/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
AlignFrame alignFrame;
- private Preset preset;
+ private WsParamSetI preset;
private List<Argument> paramset;
return;
}
server = sh.service;
- if (preset!=null) {
- if (preset instanceof JabaPreset){
- this.preset = ((JabaPreset)preset).p;
- } else
- if (preset instanceof JabaWsParamSet) {
- JabaWsParamSet pset = ((JabaWsParamSet)preset);
- if (arguments!=null && arguments.size()>0)
+ this.preset=preset;
+ if (preset != null)
+ {
+ if (!((preset instanceof JabaPreset) || preset instanceof JabaWsParamSet)) {
+ /*{
+ this.preset = ((JabaPreset) preset).p;
+ }
+ else if (preset instanceof JabaWsParamSet)
+ {
+ List<Argument> newargs = new ArrayList<Argument>();
+ JabaWsParamSet pset = ((JabaWsParamSet) preset);
+ for (Option opt : pset.getjabaArguments())
+ {
+ newargs.add(opt);
+ }
+ if (arguments != null && arguments.size() > 0)
+ {
+ // merge arguments with preset's own arguments.
+ for (Argument opt : arguments)
{
- // merge arguments with preset's own arguments.
- List<Argument> oldargs = arguments;
- arguments = new ArrayList<Argument>();
- for (Option opt : pset.getjabaArguments()) {
- arguments.add(opt);
- }
- for (Argument opt: oldargs)
- {
- arguments.add(opt);
- }
+ newargs.add(opt);
}
-
- }else{
- throw new Error("Implementation error: Can only instantiate Jaba parameter sets.");
+ }
+ paramset = newargs;
}
+ else
+ {*/
+ throw new Error(
+ "Implementation error: Can only instantiate Jaba parameter sets.");
+ }
+ }
+ else
+ {
+ // just provided with a bunch of arguments
+ this.paramset = arguments;
}
- this.paramset = arguments;
if (editParams)
{
- if (sh.paramStore==null)
+ if (sh.paramStore == null)
{
- sh.paramStore = new JabaParamStore(sh);
+ sh.paramStore = new JabaParamStore(sh,
+ Desktop.getUserParameterStore());
}
WsJobParameters jobParams = new WsJobParameters(sh, preset);
if (!jobParams.showRunDialog())
return;
}
WsParamSetI prset = jobParams.getPreset();
- if (prset==null)
+ if (prset == null)
+ {
+ paramset = JabaParamStore.getJabafromJwsArgs(jobParams
+ .getJobParams());
+ }
+ else
{
- paramset = JabaParamStore.getJabafromJwsArgs(jobParams.getJobParams());
- } else {
- this.preset = ((JabaPreset)prset).p;
+ this.preset = prset; // ((JabaPreset) prset).p;
paramset = null; // no user supplied parameters.
}
}
rmsawsmenu.add(msawsmenu);
calcName = "";
}
-
+ boolean hasparams = service.hasParameters();
do
{
+ String action = "Align ";
if (submitGaps == true)
{
- msawsmenu = new JMenu("profile " + svcname);
+ action = "Realign ";
+ msawsmenu = new JMenu("Realign with " + svcname);
+ msawsmenu
+ .setToolTipText("Align sequences to an existing alignment");
rmsawsmenu.add(msawsmenu);
}
final boolean withGaps = submitGaps;
- JMenuItem method = new JMenuItem(calcName + "Defaults");
- method.setToolTipText("Align with default settings");
+
+ JMenuItem method = new JMenuItem(calcName + "with Defaults");
+ method.setToolTipText(action + "with default settings");
method.addActionListener(new ActionListener()
{
}
});
msawsmenu.add(method);
- method = new JMenuItem(calcName + "Edit and run ...");
- method.setToolTipText("View and change the parameters before alignment.");
-
- method.addActionListener(new ActionListener()
+ if (hasparams)
{
- public void actionPerformed(ActionEvent e)
- {
- AlignmentView msa = alignFrame.gatherSequencesForAlignment();
- new MsaWSClient(service, null, null, true, alignFrame.getTitle(),
- msa, withGaps, true, alignFrame.getViewport()
- .getAlignment().getDataset(), alignFrame);
+ // only add these menu options if the service has user-modifiable
+ // arguments
+ method = new JMenuItem("Edit settings and run ...");
+ method.setToolTipText("View and change the parameters before alignment.");
- }
- });
- msawsmenu.add(method);
- List<WsParamSetI> presets = service.getParamStore().getPresets();
- if (presets != null && presets.size() > 0)
- {
- JMenu presetlist = new JMenu(calcName + "Presets");
+ method.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentView msa = alignFrame.gatherSequencesForAlignment();
+ new MsaWSClient(service, null, null, true, alignFrame
+ .getTitle(), msa, withGaps, true, alignFrame
+ .getViewport().getAlignment().getDataset(), alignFrame);
- for (final WsParamSetI preset : presets)
+ }
+ });
+ msawsmenu.add(method);
+ List<WsParamSetI> presets = service.getParamStore().getPresets();
+ if (presets != null && presets.size() > 0)
{
- final JMenuItem methodR = new JMenuItem(preset.getName());
- methodR.setToolTipText("<html><p><strong>"
- + (preset.isModifiable() ? "User Preset"
- : "Service Preset") + "</strong><br/>"
- + preset.getDescription() + "</p></html>");
- methodR.addActionListener(new ActionListener()
+ JMenu presetlist = new JMenu("Run "+calcName + "with preset");
+
+ 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()
{
- AlignmentView msa = alignFrame.gatherSequencesForAlignment();
- new MsaWSClient(service, preset, alignFrame.getTitle(), msa,
- false, true, alignFrame.getViewport().getAlignment()
- .getDataset(), alignFrame);
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentView msa = alignFrame
+ .gatherSequencesForAlignment();
+ new MsaWSClient(service, preset, alignFrame.getTitle(),
+ msa, false, true, alignFrame.getViewport()
+ .getAlignment().getDataset(), alignFrame);
- }
+ }
- });
- presetlist.add(methodR);
+ });
+ presetlist.add(methodR);
+ }
+ msawsmenu.add(presetlist);
}
- msawsmenu.add(presetlist);
}
if (!submitGaps && canSubmitGaps())
{
git://source.jalview.org / jalview.git / blobdiff