/*
- * 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.
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.util.ArrayList;
import java.util.List;
import javax.swing.*;
import jalview.gui.*;
import compbio.data.msa.MsaWS;
import compbio.metadata.Argument;
+import compbio.metadata.Option;
import compbio.metadata.Preset;
import compbio.metadata.PresetManager;
import jalview.ws.jws2.Jws2Discoverer.Jws2Instance;
+import jalview.ws.jws2.dm.JabaWsParamSet;
+import jalview.ws.params.WsParamSetI;
/**
* DOCUMENT ME!
// TODO Auto-generated constructor stub
}
- public MsaWSClient(Jws2Discoverer.Jws2Instance sh, Preset preset,
+ public MsaWSClient(Jws2Discoverer.Jws2Instance sh, WsParamSetI preset,
String altitle, jalview.datamodel.AlignmentView msa,
boolean submitGaps, boolean preserveOrder, Alignment seqdataset,
AlignFrame _alignFrame)
* DOCUMENT ME!
*/
- public MsaWSClient(Jws2Discoverer.Jws2Instance sh, Preset preset,
+ public MsaWSClient(Jws2Discoverer.Jws2Instance sh, WsParamSetI preset,
List<Argument> arguments, boolean editParams, String altitle,
jalview.datamodel.AlignmentView msa, boolean submitGaps,
boolean preserveOrder, Alignment seqdataset,
return;
}
server = sh.service;
- this.preset = preset;
- this.paramset = arguments;
+ if (preset != null)
+ {
+ if (preset instanceof JabaPreset)
+ {
+ 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)
+ {
+ newargs.add(opt);
+ }
+ }
+ 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;
+ }
if (editParams)
{
+ if (sh.paramStore == null)
+ {
+ sh.paramStore = new JabaParamStore(sh,
+ Desktop.getUserParameterStore());
+ }
WsJobParameters jobParams = new WsJobParameters(sh, preset);
if (!jobParams.showRunDialog())
{
return;
}
- preset = null;
- paramset = jobParams.getJobParams();
+ WsParamSetI prset = jobParams.getPreset();
+ if (prset == null)
+ {
+ paramset = JabaParamStore.getJabafromJwsArgs(jobParams
+ .getJobParams());
+ }
+ else
+ {
+ this.preset = ((JabaPreset) prset).p;
+ paramset = null; // no user supplied parameters.
+ }
}
if ((wsInfo = setWebService(sh, false)) == null)
String svcname = WebServiceName;
if (svcname.endsWith("WS"))
{
- svcname = svcname.substring(0,svcname.length()-2);
+ svcname = svcname.substring(0, svcname.length() - 2);
}
String calcName = svcname + " ";
if (canSubmitGaps())
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");
+ 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(calcName + "Edit and run ...");
+ method.setToolTipText("View and change the parameters before alignment.");
- }
- });
- msawsmenu.add(method);
- PresetManager presets = service.getPresets();
- if (presets != null && presets.getPresets().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 Preset preset : (List<Preset>) presets.getPresets())
+ }
+ });
+ 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>"+preset.getDescription()+"</p></html>");
- methodR.addActionListener(new ActionListener()
+ JMenu presetlist = new JMenu(calcName + "Presets");
+
+ 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