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 implements Runnable, WSMenuEntryProviderI
  20 {
  21   private static SlivkaWSDiscoverer instance = null;
  22
  23   private SlivkaClient client;
  24
  25   private SlivkaWSDiscoverer()
  26   {
  27     try
  28     {
  29       client = new SlivkaClient("gjb-www-1.cluster.lifesci.dundee.ac.uk", 3203);
  30     } catch (URISyntaxException e)
  31     {
  32       throw new RuntimeException(e);
  33     }
  34   }
  35
  36   public static SlivkaWSDiscoverer getInstance()
  37   {
  38     if (instance == null)
  39     {
  40       instance = new SlivkaWSDiscoverer();
  41     }
  42     return instance;
  43   }
  44
  45   @Override
  46   public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
  47   {
  48     JMenu slivkaMenu = new JMenu("Slivka");
  49     wsmenu.add(slivkaMenu);
  50     JMenu categoryMenu = new JMenu("Alignment");
  51     slivkaMenu.add(categoryMenu);
  52
  53     try
  54     {
  55       for (SlivkaService service : client.getServices())
  56       {
  57         msaClassifier:
  58         {
  59           for (String classifier : service.classifiers)
  60           {
  61             if (classifier.contains("Multiple sequence alignment"))
  62             {
  63               break msaClassifier;
  64             }
  65           }
  66           continue;
  67         }
  68         SlivkaMsaServiceInstance instance = new SlivkaMsaServiceInstance(client, service);
  69         JMenuItem defaultEntry = new JMenuItem(String.format("%s with defaults", service.label));
  70         defaultEntry.addActionListener((ActionEvent evt) -> {
  71           AlignmentView msa = alignFrame.gatherSequencesForAlignment();
  72           if (msa != null)
  73           {
  74             new MsaWSClient(instance, alignFrame.getTitle(), msa, false, true,
  75                 alignFrame.getViewport().getAlignment().getDataset(), alignFrame);
  76           }
  77         });
  78         categoryMenu.add(defaultEntry);
  79
  80         JMenuItem customEntry = new JMenuItem(String.format("%s with custom parameters", service.label));
  81         customEntry.addActionListener((ActionEvent evt) -> {
  82           AlignmentView msa = alignFrame.gatherSequencesForAlignment();
  83           if (msa != null)
  84           {
  85             try
  86             {
  87               SlivkaParamSet paramSet = new SlivkaParamSet(service);
  88               new MsaWSClient(instance, paramSet, null, true, alignFrame.getTitle(), msa, false, true,
  89                   alignFrame.getViewport().getAlignment().getDataset(), alignFrame);
  90             } catch (IOException exc)
  91             {
  92               throw new IOError(exc);
  93             }
  94           }
  95         });
  96         categoryMenu.add(customEntry);
  97
  98         categoryMenu.addSeparator();
  99       }
 100     } catch (IOException e)
 101     {
 102       // TODO Auto-generated catch block
 103       e.printStackTrace();
 104     }
 105   }
 106
 107   @Override
 108   public void run()
 109   {
 110
 111   }
 112 }