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   @Override
  44   public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
  45   {
  46     JMenu slivkaMenu = new JMenu("Slivka");
  47     wsmenu.add(slivkaMenu);
  48
  49     JMenu alignmentMenu = new JMenu("Sequence Alignment");
  50     slivkaMenu.add(alignmentMenu);
  51     try
  52     {
  53       for (SlivkaService service : slivkaClient.getServices())
  54       {
  55         msaClassifier:
  56         {
  57           for (String classifier : service.classifiers)
  58           {
  59             if (classifier.contains("Multiple sequence alignment"))
  60             {
  61               break msaClassifier;
  62             }
  63           }
  64           continue;
  65         }
  66         SlivkaMsaServiceInstance instance = new SlivkaMsaServiceInstance(slivkaClient, service);
  67         MsaWSClient client = new MsaWSClient();
  68         client.attachWSMenuEntry(alignmentMenu, instance, alignFrame);
  69         alignmentMenu.addSeparator();
  70       }
  71     } catch (IOException e)
  72     {
  73       // TODO Auto-generated catch block
  74       e.printStackTrace();
  75     }
  76
  77     JMenu disorderMenu = new JMenu("Protein sequence analysis");
  78     slivkaMenu.add(disorderMenu);
  79     try
  80     {
  81       for (SlivkaService service : slivkaClient.getServices())
  82       {
  83         msaClassifier:
  84         {
  85           for (String classifier : service.classifiers)
  86           {
  87             if (classifier.contains("Protein sequence analysis"))
  88             {
  89               break msaClassifier;
  90             }
  91           }
  92           continue;
  93         }
  94         SlivkaAnnotationServiceInstance serviceInstance = new SlivkaAnnotationServiceInstance(slivkaClient, service);
  95         SequenceAnnotationWSClient client = new SequenceAnnotationWSClient();
  96         client.attachWSMenuEntry(disorderMenu, serviceInstance, alignFrame);
  97         disorderMenu.addSeparator();
  98       }
  99     } catch (IOException e)
 100     {
 101       throw new IOError(e);
 102     }
 103   }
 104
 105   @Override
 106   public void run()
 107   {
 108
 109   }
 110 }