/*
- * 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.
*
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.util.ArrayList;
+import java.util.List;
import javax.swing.*;
import jalview.datamodel.*;
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!
* server is a WSDL2Java generated stub for an archetypal MsaWSI service.
*/
MsaWS server;
+
AlignFrame alignFrame;
+ private WsParamSetI preset;
+
+ private List<Argument> paramset;
+
+ public MsaWSClient(Jws2Discoverer.Jws2Instance sh, String altitle,
+ jalview.datamodel.AlignmentView msa, boolean submitGaps,
+ boolean preserveOrder, Alignment seqdataset,
+ AlignFrame _alignFrame)
+ {
+ this(sh, null, null, false, altitle, msa, submitGaps, preserveOrder,
+ seqdataset, _alignFrame);
+ // TODO Auto-generated constructor stub
+ }
+
+ public MsaWSClient(Jws2Discoverer.Jws2Instance sh, WsParamSetI preset,
+ String altitle, jalview.datamodel.AlignmentView msa,
+ boolean submitGaps, boolean preserveOrder, Alignment seqdataset,
+ AlignFrame _alignFrame)
+ {
+ this(sh, preset, null, false, altitle, msa, submitGaps, preserveOrder,
+ seqdataset, _alignFrame);
+ // TODO Auto-generated constructor stub
+ }
+
/**
* Creates a new MsaWSClient object that uses a service given by an externally
* retrieved ServiceHandle
* DOCUMENT ME!
*/
- public MsaWSClient(Jws2Discoverer.Jws2Instance sh, String altitle,
+ public MsaWSClient(Jws2Discoverer.Jws2Instance sh, WsParamSetI preset,
+ List<Argument> arguments, boolean editParams, String altitle,
jalview.datamodel.AlignmentView msa, boolean submitGaps,
boolean preserveOrder, Alignment seqdataset,
AlignFrame _alignFrame)
return;
}
server = sh.service;
+ 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)
+ {
+ 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;
+ }
+ WsParamSetI prset = jobParams.getPreset();
+ if (prset == null)
+ {
+ paramset = JabaParamStore.getJabafromJwsArgs(jobParams
+ .getJobParams());
+ }
+ else
+ {
+ this.preset = prset; // ((JabaPreset) prset).p;
+ paramset = null; // no user supplied parameters.
+ }
+ }
+
if ((wsInfo = setWebService(sh, false)) == null)
{
JOptionPane.showMessageDialog(Desktop.desktop,
private void startMsaWSClient(String altitle, AlignmentView msa,
boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
{
- //if (!locateWebService())
- // {
- // return;
- // }
+ // if (!locateWebService())
+ // {
+ // return;
+ // }
wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")
+ " of " + altitle + "\nJob details\n");
+ "alignment of " + altitle;
}
- MsaWSThread msathread = new MsaWSThread(server, WsURL, wsInfo,
- alignFrame, WebServiceName, jobtitle, msa, submitGaps,
- preserveOrder, seqdataset);
+ MsaWSThread msathread = new MsaWSThread(server, preset, paramset,
+ WsURL, wsInfo, alignFrame, WebServiceName, jobtitle, msa,
+ submitGaps, preserveOrder, seqdataset);
wsInfo.setthisService(msathread);
msathread.start();
}
return (WebServiceName.indexOf("lustal") > -1); // cheat!
}
- public void attachWSMenuEntry(JMenu msawsmenu,
+ public void attachWSMenuEntry(JMenu rmsawsmenu,
final Jws2Instance service, final AlignFrame alignFrame)
{
setWebService(service, true); // headless
- JMenuItem method = new JMenuItem(WebServiceName);
- method.setToolTipText(WsURL);
- method.addActionListener(new ActionListener()
+ boolean finished = true, submitGaps = false;
+ JMenu msawsmenu = rmsawsmenu;
+ String svcname = WebServiceName;
+ if (svcname.endsWith("WS"))
{
- public void actionPerformed(ActionEvent e)
+ svcname = svcname.substring(0, svcname.length() - 2);
+ }
+ String calcName = svcname + " ";
+ if (canSubmitGaps())
+ {
+ msawsmenu = new JMenu(svcname);
+ rmsawsmenu.add(msawsmenu);
+ calcName = "";
+ }
+ boolean hasparams = service.hasParameters();
+ do
+ {
+ String action = "Align ";
+ if (submitGaps == true)
{
- AlignmentView msa = alignFrame.gatherSequencesForAlignment();
- new MsaWSClient(service, alignFrame.getTitle(),
- msa, false, true, alignFrame.getViewport().getAlignment()
- .getDataset(), alignFrame);
-
+ action = "Realign ";
+ msawsmenu = new JMenu("Realign with " + svcname);
+ msawsmenu
+ .setToolTipText("Align sequences to an existing alignment");
+ rmsawsmenu.add(msawsmenu);
}
+ final boolean withGaps = submitGaps;
- });
- msawsmenu.add(method);
- if (canSubmitGaps())
- {
- // We know that ClustalWS can accept partial alignments for refinement.
- final JMenuItem methodR = new JMenuItem(WebServiceName
- + " (With Gaps)");
- methodR.setToolTipText(WsURL);
- methodR.addActionListener(new ActionListener()
+ JMenuItem method = new JMenuItem(calcName + "with Defaults");
+ method.setToolTipText(action + "with default settings");
+
+ method.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
AlignmentView msa = alignFrame.gatherSequencesForAlignment();
- new MsaWSClient(service, alignFrame.getTitle(),
- msa, true, true, alignFrame.getViewport().getAlignment()
+ new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
+ true, alignFrame.getViewport().getAlignment()
.getDataset(), alignFrame);
}
-
});
- msawsmenu.add(methodR);
+ msawsmenu.add(method);
+ if (hasparams)
+ {
+ // 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()
+ {
+ 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);
- }
+ }
+ });
+ msawsmenu.add(method);
+ List<WsParamSetI> presets = service.getParamStore().getPresets();
+ if (presets != null && presets.size() > 0)
+ {
+ JMenu presetlist = new JMenu("Run "+calcName + "with preset");
+
+ for (final WsParamSetI preset : presets)
+ {
+ 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()
+ {
+ 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);
+ }
+ msawsmenu.add(presetlist);
+ }
+ }
+ if (!submitGaps && canSubmitGaps())
+ {
+ submitGaps = true;
+ finished = false;
+ }
+ else
+ {
+ finished = true;
+ }
+ } while (!finished);
+ }
}
git://source.jalview.org / jalview.git / blobdiff