/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 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.
*
*/
package jalview.ws.jws2;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.List;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
+
+import compbio.metadata.Argument;
import jalview.api.AlignCalcWorkerI;
import jalview.bin.Cache;
import jalview.gui.AlignFrame;
import jalview.ws.params.WsParamSetI;
import jalview.ws.uimodel.AlignAnalysisUIText;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.List;
-
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.event.MenuEvent;
-import javax.swing.event.MenuListener;
-
-import compbio.metadata.Argument;
-
/**
* provides metadata for a jabaws2 service instance - resolves names, etc.
*
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(null, sh, null, paramset)
+ : new WsJobParameters(sh, preset);
if (adjustingExisting)
{
jobParams.setName(MessageManager
WsParamSetI prset = jobParams.getPreset();
if (prset == null)
{
- paramset = jobParams.isServiceDefaults() ? null : JabaParamStore
- .getJabafromJwsArgs(jobParams.getJobParams());
+ paramset =
+ /* JAL-3739 always take values from input form */
+ /* jobParams.isServiceDefaults() ? null : */
+ JabaParamStore.getJabafromJwsArgs(jobParams.getJobParams());
this.preset = null;
}
else
WsURL = serv.hosturl;
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 "
+ + serv.hosturl + "\n"
+ + (serv.description != null ? serv.description : ""),
+ false);
}
return null;
}
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);
{
if (service != null)
{
- if (!service.serviceType.toString().equals(
- compbio.ws.client.Services.AAConWS.toString()))
+ if (!service.serviceType.toString()
+ .equals(compbio.ws.client.Services.AAConWS.toString()))
{
- Cache.log
- .warn("Ignoring invalid preferred service for AACon calculations (service type was "
+ Cache.log.warn(
+ "Ignoring invalid preferred service for AACon calculations (service type was "
+ service.serviceType + ")");
service = null;
}