/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 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.
- *
+ * 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 java.util.Locale;
+
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.util.ArrayList;
+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.ToolTipManager;
-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.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;
/**
*/
MsaWS server;
- AlignFrame alignFrame;
-
- private WsParamSetI preset;
-
- private List<Argument> paramset;
-
- public MsaWSClient(Jws2Discoverer.Jws2Instance sh, String altitle,
+ public MsaWSClient(Jws2Instance sh, String altitle,
jalview.datamodel.AlignmentView msa, boolean submitGaps,
- boolean preserveOrder, Alignment seqdataset,
+ boolean preserveOrder, AlignmentI seqdataset,
AlignFrame _alignFrame)
{
this(sh, null, null, false, altitle, msa, submitGaps, preserveOrder,
// TODO Auto-generated constructor stub
}
- public MsaWSClient(Jws2Discoverer.Jws2Instance sh, WsParamSetI preset,
- String altitle, jalview.datamodel.AlignmentView msa,
- boolean submitGaps, boolean preserveOrder, Alignment seqdataset,
+ 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,
* DOCUMENT ME!
*/
- public MsaWSClient(Jws2Discoverer.Jws2Instance sh, WsParamSetI preset,
+ public MsaWSClient(Jws2Instance sh, WsParamSetI preset,
List<Argument> arguments, boolean editParams, String altitle,
jalview.datamodel.AlignmentView msa, boolean submitGaps,
- boolean preserveOrder, Alignment seqdataset,
+ boolean preserveOrder, AlignmentI 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);
+ 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 = 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.
- }
- }
-
+ 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);
+ 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);
}
}
private void startMsaWSClient(String altitle, AlignmentView msa,
- boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
+ boolean submitGaps, boolean preserveOrder, AlignmentI seqdataset)
{
// if (!locateWebService())
// {
wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")
+ " of " + altitle + "\nJob details\n");
- String jobtitle = WebServiceName.toLowerCase();
+ String jobtitle = WebServiceName.toLowerCase(Locale.ROOT);
if (jobtitle.endsWith("alignment"))
{
- if (submitGaps
- && (!jobtitle.endsWith("realignment") || jobtitle
- .indexOf("profile") == -1))
+ if (submitGaps && (!jobtitle.endsWith("realignment")
+ || jobtitle.indexOf("profile") == -1))
{
int pos = jobtitle.indexOf("alignment");
jobtitle = WebServiceName.substring(0, pos) + "re-alignment of "
+ "alignment of " + altitle;
}
- MsaWSThread msathread = new MsaWSThread(server, preset, paramset,
- 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
+ {
+ 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 (WebServiceName.indexOf("lustal") > -1); // cheat!
}
+ @Override
public void attachWSMenuEntry(JMenu rmsawsmenu,
- final Jws2Instance service, final AlignFrame alignFrame)
+ 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;
if (submitGaps == true)
{
action = "Realign ";
- msawsmenu = new JMenu("Realign with " + svcname);
- msawsmenu
- .setToolTipText("Align sequences to an existing alignment");
+ 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(calcName + "with Defaults");
- method.setToolTipText(action + "with default settings");
+ 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 = alignFrame.gatherSequencesForAlignment();
- new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
- true, alignFrame.getViewport().getAlignment()
- .getDataset(), alignFrame);
+ AlignmentView msa = af.gatherSequencesForAlignment();
+
+ if (msa != null)
+ {
+ new MsaWSClient(service, af.getTitle(), msa, withGaps,
+ true,
+ af.getViewport().getAlignment().getDataset(),
+ af);
+ }
}
});
{
// 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 = 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 = alignFrame.gatherSequencesForAlignment();
- new MsaWSClient(service, null, null, true, alignFrame
- .getTitle(), msa, withGaps, true, alignFrame
- .getViewport().getAlignment().getDataset(), alignFrame);
+ AlignmentView msa = af.gatherSequencesForAlignment();
+ if (msa != null)
+ {
+ startJob(service, af, withGaps, msa);
+ }
}
});
List<WsParamSetI> presets = service.getParamStore().getPresets();
if (presets != null && presets.size() > 0)
{
- JMenu presetlist = new JMenu("Run "+calcName + "with preset");
+ JMenu presetlist = new JMenu(MessageManager.formatMessage(
+ "label.run_with_preset_params", new String[]
+ { calcName }));
- for (final WsParamSetI preset : presets)
+ final int showToolTipFor = ToolTipManager.sharedInstance()
+ .getDismissDelay();
+ 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>");
+ 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, "<strong>"
+ + (preSet.isModifiable()
+ ? MessageManager.getString("label.user_preset")
+ : MessageManager
+ .getString("label.service_preset"))
+ + "</strong><br/>" + preSet.getDescription());
+ methodR.setToolTipText(tooltip);
methodR.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- AlignmentView msa = alignFrame
+ AlignmentView msa = af
.gatherSequencesForAlignment();
- new MsaWSClient(service, preset, alignFrame.getTitle(),
- msa, false, true, alignFrame.getViewport()
- .getAlignment().getDataset(), alignFrame);
+
+ if (msa != null)
+ {
+ MsaWSClient msac = new MsaWSClient(service, preSet,
+ af.getTitle(), msa, false, true,
+ af.getViewport().getAlignment()
+ .getDataset(),
+ af);
+ }
}
}
} 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);
+
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff