/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.gui.WebserviceInfo;
import jalview.gui.WsJobParameters;
import jalview.util.MessageManager;
+import jalview.ws.api.UIinfo;
import jalview.ws.jws2.dm.AAConSettings;
import jalview.ws.jws2.dm.JabaWsParamSet;
import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ParamDatastoreI;
import jalview.ws.params.WsParamSetI;
import jalview.ws.uimodel.AlignAnalysisUIText;
this.preset = preset;
if (preset != null)
{
- if (!((preset instanceof JabaPreset) || preset instanceof JabaWsParamSet))
+ if (!((preset instanceof JabaPreset)
+ || preset instanceof JabaWsParamSet))
{
/*
* { this.preset = ((JabaPreset) preset).p; } else if (preset instanceof
* arguments. for (Argument opt : arguments) { newargs.add(opt); } }
* paramset = newargs; } else {
*/
- throw new Error(MessageManager.getString("error.implementation_error_can_only_instantiate_jaba_param_sets"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_can_only_instantiate_jaba_param_sets"));
}
}
else
sh.paramStore = new JabaParamStore(sh,
Desktop.getUserParameterStore());
}
- WsJobParameters jobParams = (preset == null && paramset != null && paramset
- .size() > 0) ? new WsJobParameters(null, sh, null, paramset)
- : new WsJobParameters(sh, preset);
+ WsJobParameters jobParams = (preset == null && paramset != null
+ && paramset.size() > 0)
+ ? new WsJobParameters((ParamDatastoreI) null, sh,
+ (WsParamSetI) null,
+ paramset)
+ : new WsJobParameters((ParamDatastoreI) null, sh,
+ preset,
+ (List<Argument>) null);
if (adjustingExisting)
{
jobParams.setName(MessageManager
}
if (!jobParams.showRunDialog())
{
- return false;
+ return false; // dialog cancelled
}
+
WsParamSetI prset = jobParams.getPreset();
if (prset == null)
{
- paramset = jobParams.isServiceDefaults() ? null : JabaParamStore
- .getJabafromJwsArgs(jobParams.getJobParams());
+ paramset = jobParams.isServiceDefaults() ? null
+ : JabaParamStore
+ .getJabafromJwsArgs(jobParams.getJobParams());
this.preset = null;
}
else
// anonymous constructor - used for headless method calls only
}
- protected WebserviceInfo setWebService(Jws2Instance serv, boolean b)
+ protected WebserviceInfo setWebService(UIinfo serv, boolean b)
{
- // serviceHandle = serv;
- String serviceInstance = serv.action; // serv.service.getClass().getName();
- WebServiceName = serv.serviceType;
+ // TODO pullup
+ WebServiceName = serv.getName();
WebServiceJobTitle = serv.getActionText();
- WsURL = serv.hosturl;
+ WsURL = serv.getHostURL();
if (!b)
{
- return new WebserviceInfo(WebServiceJobTitle, WebServiceJobTitle
- + " using service hosted at " + serv.hosturl + "\n"
- + (serv.description != null ? serv.description : ""), false);
+ return new WebserviceInfo(WebServiceJobTitle,
+ WebServiceJobTitle + " using service hosted at "
+ + WsURL + "\n"
+ + (serv.getDescription() != null
+ ? serv.getDescription()
+ : ""),
+ false);
}
return null;
}
*/
abstract void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
final AlignFrame alignFrame);
-
- protected boolean registerAAConWSInstance(final JMenu wsmenu,
+ static boolean registerAAConWSInstance(final JMenu wsmenu,
final Jws2Instance service, final AlignFrame alignFrame)
{
final AlignAnalysisUIText aaui = service.getAlignAnalysisUI(); // null ; //
{
AbstractJabaCalcWorker worker = (AbstractJabaCalcWorker) aaconClient
.get(0);
- if (!worker.service.hosturl.equals(service.hosturl))
+ if (!worker.service.getHostURL().equals(service.getHostURL()))
{
// javax.swing.SwingUtilities.invokeLater(new Runnable()
{
removeCurrentAAConWorkerFor(aaui, alignFrame);
buildCurrentAAConWorkerFor(aaui, alignFrame, service);
}
- }// );
+ } // );
}
}
}
final JCheckBoxMenuItem aaConEnabled = new JCheckBoxMenuItem(
aaui.getAAconToggle());
- aaConEnabled.setToolTipText(JvSwingUtils.wrapTooltip(true, aaui.getAAconToggleTooltip()));
+ aaConEnabled.setToolTipText(
+ JvSwingUtils.wrapTooltip(true, aaui.getAAconToggleTooltip()));
aaConEnabled.addActionListener(new ActionListener()
{
@Override
});
wsmenu.add(aaConEnabled);
- final JMenuItem modifyParams = new JMenuItem(aaui.getAAeditSettings());
- modifyParams.setToolTipText("<html><p>"
- + JvSwingUtils.wrapTooltip(false, aaui.getAAeditSettingsTooltip()
- + "</p>") + "</html>");
+ final JMenuItem modifyParams = new JMenuItem(
+ aaui.getAAeditSettings());
+ modifyParams.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ aaui.getAAeditSettingsTooltip()));
modifyParams.addActionListener(new ActionListener()
{
public void menuSelected(MenuEvent arg0)
{
// TODO: refactor to the implementing class.
- if (alignFrame.getViewport().getAlignment().isNucleotide() ? aaui
- .isNa() : aaui.isPr())
+ if (alignFrame.getViewport().getAlignment().isNucleotide()
+ ? aaui.isNa()
+ : aaui.isPr())
{
aaConEnabled.setEnabled(true);
modifyParams.setEnabled(true);
else
{
if (service != null
- && !fave.getService().hosturl.equals(service.hosturl))
+ && !fave.getService().getHostURL()
+ .equals(service.getHostURL()))
{
- Cache.log.debug("Changing AACon service to " + service.hosturl
- + " from " + fave.getService().hosturl);
+ Cache.log.debug("Changing AACon service to " + service.getHostURL()
+ + " from " + fave.getService().getHostURL());
fave.setService(service);
}
}
{
if (service != null)
{
- if (!service.serviceType.toString().equals(
- compbio.ws.client.Services.AAConWS.toString()))
+ if (!service.getServiceType()
+ .equals(compbio.ws.client.Services.AAConWS.toString()))
{
- Cache.log
- .warn("Ignoring invalid preferred service for AACon calculations (service type was "
- + service.serviceType + ")");
+ Cache.log.warn(
+ "Ignoring invalid preferred service for AACon calculations (service type was "
+ + service.getServiceType() + ")");
service = null;
}
else
{
// TODO raise dialog box explaining error, and/or open the JABA
// preferences menu.
- throw new Error(MessageManager.getString("error.no_aacon_service_found"));
+ throw new Error(
+ MessageManager.getString("error.no_aacon_service_found"));
}
return new AAConSettings(true, service, null, null);
}