/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see .
*/
package jalview.ws.jws2;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
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.Preset;
import compbio.metadata.PresetManager;
import jalview.ws.jws2.Jws2Discoverer.Jws2Instance;
/**
* DOCUMENT ME!
*
* @author $author$
* @version $Revision$
*/
public class MsaWSClient extends Jws2Client
{
/**
* server is a WSDL2Java generated stub for an archetypal MsaWSI service.
*/
MsaWS server;
AlignFrame alignFrame;
private Preset preset;
private List paramset;
public MsaWSClient(Jws2Discoverer.Jws2Instance sh, String altitle,
jalview.datamodel.AlignmentView msa, boolean submitGaps,
boolean preserveOrder, Alignment seqdataset,
AlignFrame _alignFrame)
{
this(sh, null, null, altitle, msa, submitGaps, preserveOrder, seqdataset, _alignFrame);
// TODO Auto-generated constructor stub
}
public MsaWSClient(Jws2Discoverer.Jws2Instance sh, Preset preset, String altitle,
jalview.datamodel.AlignmentView msa, boolean submitGaps,
boolean preserveOrder, Alignment seqdataset,
AlignFrame _alignFrame)
{
this(sh, preset, null, 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
*
* @param sh
* service handle of type AbstractName(MsaWS)
* @param altitle
* DOCUMENT ME!
* @param msa
* DOCUMENT ME!
* @param submitGaps
* DOCUMENT ME!
* @param preserveOrder
* DOCUMENT ME!
*/
public MsaWSClient(Jws2Discoverer.Jws2Instance sh, Preset preset, List arguments, String altitle,
jalview.datamodel.AlignmentView msa, boolean submitGaps,
boolean preserveOrder, Alignment seqdataset,
AlignFrame _alignFrame) {
super();
alignFrame = _alignFrame;
if (!(sh.service instanceof MsaWS))
{
// redundant at mo - but may change
JOptionPane
.showMessageDialog(
Desktop.desktop,
"The Service called \n"
+ sh.serviceType
+ "\nis not a \nMultiple Sequence Alignment Service !",
"Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
return;
}
server = sh.service;
this.preset = preset;
this.paramset = arguments;
if ((wsInfo = setWebService(sh, false)) == null)
{
JOptionPane.showMessageDialog(Desktop.desktop,
"The Multiple Sequence Alignment Service named "
+ sh.serviceType + " is unknown",
"Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
return;
}
startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);
}
public MsaWSClient()
{
super();
// add a class reference to the list
}
private void startMsaWSClient(String altitle, AlignmentView msa,
boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
{
//if (!locateWebService())
// {
// return;
// }
wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")
+ " of " + altitle + "\nJob details\n");
String jobtitle = WebServiceName.toLowerCase();
if (jobtitle.endsWith("alignment"))
{
if (submitGaps
&& (!jobtitle.endsWith("realignment") || jobtitle
.indexOf("profile") == -1))
{
int pos = jobtitle.indexOf("alignment");
jobtitle = WebServiceName.substring(0, pos) + "re-alignment of "
+ altitle;
}
else
{
jobtitle = WebServiceName + " of " + altitle;
}
}
else
{
jobtitle = WebServiceName + (submitGaps ? " re" : " ")
+ "alignment of " + altitle;
}
MsaWSThread msathread = new MsaWSThread(server, preset, paramset, WsURL, wsInfo,
alignFrame, WebServiceName, jobtitle, msa, submitGaps,
preserveOrder, seqdataset);
wsInfo.setthisService(msathread);
msathread.start();
}
protected String getServiceActionKey()
{
return "MsaWS";
}
protected String getServiceActionDescription()
{
return "Multiple Sequence Alignment";
}
/**
* look at ourselves and work out if we are a service that can take a profile
* and align to it
*
* @return true if we can send gapped sequences to the alignment service
*/
private boolean canSubmitGaps()
{
// TODO: query service or extract service handle props to check if we can
// realign
return (WebServiceName.indexOf("lustal") > -1); // cheat!
}
public void attachWSMenuEntry(JMenu msawsmenu,
final Jws2Instance service, final AlignFrame alignFrame)
{
setWebService(service, true); // headless
JMenuItem method = new JMenuItem(WebServiceName);
method.setToolTipText(WsURL);
method.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
AlignmentView msa = alignFrame.gatherSequencesForAlignment();
new MsaWSClient(service, alignFrame.getTitle(),
msa, false, true, alignFrame.getViewport().getAlignment()
.getDataset(), alignFrame);
}
});
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()
{
public void actionPerformed(ActionEvent e)
{
AlignmentView msa = alignFrame.gatherSequencesForAlignment();
new MsaWSClient(service, alignFrame.getTitle(),
msa, true, true, alignFrame.getViewport().getAlignment()
.getDataset(), alignFrame);
}
});
msawsmenu.add(methodR);
}
PresetManager presets = service.getPresets();
if (presets!=null && presets.getPresets().size()>0)
{
JMenu presetlist = new JMenu("Presets for "+WebServiceName+"(Without gaps)");
for (final Preset preset : (List) presets.getPresets())
{
final JMenuItem methodR = new JMenuItem(preset.getName());
methodR.setToolTipText(preset.getDescription());
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);
}
}
}