import jalview.gui.Desktop;
import jalview.gui.JvSwingUtils;
import jalview.util.MessageManager;
-import jalview.ws.jws2.dm.AAConSettings;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.api.ServiceWithParameters;
+import jalview.ws.params.AutoCalcSetting;
import jalview.ws.params.WsParamSetI;
import jalview.ws.uimodel.AlignAnalysisUIText;
// TODO Auto-generated constructor stub
}
- public SequenceAnnotationWSClient(final Jws2Instance sh,
+ public SequenceAnnotationWSClient(final ServiceWithParameters sh,
AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
{
super(alignFrame, preset, null);
// dan think. Do I need to change this method to run RNAalifold through the
// GUI
- public void initSequenceAnnotationWSClient(final Jws2Instance sh,
+ public void initSequenceAnnotationWSClient(final ServiceWithParameters sh,
AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
{
// dan changed! dan test. comment out if conditional
// if (alignFrame.getViewport().getAlignment().isNucleotide())
// {
- // JOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
+ // JvOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
// + " can only be used\nfor amino acid alignments.",
- // "Wrong type of sequences!", JOptionPane.WARNING_MESSAGE);
+ // "Wrong type of sequences!", JvOptionPane.WARNING_MESSAGE);
// return;
//
// }
// columns
List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
- .getCalcManager().getRegisteredWorkersOfClass(clientClass);
- AbstractJabaCalcWorker worker;
- if (clnts == null || clnts.size() == 0)
+ .getCalcManager()
+ .getRegisteredWorkersOfClass(SeqAnnotationServiceCalcWorker.class);
+
+ SeqAnnotationServiceCalcWorker worker = null;
+ if (clnts != null)
+ {
+ for (AlignCalcWorkerI _worker : clnts)
+ {
+ worker = (SeqAnnotationServiceCalcWorker) _worker;
+ if (worker.hasService()
+ && worker.getService().getClass().equals(clientClass))
+ {
+ break;
+ }
+ worker = null;
+ }
+ }
+ if (worker == null)
{
if (!processParams(sh, editParams))
{
}
try
{
- worker = (AbstractJabaCalcWorker) (clientClass
- .getConstructor(new Class[] { Jws2Instance.class,
- AlignFrame.class, WsParamSetI.class, List.class })
- .newInstance(new Object[] { sh, alignFrame, this.preset,
- paramset }));
+ worker = new SeqAnnotationServiceCalcWorker(sh, alignFrame, this.preset,
+ paramset);
} catch (Exception x)
{
x.printStackTrace();
throw new Error(
- MessageManager.getString("error.implementation_error"), x);
+ MessageManager.getString("error.implementation_error"),
+ x);
}
alignFrame.getViewport().getCalcManager().registerWorker(worker);
alignFrame.getViewport().getCalcManager().startWorker(worker);
}
else
{
- worker = (AbstractJabaCalcWorker) clnts.get(0);
if (editParams)
{
paramset = worker.getArguments();
worker.updateParameters(this.preset, paramset);
}
}
- if (sh.action.toLowerCase().contains("disorder"))
+ if (!sh.isInteractiveUpdate())
{
// build IUPred style client. take sequences, returns annotation per
// sequence.
return;
}
- alignFrame
- .getViewport()
- .getCalcManager()
- .startWorker(
- new AADisorderClient(sh, alignFrame, preset, paramset));
+ alignFrame.getViewport().getCalcManager().startWorker(
+ new SeqAnnotationServiceCalcWorker(sh, alignFrame, preset, paramset));
}
}
- public SequenceAnnotationWSClient(AAConSettings fave,
+ public SequenceAnnotationWSClient(AutoCalcSetting fave,
AlignFrame alignFrame, boolean b)
{
- super(alignFrame, fave.getPreset(), fave.getJobArgset());
+ super(alignFrame, fave.getPreset(), fave.getArgumentSet());
initSequenceAnnotationWSClient(fave.getService(), alignFrame,
fave.getPreset(), b);
}
* @see jalview.ws.jws2.Jws2Client#attachWSMenuEntry(javax.swing.JMenu,
* jalview.ws.jws2.jabaws2.Jws2Instance, jalview.gui.AlignFrame)
*/
- public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
+ @Override
+ public void attachWSMenuEntry(JMenu wsmenu,
+ final ServiceWithParameters service,
final AlignFrame alignFrame)
{
- if (registerAAConWSInstance(wsmenu, service, alignFrame))
+ if (Jws2ClientFactory.registerAAConWSInstance(wsmenu,
+ service, alignFrame))
{
// Alignment dependent analysis calculation WS gui
return;
}
boolean hasparams = service.hasParameters();
- // Assume name ends in WS
- String calcName = service.serviceType.substring(0,
- service.serviceType.length() - 2);
+ String calcName = service.getName();
+ if (calcName.endsWith("WS"))
+ {
+ // Remove "WS" suffix
+ calcName = calcName.substring(0, calcName.length() - 2);
+ }
JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage(
- "label.calcname_with_default_settings",
- new String[] { calcName }));
+ "label.calcname_with_default_settings", new String[]
+ { calcName }));
annotservice.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- new SequenceAnnotationWSClient(service, alignFrame, null, false);
+ new SequenceAnnotationWSClient(service, alignFrame,
+ null, false);
}
});
wsmenu.add(annotservice);
// arguments
annotservice = new JMenuItem(
MessageManager.getString("label.edit_settings_and_run"));
- annotservice
- .setToolTipText(MessageManager
- .getString("label.view_and_change_parameters_before_running_calculation"));
+ annotservice.setToolTipText(MessageManager.getString(
+ "label.view_and_change_parameters_before_running_calculation"));
annotservice.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- new SequenceAnnotationWSClient(service, alignFrame, null, true);
+ new SequenceAnnotationWSClient(service, alignFrame,
+ null, true);
}
});
wsmenu.add(annotservice);
List<WsParamSetI> presets = service.getParamStore().getPresets();
if (presets != null && presets.size() > 0)
{
- JMenu presetlist = new JMenu(MessageManager.formatMessage(
- "label.run_with_preset", new String[] { calcName }));
+ JMenu presetlist = new JMenu(MessageManager
+ .formatMessage("label.run_with_preset", new String[]
+ { calcName }));
for (final WsParamSetI preset : presets)
{
final JMenuItem methodR = new JMenuItem(preset.getName());
- methodR.setToolTipText(JvSwingUtils.wrapTooltip(
- true,
- "<strong>"
- + (preset.isModifiable() ? MessageManager
- .getString("label.user_preset")
- : MessageManager
- .getString("label.service_preset"))
- + "</strong><br/>" + preset.getDescription()));
+ methodR.setToolTipText(JvSwingUtils.wrapTooltip(true, "<strong>"
+ + (preset.isModifiable()
+ ? MessageManager.getString("label.user_preset")
+ : MessageManager
+ .getString("label.service_preset"))
+ + "</strong><br/>" + preset.getDescription()));
methodR.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- new SequenceAnnotationWSClient(service, alignFrame, preset,
+ new SequenceAnnotationWSClient(service,
+ alignFrame, preset,
false);
}
{
annotservice = new JMenuItem(
MessageManager.getString("label.view_documentation"));
- if (service.docUrl != null)
+ if (service != null && service.hasDocumentationUrl())
{
annotservice.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent arg0)
{
- Desktop.instance.showUrl(service.docUrl);
+ Desktop.instance.showUrl(service.getDocumentationUrl());
}
});
- annotservice.setToolTipText(JvSwingUtils.wrapTooltip(true,
- MessageManager.formatMessage("label.view_service_doc_url",
- new String[] { service.docUrl, service.docUrl })));
+ annotservice.setToolTipText(
+ JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage(
+ "label.view_service_doc_url", new String[]
+ { service.getDocumentationUrl(),
+ service.getDocumentationUrl() })));
wsmenu.add(annotservice);
}
}