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     {
  48       // clustalo menu entry
  49       JMenuItem noParamMenuItem = new JMenuItem("ClustalO with defaults");
  50       SlivkaWSInstance clustalo;
  51       try
  52       {
  53         clustalo = new SlivkaWSInstance(client, client.getService("clustalo"));
  54       } catch (IOException e)
  55       {
  56         throw new IOError(e);
  57       }
  58       noParamMenuItem.addActionListener((ActionEvent e) -> {
  59         AlignmentView msa = alignFrame.gatherSequencesForAlignment();
  60         if (msa != null)
  61         {
  62           new MsaWSClient(
  63               clustalo, alignFrame.getTitle(), msa, false, true, alignFrame.getViewport().getAlignment().getDataset(),
  64               alignFrame
  65           );
  66         }
  67       });
  68       submenu.add(noParamMenuItem);
  69
  70       JMenuItem parametrisedMenuItem = new JMenuItem("ClustalO with custom parameters");
  71       parametrisedMenuItem.addActionListener((ActionEvent evt) -> {
  72         AlignmentView msa = alignFrame.gatherSequencesForAlignment();
  73         if (msa != null)
  74         {
  75           try
  76           {
  77             SlivkaParamSet paramSet = new SlivkaParamSet(clustalo.getService());
  78             new MsaWSClient(
  79                 clustalo, paramSet, null, true, alignFrame.getTitle(), msa, false, true,
  80                 alignFrame.getViewport().getAlignment().getDataset(), alignFrame
  81             );
  82           } catch (IOException e)
  83           {
  84             e.printStackTrace();
  85           }
  86         }
  87       });
  88       submenu.add(parametrisedMenuItem);
  89     }
  90
  91     {
  92       // clustalw2 menu entry
  93       JMenuItem noParamMenuItem = new JMenuItem("ClustalW2 with defaults");
  94       SlivkaWSInstance clustalo;
  95       try
  96       {
  97         clustalo = new SlivkaWSInstance(client, client.getService("clustalw"));
  98       } catch (IOException e)
  99       {
 100         throw new IOError(e);
 101       }
 102       noParamMenuItem.addActionListener((ActionEvent e) -> {
 103         AlignmentView msa = alignFrame.gatherSequencesForAlignment();
 104         if (msa != null)
 105         {
 106           new MsaWSClient(
 107               clustalo, alignFrame.getTitle(), msa, false, true, alignFrame.getViewport().getAlignment().getDataset(),
 108               alignFrame
 109           );
 110         }
 111       });
 112       submenu.add(noParamMenuItem);
 113
 114       JMenuItem parametrisedMenuItem = new JMenuItem("ClustalW2 with custom parameters");
 115       parametrisedMenuItem.addActionListener((ActionEvent evt) -> {
 116         AlignmentView msa = alignFrame.gatherSequencesForAlignment();
 117         if (msa != null)
 118         {
 119           try
 120           {
 121             SlivkaParamSet paramSet = new SlivkaParamSet(clustalo.getService());
 122             new MsaWSClient(
 123                 clustalo, paramSet, null, true, alignFrame.getTitle(), msa, false, true,
 124                 alignFrame.getViewport().getAlignment().getDataset(), alignFrame
 125             );
 126           } catch (IOException e)
 127           {
 128             e.printStackTrace();
 129           }
 130         }
 131       });
 132       submenu.add(parametrisedMenuItem);
 133     }
 134
 135     wsmenu.add(submenu);
 136   }
 137
 138   @Override
 139   public void run()
 140   {
 141
 142   }
 143 }