src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java

   1 package jalview.ws.slivkaws;
   2
   3 import jalview.datamodel.AlignmentView;
   4 import jalview.gui.AlignFrame;
   5 import jalview.ws.WSMenuEntryProviderI;
   6 import jalview.ws.jws2.MsaWSClient;
   7
   8 import java.awt.event.ActionEvent;
   9 import java.net.URISyntaxException;
  10
  11 import javax.swing.JMenu;
  12 import javax.swing.JMenuItem;
  13
  14 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  15
  16 public class SlivkaWSDiscoverer
  17   implements Runnable, WSMenuEntryProviderI
  18 {
  19   private static SlivkaWSDiscoverer instance = null;
  20   private SlivkaClient client;
  21   private ClustaloWS clustalo;
  22
  23   private SlivkaWSDiscoverer() {
  24     try
  25     {
  26       client = new SlivkaClient("gjb-www-1.cluster.lifesci.dundee.ac.uk", 3203);
  27     } catch (URISyntaxException e)
  28     {
  29       throw new RuntimeException(e);
  30     }
  31     clustalo = new ClustaloWS(client);
  32   }
  33
  34   public static SlivkaWSDiscoverer getInstance()
  35   {
  36     if (instance == null) {
  37                 instance = new SlivkaWSDiscoverer();
  38         }
  39     return instance;
  40   }
  41
  42   @Override
  43   public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
  44   {
  45     JMenu submenu = new JMenu("Slivka");
  46     JMenuItem menuItem = new JMenuItem("ClustalO with defaults");
  47     menuItem.addActionListener((ActionEvent e) -> {
  48
  49       AlignmentView msa = alignFrame.gatherSequencesForAlignment();
  50
  51       if (msa != null)
  52       {
  53         new MsaWSClient(clustalo, alignFrame.getTitle(), msa, false,
  54             true,
  55             alignFrame.getViewport().getAlignment().getDataset(),
  56             alignFrame);
  57       }
  58 //
  59 //      List<SequenceI> sequences = alignFrame.getViewport().getAlignment().getSequences();
  60 //      try
  61 //      {
  62 //        clustalo.align(sequences, null, null);
  63 //      } catch (FormValidationException | IOException exc)
  64 //      {
  65 //        throw new RuntimeException(exc);
  66 //      }
  67     });
  68     submenu.add(menuItem);
  69     wsmenu.add(submenu);
  70   }
  71
  72   @Override
  73   public void run()
  74   {
  75
  76   }
  77 }