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 import jalview.ws.jws2.SequenceAnnotationWSClient;
   8
   9 import java.awt.event.ActionEvent;
  10 import java.io.IOError;
  11 import java.io.IOException;
  12 import java.net.URISyntaxException;
  13
  14 import javax.swing.JMenu;
  15 import javax.swing.JMenuItem;
  16
  17 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  18 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  19
  20 public class SlivkaWSDiscoverer implements Runnable, WSMenuEntryProviderI
  21 {
  22   private static SlivkaWSDiscoverer instance = null;
  23
  24   private SlivkaClient client;
  25
  26   private SlivkaWSDiscoverer()
  27   {
  28     try
  29     {
  30       client = new SlivkaClient("gjb-www-1.cluster.lifesci.dundee.ac.uk", 3203);
  31     } catch (URISyntaxException e)
  32     {
  33       throw new RuntimeException(e);
  34     }
  35   }
  36
  37   public static SlivkaWSDiscoverer getInstance()
  38   {
  39     if (instance == null)
  40     {
  41       instance = new SlivkaWSDiscoverer();
  42     }
  43     return instance;
  44   }
  45
  46   @Override
  47   public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
  48   {
  49     JMenu slivkaMenu = new JMenu("Slivka");
  50     wsmenu.add(slivkaMenu);
  51
  52     JMenu alignmentMenu = new JMenu("Sequence Alignment");
  53     slivkaMenu.add(alignmentMenu);
  54     try
  55     {
  56       for (SlivkaService service : client.getServices())
  57       {
  58         msaClassifier:
  59         {
  60           for (String classifier : service.classifiers)
  61           {
  62             if (classifier.contains("Multiple sequence alignment"))
  63             {
  64               break msaClassifier;
  65             }
  66           }
  67           continue;
  68         }
  69         SlivkaMsaServiceInstance instance = new SlivkaMsaServiceInstance(client, service);
  70         JMenuItem defaultEntry = new JMenuItem(String.format("%s with defaults", service.label));
  71         defaultEntry.addActionListener((ActionEvent evt) -> {
  72           AlignmentView msa = alignFrame.gatherSequencesForAlignment();
  73           if (msa != null)
  74           {
  75             new MsaWSClient(instance, alignFrame.getTitle(), msa, false, true,
  76                 alignFrame.getViewport().getAlignment().getDataset(), alignFrame);
  77           }
  78         });
  79         alignmentMenu.add(defaultEntry);
  80
  81         JMenuItem customEntry = new JMenuItem(String.format("%s with custom parameters", service.label));
  82         customEntry.addActionListener((ActionEvent evt) -> {
  83           AlignmentView msa = alignFrame.gatherSequencesForAlignment();
  84           if (msa != null)
  85           {
  86             try
  87             {
  88               SlivkaParamSet paramSet = new SlivkaParamSet(service);
  89               new MsaWSClient(instance, paramSet, null, true, alignFrame.getTitle(), msa, false, true,
  90                   alignFrame.getViewport().getAlignment().getDataset(), alignFrame);
  91             } catch (IOException exc)
  92             {
  93               throw new IOError(exc);
  94             }
  95           }
  96         });
  97         alignmentMenu.add(customEntry);
  98
  99         alignmentMenu.addSeparator();
 100       }
 101     } catch (IOException e)
 102     {
 103       // TODO Auto-generated catch block
 104       e.printStackTrace();
 105     }
 106
 107     JMenu disorderMenu = new JMenu("Protein sequence analysis");
 108     slivkaMenu.add(disorderMenu);
 109     try
 110     {
 111       for (SlivkaService service : client.getServices())
 112       {
 113         msaClassifier:
 114         {
 115           for (String classifier : service.classifiers)
 116           {
 117             if (classifier.contains("Protein sequence analysis"))
 118             {
 119               break msaClassifier;
 120             }
 121           }
 122           continue;
 123         }
 124         JMenuItem menuEntry = new JMenuItem(String.format("%s with custom parameters", service.label));
 125         disorderMenu.add(menuEntry);
 126         SlivkaAnnotationServiceInstance serviceInstance = new SlivkaAnnotationServiceInstance(client, service);
 127         menuEntry.addActionListener((ActionEvent evt) -> {
 128           try
 129           {
 130             SlivkaParamSet paramSet = new SlivkaParamSet(service);
 131             SequenceAnnotationWSClient client = new SequenceAnnotationWSClient();
 132             client.initSequenceAnnotationWSClient(serviceInstance, alignFrame, paramSet, true);
 133           } catch (IOException e)
 134           {
 135             throw new IOError(e);
 136           }
 137
 138         });
 139       }
 140     } catch (IOException e)
 141     {
 142       throw new IOError(e);
 143     }
 144   }
 145
 146   @Override
 147   public void run()
 148   {
 149
 150   }
 151 }