/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
import java.util.Locale;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.util.List;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
import javax.swing.ToolTipManager;
import compbio.data.msa.MsaWS;
import compbio.metadata.Argument;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.gui.JvSwingUtils;
import jalview.util.MessageManager;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
/**
* DOCUMENT ME!
*
* @author $author$
* @version $Revision$
*/
public class MsaWSClient extends Jws2Client
{
/**
* server is a WSDL2Java generated stub for an archetypal MsaWSI service.
*/
MsaWS server;
public MsaWSClient(Jws2Instance sh, String altitle,
jalview.datamodel.AlignmentView msa, boolean submitGaps,
boolean preserveOrder, AlignmentI seqdataset,
AlignFrame _alignFrame)
{
this(sh, null, null, false, altitle, msa, submitGaps, preserveOrder,
seqdataset, _alignFrame);
// TODO Auto-generated constructor stub
}
public MsaWSClient(Jws2Instance sh, WsParamSetI preset, String altitle,
jalview.datamodel.AlignmentView msa, boolean submitGaps,
boolean preserveOrder, AlignmentI 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
*
* @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(Jws2Instance sh, WsParamSetI preset,
List arguments, boolean editParams, String altitle,
jalview.datamodel.AlignmentView msa, boolean submitGaps,
boolean preserveOrder, AlignmentI seqdataset,
AlignFrame _alignFrame)
{
super(_alignFrame, preset, arguments);
if (!processParams(sh, editParams))
{
return;
}
if (!(sh.service instanceof MsaWS))
{
// redundant at mo - but may change
JvOptionPane.showMessageDialog(Desktop.desktop,
MessageManager.formatMessage(
"label.service_called_is_not_msa_service",
new String[]
{ sh.serviceType }),
MessageManager.getString("label.internal_jalview_error"),
JvOptionPane.WARNING_MESSAGE);
return;
}
server = (MsaWS) sh.service;
if ((wsInfo = setWebService(sh, false)) == null)
{
JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.msa_service_is_unknown", new String[]
{ sh.serviceType }),
MessageManager.getString("label.internal_jalview_error"),
JvOptionPane.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, AlignmentI seqdataset)
{
// if (!locateWebService())
// {
// return;
// }
wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")
+ " of " + altitle + "\nJob details\n");
String jobtitle = WebServiceName.toLowerCase(Locale.ROOT);
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);
if (msathread.hasValidInput())
{
wsInfo.setthisService(msathread);
wsInfo.setVisible(true);
msathread.start();
}
else
{
wsInfo.setVisible(false);
JvOptionPane.showMessageDialog(alignFrame,
MessageManager.getString("info.invalid_msa_input_mininfo"),
MessageManager.getString("info.invalid_msa_notenough"),
JvOptionPane.INFORMATION_MESSAGE);
}
}
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!
}
@Override
public void attachWSMenuEntry(JMenu rmsawsmenu,
final Jws2Instance service, final AlignFrame af)
{
if (registerAAConWSInstance(rmsawsmenu, service, af))
{
// Alignment dependent analysis calculation WS gui
return;
}
setWebService(service, true); // headless
boolean finished = true, submitGaps = false;
JMenu msawsmenu = rmsawsmenu;
String svcname = WebServiceName;
if (svcname.endsWith("WS"))
{
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)
{
action = "Realign ";
msawsmenu = new JMenu(MessageManager
.formatMessage("label.realign_with_params", new String[]
{ svcname }));
msawsmenu.setToolTipText(MessageManager
.getString("label.align_sequences_to_existing_alignment"));
rmsawsmenu.add(msawsmenu);
}
final boolean withGaps = submitGaps;
JMenuItem method = new JMenuItem(MessageManager.formatMessage(
"label.calcname_with_default_settings", new String[]
{ calcName }));
method.setToolTipText(MessageManager.formatMessage(
"label.action_with_default_settings", new String[]
{ action }));
method.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
AlignmentView msa = af.gatherSequencesForAlignment();
if (msa != null)
{
new MsaWSClient(service, af.getTitle(), msa, withGaps, true,
af.getViewport().getAlignment().getDataset(), af);
}
}
});
msawsmenu.add(method);
if (hasparams)
{
// only add these menu options if the service has user-modifiable
// arguments
method = new JMenuItem(
MessageManager.getString("label.edit_settings_and_run"));
method.setToolTipText(MessageManager.getString(
"label.view_and_change_parameters_before_alignment"));
method.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
AlignmentView msa = af.gatherSequencesForAlignment();
if (msa != null)
{
startJob(service, af, withGaps, msa);
}
}
});
msawsmenu.add(method);
List presets = service.getParamStore().getPresets();
if (presets != null && presets.size() > 0)
{
JMenu presetlist = new JMenu(MessageManager.formatMessage(
"label.run_with_preset_params", new String[]
{ calcName }));
final int showToolTipFor = ToolTipManager.sharedInstance()
.getDismissDelay();
for (final WsParamSetI preSet : presets)
{
final JMenuItem methodR = new JMenuItem(preSet.getName());
final int QUICK_TOOLTIP = 1500;
// JAL-1582 shorten tooltip display time in these menu items as
// they can obscure other options
methodR.addMouseListener(new MouseAdapter()
{
@Override
public void mouseEntered(MouseEvent e)
{
ToolTipManager.sharedInstance()
.setDismissDelay(QUICK_TOOLTIP);
}
@Override
public void mouseExited(MouseEvent e)
{
ToolTipManager.sharedInstance()
.setDismissDelay(showToolTipFor);
}
});
String tooltip = JvSwingUtils.wrapTooltip(true, ""
+ (preSet.isModifiable()
? MessageManager.getString("label.user_preset")
: MessageManager
.getString("label.service_preset"))
+ "
" + preSet.getDescription());
methodR.setToolTipText(tooltip);
methodR.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
AlignmentView msa = af.gatherSequencesForAlignment();
if (msa != null)
{
MsaWSClient msac = new MsaWSClient(service, preSet,
af.getTitle(), msa, false, true,
af.getViewport().getAlignment().getDataset(), af);
}
}
});
presetlist.add(methodR);
}
msawsmenu.add(presetlist);
}
}
if (!submitGaps && canSubmitGaps())
{
submitGaps = true;
finished = false;
}
else
{
finished = true;
}
} while (!finished);
}
protected void startJob(final Jws2Instance service, final AlignFrame af,
final boolean withGaps, AlignmentView msa)
{
try
{
new MsaWSClient(service, null, null, true, af.getTitle(), msa,
withGaps, true, af.getViewport().getAlignment().getDataset(),
af);
} catch (Exception e)
{
JvOptionPane.showMessageDialog(alignFrame, e.getMessage(),
MessageManager.getString("label.state_job_error"),
JvOptionPane.WARNING_MESSAGE);
}
}
}