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 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  18
  19 public class SlivkaWSDiscoverer
  20   implements Runnable, WSMenuEntryProviderI
  21 {
  22   private static SlivkaWSDiscoverer instance = null;
  23   private SlivkaClient client;
  24
  25   private SlivkaWSDiscoverer() {
  26     try
  27     {
  28       client = new SlivkaClient("gjb-www-1.cluster.lifesci.dundee.ac.uk", 3203);
  29     } catch (URISyntaxException e)
  30     {
  31       throw new RuntimeException(e);
  32     }
  33   }
  34
  35   public static SlivkaWSDiscoverer getInstance()
  36   {
  37     if (instance == null) {
  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     JMenu categoryMenu = new JMenu("Alignment");
  49     slivkaMenu.add(categoryMenu);
  50
  51     try
  52     {
  53       for (SlivkaService service: client.getServices()) {
  54         msaClassifier: {
  55           for (String classifier: service.classifiers) {
  56             if (classifier.contains("Multiple sequence alignment")) {
  57               break msaClassifier;
  58             }
  59           }
  60           continue;
  61         }
  62         SlivkaWSInstance instance = new SlivkaWSInstance(client, service);
  63         JMenuItem defaultEntry = new JMenuItem(String.format("%s with defaults", service.label));
  64         defaultEntry.addActionListener((ActionEvent evt) -> {
  65           AlignmentView msa = alignFrame.gatherSequencesForAlignment();
  66           if (msa != null) {
  67             new MsaWSClient(
  68                 instance, alignFrame.getTitle(), msa, false, true,
  69                 alignFrame.getViewport().getAlignment().getDataset(),
  70                 alignFrame
  71             );
  72           }
  73         });
  74         categoryMenu.add(defaultEntry);
  75
  76         JMenuItem customEntry = new JMenuItem(String.format("%s with custom parameters", service.label));
  77         customEntry.addActionListener((ActionEvent evt) -> {
  78           AlignmentView msa = alignFrame.gatherSequencesForAlignment();
  79           if (msa != null) {
  80             try
  81             {
  82             SlivkaParamSet paramSet = new SlivkaParamSet(service);
  83               new MsaWSClient(
  84                   instance, paramSet, null, true, alignFrame.getTitle(), msa, false, true,
  85                   alignFrame.getViewport().getAlignment().getDataset(), alignFrame);
  86             } catch (IOException exc)
  87             {
  88               throw new IOError(exc);
  89             }
  90           }
  91         });
  92         categoryMenu.add(customEntry);
  93
  94         categoryMenu.addSeparator();
  95       }
  96     } catch (IOException e)
  97     {
  98       // TODO Auto-generated catch block
  99       e.printStackTrace();
 100     }
 101   }
 102
 103   @Override
 104   public void run()
 105   {
 106
 107   }
 108 }