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 (sh.serviceType.toLowerCase().contains("aaconws"))
  45     {
  46       // Build an AACons client
  47       if (alignFrame.getViewport().getAlignment().isNucleotide())
  48       {
  49         JOptionPane
  50                 .showMessageDialog(
  51                         Desktop.desktop,
  52                         "AACons can only be used\nfor amino acid alignments.\nSorry about that!",
  53                         "Wrong type of sequences!",
  54                         JOptionPane.WARNING_MESSAGE);
  55         return;
  56
  57       }
  58       List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
  59               .getCalcManager()
  60               .getRegisteredWorkersOfClass(AAConsClient.class);
  61       if (clnts == null || clnts.size() == 0)
  62       {
  63         if (!processParams(sh, editParams))
  64         {
  65           return;
  66         }
  67         alignFrame
  68                 .getViewport()
  69                 .getCalcManager()
  70                 .registerWorker(
  71                         new AAConsClient(sh, alignFrame, preset, paramset));
  72       }
  73       else
  74       {
  75         AAConsClient worker = (AAConsClient) clnts.get(0);
  76         if (editParams)
  77         {
  78           paramset = worker.getArguments();
  79           preset = worker.getPreset();
  80         }
  81
  82         if (!processParams(sh, editParams, true))
  83           return;
  84         // reinstate worker if it was blacklisted (might have happened due to
  85         // invalid parameters)
  86         alignFrame.getViewport().getCalcManager().workerMayRun(worker);
  87         worker.updateParameters(preset, paramset);
  88
  89       }
  90     }
  91
  92   }
  93
  94   /*
  95    * (non-Javadoc)
  96    *
  97    * @see jalview.ws.jws2.Jws2Client#attachWSMenuEntry(javax.swing.JMenu,
  98    * jalview.ws.jws2.jabaws2.Jws2Instance, jalview.gui.AlignFrame)
  99    */
 100   public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
 101           final AlignFrame alignFrame)
 102   {
 103     if (service.serviceType.toLowerCase().contains("aaconws"))
 104     {
 105       boolean hasparams = service.hasParameters();
 106       String calcName = "AACons";
 107       JMenuItem aacons = new JMenuItem("AACons Defaults");
 108       aacons.addActionListener(new ActionListener()
 109       {
 110
 111         @Override
 112         public void actionPerformed(ActionEvent e)
 113         {
 114           new SequenceAnnotationWSClient(service, alignFrame, null, false);
 115         }
 116       });
 117       wsmenu.add(aacons);
 118       if (hasparams)
 119       {
 120         // only add these menu options if the service has user-modifiable
 121         // arguments
 122         aacons = new JMenuItem("Edit settings and run ...");
 123         aacons.setToolTipText("View and change the parameters before alignment.");
 124
 125         aacons.addActionListener(new ActionListener()
 126         {
 127           public void actionPerformed(ActionEvent e)
 128           {
 129             new SequenceAnnotationWSClient(service, alignFrame, null, true);
 130           }
 131         });
 132         wsmenu.add(aacons);
 133         List<WsParamSetI> presets = service.getParamStore().getPresets();
 134         if (presets != null && presets.size() > 0)
 135         {
 136           JMenu presetlist = new JMenu("Run " + calcName + "with preset");
 137
 138           for (final WsParamSetI preset : presets)
 139           {
 140             final JMenuItem methodR = new JMenuItem(preset.getName());
 141             methodR.setToolTipText("<html><p>"
 142                     + JvSwingUtils.wrapTooltip("<strong>"
 143                             + (preset.isModifiable() ? "User Preset"
 144                                     : "Service Preset") + "</strong><br/>"
 145                             + preset.getDescription() + "</p>") + "</html>");
 146             methodR.addActionListener(new ActionListener()
 147             {
 148               public void actionPerformed(ActionEvent e)
 149               {
 150                 new SequenceAnnotationWSClient(service, alignFrame, preset,
 151                         false);
 152               }
 153
 154             });
 155             presetlist.add(methodR);
 156           }
 157           wsmenu.add(presetlist);
 158         }
 159       }
 160
 161     }
 162   }
 163 }