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.io.IOError;
  10 import java.io.IOException;
  11 import java.net.URISyntaxException;
  12
  13 import javax.swing.JMenu;
  14 import javax.swing.JMenuItem;
  15
  16 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  17
  18 public class SlivkaWSDiscoverer
  19   implements Runnable, WSMenuEntryProviderI
  20 {
  21   private static SlivkaWSDiscoverer instance = null;
  22   private SlivkaClient client;
  23
  24   private SlivkaWSDiscoverer() {
  25     try
  26     {
  27       client = 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                 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
  47     String[] services = { "clustalo", "clustalw", "probcons", "muscle", "mafft", "tcoffee" };
  48     String[] names = { "ClustalO", "ClustalW2", "Probcons", "Muscle", "Mafft", "TCoffe" };
  49
  50     for (int i = 0; i < services.length; i++)
  51     {
  52       try
  53       {
  54         SlivkaWSInstance instance = new SlivkaWSInstance(client,
  55             client.getService(services[i]));
  56
  57         JMenuItem defaultMenuItem = new JMenuItem(
  58             String.format("%s with defaults", names[i]));
  59         defaultMenuItem.addActionListener((ActionEvent e) -> {
  60           AlignmentView msa = alignFrame.gatherSequencesForAlignment();
  61           if (msa != null)
  62           {
  63             new MsaWSClient(instance, alignFrame.getTitle(), msa, false, true,
  64                 alignFrame.getViewport().getAlignment().getDataset(),
  65                 alignFrame);
  66           }
  67         });
  68         submenu.add(defaultMenuItem);
  69
  70         JMenuItem customMenuItem = new JMenuItem(
  71             String.format("%s with custom parameters", names[i]));
  72         customMenuItem.addActionListener((ActionEvent e) -> {
  73           AlignmentView msa = alignFrame.gatherSequencesForAlignment();
  74           if (msa != null)
  75           {
  76             try
  77             {
  78               SlivkaParamSet paramSet = new SlivkaParamSet(
  79                   instance.getService());
  80               new MsaWSClient(instance, paramSet, null, true,
  81                   alignFrame.getTitle(), msa, false, true,
  82                   alignFrame.getViewport().getAlignment().getDataset(),
  83                   alignFrame);
  84             } catch (IOException e1)
  85             {
  86               throw new IOError(e1);
  87             }
  88
  89           }
  90         });
  91         submenu.add(customMenuItem);
  92       } catch (IOException e)
  93       {
  94         // TODO Auto-generated catch block
  95         e.printStackTrace();
  96       }
  97     }
  98
  99     wsmenu.add(submenu);
 100   }
 101
 102   @Override
 103   public void run()
 104   {
 105
 106   }
 107 }