviceInstance = new SlivkaAnnotationServiceInstance(
  57             slivkaClient, service, false);
  58     SequenceAnnotationWSClient client = new SequenceAnnotationWSClient();
  59     client.attachWSMenuEntry(disorderMenu, serviceInstance, alignFrame);
  60     disorderMenu.addSeparator();
  61   }
  62
  63   private void addConservationServiceClient(JMenu conservationMenu,
  64           SlivkaService service, AlignFrame alignFrame)
  65   {
  66     SlivkaAnnotationServiceInstance serviceInstance = new SlivkaAnnotationServiceInstance(
  67             slivkaClient, service, true);
  68     SequenceAnnotationWSClient client = new SequenceAnnotationWSClient();
  69     client.attachWSMenuEntry(conservationMenu, serviceInstance, alignFrame);
  70     conservationMenu.addSeparator();
  71   }
  72
  73   @Override
  74   public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
  75   {
  76     JMenu slivkaMenu = new JMenu("Slivka");
  77     wsmenu.add(slivkaMenu);
  78
  79     JMenu alignmentMenu = new JMenu("Sequence Alignment");
  80     slivkaMenu.add(alignmentMenu);
  81     JMenu disorderMenu = new JMenu("Protein sequence analysis");
  82     slivkaMenu.add(disorderMenu);
  83     JMenu conservationMenu = new JMenu("Conservation");
  84     slivkaMenu.add(conservationMenu);
  85     try
  86     {
  87       for (SlivkaService service : slivkaClient.getServices())
  88       {
  89         for (String classifier : service.classifiers)
  90         {
  91           if (classifier.contains("Multiple sequence alignment"))
  92           {
  93             addMsaServiceClient(alignmentMenu, service, alignFrame);
  94           }
  95           else if (classifier.contains("Protein sequence analysis"))
  96           {
  97             addDisorderServiceClient(disorderMenu, service, alignFrame);
  98           }
  99           else if (classifier
 100                   .contains("Sequence alignment analysis (conservation)"))
 101           {
 102             addConservationServiceClient(conservationMenu, service,
 103                     alignFrame);
 104           }
 105
 106         }
 107       }
 108     } catch (IOException e)
 109     {
 110       throw new IOError(e);
 111     }
 112   }
 113
 114   @Override
 115   public void run()
 116   {
 117
 118   }
 119 }