src/jalview/ws/jws2/SequenceAnnotationWSClient.java

   1 /**
   2  *
   3  */
   4 package jalview.ws.jws2;
   5
   6 import java.awt.event.ActionEvent;
   7 import java.awt.event.ActionListener;
   8 import java.util.List;
   9
  10 import javax.swing.JMenu;
  11 import javax.swing.JMenuItem;
  12 import javax.swing.JOptionPane;
  13
  14 import compbio.metadata.Argument;
  15
  16 import jalview.api.AlignCalcWorkerI;
  17 import jalview.datamodel.AlignmentView;
  18 import jalview.gui.AlignFrame;
  19 import jalview.gui.Desktop;
  20 import jalview.gui.JalviewDialog;
  21 import jalview.gui.JvSwingUtils;
  22 import jalview.ws.jws2.jabaws2.Jws2Instance;
  23 import jalview.ws.params.WsParamSetI;
  24
  25 /**
  26  * @author jimp
  27  *
  28  */
  29 public class SequenceAnnotationWSClient extends Jws2Client
  30 {
  31
  32   /**
  33    * initialise a client so its attachWSMenuEntry method can be called.
  34    */
  35   public SequenceAnnotationWSClient()
  36   {
  37     // TODO Auto-generated constructor stub
  38   }
  39
  40   public SequenceAnnotationWSClient(final Jws2Instance sh,
  41           AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
  42   {
  43     super(alignFrame, preset, null);
  44     if (alignFrame.getViewport().getAlignment().isNucleotide())
  45     {
  46       JOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
  47               + " can only be used\nfor amino acid alignments.",
  48               "Wrong type of sequences!", JOptionPane.WARNING_MESSAGE);
  49       return;
  50
  51     }
  52     if (sh.action.toLowerCase().contains("conservation"))
  53     {
  54       // Build an AACons style client - take alignment, return annotation for
  55       // columns
  56
  57       List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
  58               .getCalcManager()
  59               .getRegisteredWorkersOfClass(AAConsClient.class);
  60       if (clnts == null || clnts.size() == 0)
  61       {
  62         if (!processParams(sh, editParams))
  63         {
  64           return;
  65         }
  66         AAConsClient worker;
  67         alignFrame
  68                 .getViewport()
  69                 .getCalcManager()
  70                 .registerWorker(
  71                         worker = new AAConsClient(sh, alignFrame, preset,
  72                                 paramset));
  73         alignFrame.getViewport().getCalcManager().startWorker(worker);
  74
  75       }
  76       else
  77       {
  78         AAConsClient worker = (AAConsClient) clnts.get(0);
  79         if (editParams)
  80         {
  81           paramset = worker.getArguments();
  82           preset = worker.getPreset();
  83         }
  84
  85         if (!processParams(sh, editParams, true))
  86           return;
  87         // reinstate worker if it was blacklisted (might have happened due to
  88         // invalid parameters)
  89         alignFrame.getViewport().getCalcManager().workerMayRun(worker);
  90         worker.updateParameters(preset, paramset);
  91
  92       }
  93     }
  94     if (sh.action.toLowerCase().contains("disorder"))
  95     {
  96       // build IUPred style client. take sequences, returns annotation per
  97       // sequence.
  98       if (!processParams(sh, editParams))
  99       {
 100         return;
 101       }
 102
 103       alignFrame
 104               .getViewport()
 105               .getCalcManager()
 106               .startWorker(
 107                       new AADisorderClient(sh, alignFrame, preset, paramset));
 108     }
 109
 110   }
 111
 112   /*
 113    * (non-Javadoc)
 114    *
 115    * @see jalview.ws.jws2.Jws2Client#attachWSMenuEntry(javax.swing.JMenu,
 116    * jalview.ws.jws2.jabaws2.Jws2Instance, jalview.gui.AlignFrame)
 117    */
 118   public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
 119           final AlignFrame alignFrame)
 120   {
 121     boolean hasparams = service.hasParameters();
 122     // Assume name ends in WS
 123     String calcName = service.serviceType.substring(0,
 124             service.serviceType.length() - 2);
 125
 126     JMenuItem aacons = new JMenuItem(calcName + " Defaults");
 127     aacons.addActionListener(new ActionListener()
 128     {
 129
 130       @Override
 131       public void actionPerformed(ActionEvent e)
 132       {
 133         new SequenceAnnotationWSClient(service, alignFrame, null, false);
 134       }
 135     });
 136     wsmenu.add(aacons);
 137     if (hasparams)
 138     {
 139       // only add these menu options if the service has user-modifiable
 140       // arguments
 141       aacons = new JMenuItem("Edit settings and run ...");
 142       aacons.setToolTipText("View and change parameters before running calculation");
 143
 144       aacons.addActionListener(new ActionListener()
 145       {
 146         public void actionPerformed(ActionEvent e)
 147         {
 148           new SequenceAnnotationWSClient(service, alignFrame, null, true);
 149         }
 150       });
 151       wsmenu.add(aacons);
 152       List<WsParamSetI> presets = service.getParamStore().getPresets();
 153       if (presets != null && presets.size() > 0)
 154       {
 155         JMenu presetlist = new JMenu("Run " + calcName + "with preset");
 156
 157         for (final WsParamSetI preset : presets)
 158         {
 159           final JMenuItem methodR = new JMenuItem(preset.getName());
 160           methodR.setToolTipText("<html><p>"
 161                   + JvSwingUtils.wrapTooltip("<strong>"
 162                           + (preset.isModifiable() ? "User Preset"
 163                                   : "Service Preset") + "</strong><br/>"
 164                           + preset.getDescription() + "</p>") + "</html>");
 165           methodR.addActionListener(new ActionListener()
 166           {
 167             public void actionPerformed(ActionEvent e)
 168             {
 169               new SequenceAnnotationWSClient(service, alignFrame, preset,
 170                       false);
 171             }
 172
 173           });
 174           presetlist.add(methodR);
 175         }
 176         wsmenu.add(presetlist);
 177       }
 178
 179     }
 180   }
 181 }