import javax.swing.JMenu;
import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
import compbio.metadata.Argument;
import jalview.api.AlignCalcWorkerI;
import jalview.datamodel.AlignmentView;
import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JalviewDialog;
import jalview.gui.JvSwingUtils;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
{
super(alignFrame, preset, null);
- List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
- .getCalcManager()
- .getRegisteredWorkersOfClass(AAConsClient.class);
- if (clnts == null || clnts.size() == 0)
+ if (alignFrame.getViewport().getAlignment().isNucleotide())
{
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ sh.serviceType+" can only be used\nfor amino acid alignments.",
+ "Wrong type of sequences!",
+ JOptionPane.WARNING_MESSAGE);
+ return;
+
+ }
+ if (sh.action.toLowerCase().contains("conservation"))
+ {
+ // Build an AACons style client - take alignment, return annotation for columns
+
+ List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
+ .getCalcManager()
+ .getRegisteredWorkersOfClass(AAConsClient.class);
+ if (clnts == null || clnts.size() == 0)
+ {
+ if (!processParams(sh, editParams))
+ {
+ return;
+ }
+ alignFrame
+ .getViewport()
+ .getCalcManager()
+ .registerWorker(
+ new AAConsClient(sh, alignFrame, preset, paramset));
+ }
+ else
+ {
+ AAConsClient worker = (AAConsClient) clnts.get(0);
+ if (editParams)
+ {
+ paramset = worker.getArguments();
+ preset = worker.getPreset();
+ }
+
+ if (!processParams(sh, editParams, true))
+ return;
+ // reinstate worker if it was blacklisted (might have happened due to
+ // invalid parameters)
+ alignFrame.getViewport().getCalcManager().workerMayRun(worker);
+ worker.updateParameters(preset, paramset);
+
+ }
+ }
+ if (sh.action.toLowerCase().contains("disorder"))
+ {
+ // build IUPred style client. take sequences, returns annotation per sequence.
if (!processParams(sh, editParams))
{
return;
}
+
alignFrame
.getViewport()
.getCalcManager()
- .registerWorker(
- new AAConsClient(sh, alignFrame, preset, paramset));
+ .startWorker(
+ new AADisorderClient(sh, alignFrame, preset, paramset));
}
- else
- {
- AAConsClient worker = (AAConsClient) clnts.get(0);
- if (editParams)
- {
- paramset = worker.getArguments();
- preset = worker.getPreset();
- }
-
- if (!processParams(sh, editParams, true))
- return;
- // reinstate worker if it was blacklisted (might have happened due to invalid parameters)
- alignFrame.getViewport().getCalcManager().workerMayRun(worker);
- worker.updateParameters(preset, paramset);
- }
}
/*
public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
final AlignFrame alignFrame)
{
- if (service.serviceType.toLowerCase().contains("aaconws"))
+ boolean hasparams = service.hasParameters();
+ // Assume name ends in WS
+ String calcName = service.serviceType.substring(0,service.serviceType.length()-2);
+
+ JMenuItem aacons = new JMenuItem(calcName + " Defaults");
+ aacons.addActionListener(new ActionListener()
{
- boolean hasparams = service.hasParameters();
- String calcName = "AACons";
- System.out.println("Making an aacons client!");
- JMenuItem aacons = new JMenuItem("AACons Defaults");
- aacons.addActionListener(new ActionListener()
+
+ @Override
+ public void actionPerformed(ActionEvent e)
{
+ new SequenceAnnotationWSClient(service, alignFrame, null, false);
+ }
+ });
+ wsmenu.add(aacons);
+ if (hasparams)
+ {
+ // only add these menu options if the service has user-modifiable
+ // arguments
+ aacons = new JMenuItem("Edit settings and run ...");
+ aacons.setToolTipText("View and change parameters before running calculation");
- @Override
+ aacons.addActionListener(new ActionListener()
+ {
public void actionPerformed(ActionEvent e)
{
- new SequenceAnnotationWSClient(service, alignFrame, null, false);
+ new SequenceAnnotationWSClient(service, alignFrame, null, true);
}
});
wsmenu.add(aacons);
- if (hasparams)
+ List<WsParamSetI> presets = service.getParamStore().getPresets();
+ if (presets != null && presets.size() > 0)
{
- // only add these menu options if the service has user-modifiable
- // arguments
- aacons = new JMenuItem("Edit settings and run ...");
- aacons.setToolTipText("View and change the parameters before alignment.");
+ JMenu presetlist = new JMenu("Run " + calcName + "with preset");
- aacons.addActionListener(new ActionListener()
+ for (final WsParamSetI preset : presets)
{
- public void actionPerformed(ActionEvent e)
+ final JMenuItem methodR = new JMenuItem(preset.getName());
+ methodR.setToolTipText("<html><p>"
+ + JvSwingUtils.wrapTooltip("<strong>"
+ + (preset.isModifiable() ? "User Preset"
+ : "Service Preset") + "</strong><br/>"
+ + preset.getDescription() + "</p>") + "</html>");
+ methodR.addActionListener(new ActionListener()
{
- new SequenceAnnotationWSClient(service, alignFrame, null, true);
- }
- });
- wsmenu.add(aacons);
- List<WsParamSetI> presets = service.getParamStore().getPresets();
- if (presets != null && presets.size() > 0)
- {
- JMenu presetlist = new JMenu("Run " + calcName + "with preset");
-
- for (final WsParamSetI preset : presets)
- {
- final JMenuItem methodR = new JMenuItem(preset.getName());
- methodR.setToolTipText("<html><p>"
- + JvSwingUtils.wrapTooltip("<strong>"
- + (preset.isModifiable() ? "User Preset"
- : "Service Preset") + "</strong><br/>"
- + preset.getDescription() + "</p>") + "</html>");
- methodR.addActionListener(new ActionListener()
+ public void actionPerformed(ActionEvent e)
{
- public void actionPerformed(ActionEvent e)
- {
- new SequenceAnnotationWSClient(service, alignFrame, preset,
- false);
- }
-
- });
- presetlist.add(methodR);
- }
- wsmenu.add(presetlist);
+ new SequenceAnnotationWSClient(service, alignFrame, preset,
+ false);
+ }
+
+ });
+ presetlist.add(methodR);
}
+ wsmenu.add(presetlist);
}
}