/*
- * 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 2.9.0b1)
+ * Copyright (C) 2015 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.
- *
+ * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvSwingUtils;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.WsParamSetI;
+
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.*;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.ToolTipManager;
-import jalview.datamodel.*;
-import jalview.gui.*;
import compbio.data.msa.MsaWS;
-import jalview.ws.jws2.Jws2Discoverer.Jws2Instance;
+import compbio.metadata.Argument;
/**
* DOCUMENT ME!
* server is a WSDL2Java generated stub for an archetypal MsaWSI service.
*/
MsaWS server;
- AlignFrame alignFrame;
+
+ public MsaWSClient(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(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
* DOCUMENT ME!
*/
- public MsaWSClient(Jws2Discoverer.Jws2Instance sh, String altitle,
+ public MsaWSClient(Jws2Instance sh, WsParamSetI preset,
+ List<Argument> arguments, boolean editParams, String altitle,
jalview.datamodel.AlignmentView msa, boolean submitGaps,
boolean preserveOrder, Alignment seqdataset,
AlignFrame _alignFrame)
{
- super();
- alignFrame = _alignFrame;
+ super(_alignFrame, preset, arguments);
+ if (!processParams(sh, editParams))
+ {
+ return;
+ }
+
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);
+ JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ .formatMessage("label.service_called_is_not_msa_service",
+ new String[] { sh.serviceType }), MessageManager
+ .getString("label.internal_jalview_error"),
+ JOptionPane.WARNING_MESSAGE);
return;
}
- server = sh.service;
+ server = (MsaWS) sh.service;
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);
+ JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ .formatMessage("label.msa_service_is_unknown",
+ new String[] { sh.serviceType }), MessageManager
+ .getString("label.internal_jalview_error"),
+ JOptionPane.WARNING_MESSAGE);
return;
}
+
startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);
}
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);
- wsInfo.setthisService(msathread);
- msathread.start();
+ 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
+ {
+ JOptionPane.showMessageDialog(alignFrame,
+ MessageManager.getString("info.invalid_msa_input_mininfo"),
+ MessageManager.getString("info.invalid_msa_notenough"),
+ JOptionPane.INFORMATION_MESSAGE);
+ wsInfo.setVisible(false);
+ }
+ }
+
+ public static void main(String[] args)
+ {
+ System.out.println("A".matches("(-*[a-zA-Z]-*){1}[a-zA-Z-]*"));
}
protected String getServiceActionKey()
return (WebServiceName.indexOf("lustal") > -1); // cheat!
}
- public void attachWSMenuEntry(JMenu msawsmenu,
+ public void attachWSMenuEntry(JMenu rmsawsmenu,
final Jws2Instance service, final AlignFrame alignFrame)
{
+ if (registerAAConWSInstance(rmsawsmenu, service, alignFrame))
+ {
+ // Alignment dependent analysis calculation WS gui
+ return;
+ }
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"))
+ {
+ svcname = svcname.substring(0, svcname.length() - 2);
+ }
+ String calcName = svcname + " ";
+ if (canSubmitGaps())
{
- public void actionPerformed(ActionEvent e)
+ 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(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;
- });
- 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(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()
{
public void actionPerformed(ActionEvent e)
{
AlignmentView msa = alignFrame.gatherSequencesForAlignment();
- new MsaWSClient(service, alignFrame.getTitle(),
- msa, true, true, alignFrame.getViewport().getAlignment()
- .getDataset(), alignFrame);
- }
+ if (msa != null)
+ {
+ 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(
+ MessageManager.getString("label.edit_settings_and_run"));
+ method.setToolTipText(MessageManager
+ .getString("label.view_and_change_parameters_before_alignment"));
- }
+ method.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentView msa = alignFrame.gatherSequencesForAlignment();
+ if (msa != null)
+ {
+ 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(
+ 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);
+ }
+ });
+ methodR.setToolTipText(JvSwingUtils.wrapTooltip(
+ true,
+ "<p><strong>"
+ + (preset.isModifiable() ? MessageManager
+ .getString("label.user_preset")
+ : MessageManager
+ .getString("label.service_preset"))
+ + "</strong><br/>" + preset.getDescription()
+ + "</p>"));
+ methodR.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentView msa = alignFrame
+ .gatherSequencesForAlignment();
+
+ if (msa != null)
+ {
+ MsaWSClient msac = 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