/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 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;
+ this.preset=preset;
if (preset != null)
{
- if (preset instanceof JabaPreset)
- {
+ if (!((preset instanceof JabaPreset) || preset instanceof JabaWsParamSet)) {
+ /*{
this.preset = ((JabaPreset) preset).p;
}
else if (preset instanceof JabaWsParamSet)
paramset = newargs;
}
else
- {
+ {*/
throw new Error(
"Implementation error: Can only instantiate Jaba parameter sets.");
}
}
else
{
- this.preset = ((JabaPreset) prset).p;
+ this.preset = prset; // ((JabaPreset) prset).p;
paramset = null; // no user supplied parameters.
}
}
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);
if (hasparams)
{
- // only add these menu options if the service has user-modifiable arguments
- method = new JMenuItem(calcName + "Edit and run ...");
+ // 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.");
method.addActionListener(new ActionListener()
List<WsParamSetI> presets = service.getParamStore().getPresets();
if (presets != null && presets.size() > 0)
{
- JMenu presetlist = new JMenu(calcName + "Presets");
+ JMenu presetlist = new JMenu("Run "+calcName + "with preset");
for (final WsParamSetI preset : presets)
{