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
  47               .showMessageDialog(
  48                       Desktop.desktop,
  49                       sh.serviceType+" can only be used\nfor amino acid alignments.",
  50                       "Wrong type of sequences!",
  51                       JOptionPane.WARNING_MESSAGE);
  52       return;
  53
  54     }
  55     if (sh.action.toLowerCase().contains("conservation"))
  56     {
  57       // Build an AACons style client - take alignment, return annotation for columns
  58
  59       List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
  60               .getCalcManager()
  61               .getRegisteredWorkersOfClass(AAConsClient.class);
  62       if (clnts == null || clnts.size() == 0)
  63       {
  64         if (!processParams(sh, editParams))
  65         {
  66           return;
  67         }
  68         alignFrame
  69                 .getViewport()
  70                 .getCalcManager()
  71                 .registerWorker(
  72                         new AAConsClient(sh, alignFrame, preset, paramset));
  73       }
  74       else
  75       {
  76         AAConsClient worker = (AAConsClient) clnts.get(0);
  77         if (editParams)
  78         {
  79           paramset = worker.getArguments();
  80           preset = worker.getPreset();
  81         }
  82
  83         if (!processParams(sh, editParams, true))
  84           return;
  85         // reinstate worker if it was blacklisted (might have happened due to
  86         // invalid parameters)
  87         alignFrame.getViewport().getCalcManager().workerMayRun(worker);
  88         worker.updateParameters(preset, paramset);
  89
  90       }
  91     }
  92     if (sh.action.toLowerCase().contains("disorder"))
  93     {
  94       // build IUPred style client. take sequences, returns annotation per sequence.
  95       if (!processParams(sh, editParams))
  96       {
  97         return;
  98       }
  99
 100       alignFrame
 101               .getViewport()
 102               .getCalcManager()
 103               .startWorker(
 104                       new AADisorderClient(sh, alignFrame, preset, paramset));
 105     }
 106
 107   }
 108
 109   /*
 110    * (non-Javadoc)
 111    *
 112    * @see jalview.ws.jws2.Jws2Client#attachWSMenuEntry(javax.swing.JMenu,
 113    * jalview.ws.jws2.jabaws2.Jws2Instance, jalview.gui.AlignFrame)
 114    */
 115   public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
 116           final AlignFrame alignFrame)
 117   {
 118     boolean hasparams = service.hasParameters();
 119     // Assume name ends in WS
 120     String calcName = service.serviceType.substring(0,service.serviceType.length()-2);
 121
 122     JMenuItem aacons = new JMenuItem(calcName + " Defaults");
 123     aacons.addActionListener(new ActionListener()
 124     {
 125
 126       @Override
 127       public void actionPerformed(ActionEvent e)
 128       {
 129         new SequenceAnnotationWSClient(service, alignFrame, null, false);
 130       }
 131     });
 132     wsmenu.add(aacons);
 133     if (hasparams)
 134     {
 135       // only add these menu options if the service has user-modifiable
 136       // arguments
 137       aacons = new JMenuItem("Edit settings and run ...");
 138       aacons.setToolTipText("View and change parameters before running calculation");
 139
 140       aacons.addActionListener(new ActionListener()
 141       {
 142         public void actionPerformed(ActionEvent e)
 143         {
 144           new SequenceAnnotationWSClient(service, alignFrame, null, true);
 145         }
 146       });
 147       wsmenu.add(aacons);
 148       List<WsParamSetI> presets = service.getParamStore().getPresets();
 149       if (presets != null && presets.size() > 0)
 150       {
 151         JMenu presetlist = new JMenu("Run " + calcName + "with preset");
 152
 153         for (final WsParamSetI preset : presets)
 154         {
 155           final JMenuItem methodR = new JMenuItem(preset.getName());
 156           methodR.setToolTipText("<html><p>"
 157                   + JvSwingUtils.wrapTooltip("<strong>"
 158                           + (preset.isModifiable() ? "User Preset"
 159                                   : "Service Preset") + "</strong><br/>"
 160                           + preset.getDescription() + "</p>") + "</html>");
 161           methodR.addActionListener(new ActionListener()
 162           {
 163             public void actionPerformed(ActionEvent e)
 164             {
 165               new SequenceAnnotationWSClient(service, alignFrame, preset,
 166                       false);
 167             }
 168
 169           });
 170           presetlist.add(methodR);
 171         }
 172         wsmenu.add(presetlist);
 173       }
 174
 175     }
 176   }
 177 }