-/**
+/*
+ * 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.List;
-
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.event.AncestorEvent;
-import javax.swing.event.AncestorListener;
-import javax.swing.event.MenuEvent;
-import javax.swing.event.MenuListener;
-
-import compbio.metadata.Argument;
-
import jalview.api.AlignCalcWorkerI;
-import jalview.datamodel.AlignmentView;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
-import jalview.gui.JalviewDialog;
import jalview.gui.JvSwingUtils;
-import jalview.ws.jws2.dm.AAConsSettings;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.dm.AAConSettings;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
+import jalview.ws.uimodel.AlignAnalysisUIText;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.List;
+
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
/**
- * @author jimp
+ * @author jprocter
*
*/
public class SequenceAnnotationWSClient extends Jws2Client
{
-
/**
* initialise a client so its attachWSMenuEntry method can be called.
*/
super(alignFrame, preset, null);
initSequenceAnnotationWSClient(sh, alignFrame, preset, editParams);
}
-
+
+ // dan think. Do I need to change this method to run RNAalifold through the
+ // GUI
+
public void initSequenceAnnotationWSClient(final Jws2Instance sh,
AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
{
- if (alignFrame.getViewport().getAlignment().isNucleotide())
+ // dan changed! dan test. comment out if conditional
+ // if (alignFrame.getViewport().getAlignment().isNucleotide())
+ // {
+ // JOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
+ // + " can only be used\nfor amino acid alignments.",
+ // "Wrong type of sequences!", JOptionPane.WARNING_MESSAGE);
+ // return;
+ //
+ // }
+ AlignAnalysisUIText aaui = sh.getAlignAnalysisUI();
+ if (aaui != null)
{
- JOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
- + " can only be used\nfor amino acid alignments.",
- "Wrong type of sequences!", JOptionPane.WARNING_MESSAGE);
- return;
+ Class clientClass = aaui.getClient();
- }
- if (sh.action.toLowerCase().contains("conservation"))
- {
- // Build an AACons style client - take alignment, return annotation for
+ // Build an AACon style client - take alignment, return annotation for
// columns
List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
- .getCalcManager()
- .getRegisteredWorkersOfClass(AAConsClient.class);
+ .getCalcManager().getRegisteredWorkersOfClass(clientClass);
+ AbstractJabaCalcWorker worker;
if (clnts == null || clnts.size() == 0)
{
if (!processParams(sh, editParams))
{
return;
}
- AAConsClient worker;
- alignFrame
- .getViewport()
- .getCalcManager()
- .registerWorker(
- worker = new AAConsClient(sh, alignFrame, this.preset,
- paramset));
- alignFrame.getViewport().setPreferredAAConsSettings(new AAConsSettings(true, sh, this.preset, paramset));
+ try
+ {
+ worker = (AbstractJabaCalcWorker) (clientClass
+ .getConstructor(new Class[] { Jws2Instance.class,
+ AlignFrame.class, WsParamSetI.class, List.class })
+ .newInstance(new Object[] { sh, alignFrame, this.preset,
+ paramset }));
+ } catch (Exception x)
+ {
+ x.printStackTrace();
+ throw new Error(
+ MessageManager.getString("error.implementation_error"), x);
+ }
+ alignFrame.getViewport().getCalcManager().registerWorker(worker);
alignFrame.getViewport().getCalcManager().startWorker(worker);
}
else
{
- AAConsClient worker = (AAConsClient) clnts.get(0);
+ worker = (AbstractJabaCalcWorker) clnts.get(0);
if (editParams)
{
paramset = worker.getArguments();
{
return;
}
- alignFrame.getViewport().setPreferredAAConsSettings(new AAConsSettings(true, sh, preset, paramset));
// reinstate worker if it was blacklisted (might have happened due to
// invalid parameters)
alignFrame.getViewport().getCalcManager().workerMayRun(worker);
- worker.updateParameters(preset, paramset);
-
+ worker.updateParameters(this.preset, paramset);
}
}
if (sh.action.toLowerCase().contains("disorder"))
.startWorker(
new AADisorderClient(sh, alignFrame, preset, paramset));
}
-
}
- public SequenceAnnotationWSClient(AAConsSettings fave,
+ public SequenceAnnotationWSClient(AAConSettings fave,
AlignFrame alignFrame, boolean b)
{
super(alignFrame, fave.getPreset(), fave.getJobArgset());
- initSequenceAnnotationWSClient(fave.getService(), alignFrame, fave.getPreset(), b);
+ initSequenceAnnotationWSClient(fave.getService(), alignFrame,
+ fave.getPreset(), b);
}
/*
public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
final AlignFrame alignFrame)
{
- if (service.serviceType.equals(compbio.ws.client.Services.AAConWS
- .toString()))
+ if (registerAAConWSInstance(wsmenu, service, alignFrame))
{
- registerAAConsWSInstance(wsmenu, service, alignFrame);
+ // Alignment dependent analysis calculation WS gui
return;
}
boolean hasparams = service.hasParameters();
String calcName = service.serviceType.substring(0,
service.serviceType.length() - 2);
- JMenuItem aacons = new JMenuItem(calcName + " Defaults");
- aacons.addActionListener(new ActionListener()
+ JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage(
+ "label.calcname_with_default_settings",
+ new String[] { calcName }));
+ annotservice.addActionListener(new ActionListener()
{
@Override
new SequenceAnnotationWSClient(service, alignFrame, null, false);
}
});
- wsmenu.add(aacons);
+ wsmenu.add(annotservice);
if (hasparams)
{
// only add these menu options if the service has user-modifiable
// arguments
- aacons = new JMenuItem("Edit settings and run ...");
- aacons.setToolTipText("View and change parameters before running calculation");
+ annotservice = new JMenuItem(
+ MessageManager.getString("label.edit_settings_and_run"));
+ annotservice
+ .setToolTipText(MessageManager
+ .getString("label.view_and_change_parameters_before_running_calculation"));
- aacons.addActionListener(new ActionListener()
+ annotservice.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
new SequenceAnnotationWSClient(service, alignFrame, null, true);
}
});
- wsmenu.add(aacons);
+ wsmenu.add(annotservice);
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", new String[] { calcName }));
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.setToolTipText(JvSwingUtils.wrapTooltip(
+ true,
+ "<strong>"
+ + (preset.isModifiable() ? MessageManager
+ .getString("label.user_preset")
+ : MessageManager
+ .getString("label.service_preset"))
+ + "</strong><br/>" + preset.getDescription()));
methodR.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
}
- }
-
- private final String AAconsToggle = "AACons Calculations",
- AAconsToggleTooltip = "When checked, AACons calculations are updated automatically.",
- AAeditSettings = "Change AACons Settings...",
- AAeditSettingsTooltip = "Modify settings for AACons calculations.";
-
- private SequenceAnnotationWSClient preferredAAConsClient = null;
-
- // private final enableAAConsCalculation(final AlignFrame alignFrame, )
- private void registerAAConsWSInstance(final JMenu wsmenu,
- final Jws2Instance service, final AlignFrame alignFrame)
- {
- // register this in the AACons settings set
- JCheckBoxMenuItem _aaConsEnabled = null;
- for (int i = 0; i < wsmenu.getItemCount(); i++)
- {
- JMenuItem item = wsmenu.getItem(i);
- if (item instanceof JCheckBoxMenuItem
- && item.getText().equals(AAconsToggle))
- {
- _aaConsEnabled = (JCheckBoxMenuItem) item;
- }
- }
-
- // is there a service already registered ?
- if (_aaConsEnabled == null)
+ else
{
- final JCheckBoxMenuItem aaConsEnabled = new JCheckBoxMenuItem(
- AAconsToggle);
- wsmenu.addMenuListener(new MenuListener()
+ annotservice = new JMenuItem(
+ MessageManager.getString("label.view_documentation"));
+ if (service.docUrl != null)
{
-
- @Override
- public void menuSelected(MenuEvent arg0)
- {
- wsmenu.setEnabled(!alignFrame.getViewport().getAlignment()
- .isNucleotide());
- List<AlignCalcWorkerI> aaconsClient = alignFrame.getViewport()
- .getCalcManager()
- .getRegisteredWorkersOfClass(AAConsClient.class);
- if (aaconsClient != null && aaconsClient.size() > 0)
- {
- aaConsEnabled.setSelected(true);
- }
- else
- {
- aaConsEnabled.setSelected(false);
- }
- }
-
- @Override
- public void menuDeselected(MenuEvent arg0)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void menuCanceled(MenuEvent arg0)
+ annotservice.addActionListener(new ActionListener()
{
- // TODO Auto-generated method stub
- }
- });
- aaConsEnabled.setToolTipText("<html><p>"
- + JvSwingUtils.wrapTooltip(AAconsToggleTooltip + "</p>")
- + "</html>");
- aaConsEnabled.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent arg0)
- {
- // aaConsEnabled.setSelected(!aaConsEnabled.isSelected());
- List<AlignCalcWorkerI> aaconsClient = alignFrame.getViewport()
- .getCalcManager()
- .getRegisteredWorkersOfClass(AAConsClient.class);
- if (aaconsClient != null && aaconsClient.size() > 0)
+ @Override
+ public void actionPerformed(ActionEvent arg0)
{
- removeCurrentAAConsWorkerFor(alignFrame);
+ Desktop.instance.showUrl(service.docUrl);
}
- else
- {
- buildCurrentAAConsWorkerFor(alignFrame);
-
- }
- }
-
- });
- wsmenu.add(aaConsEnabled);
- JMenuItem modifyParams = new JMenuItem(AAeditSettings);
- modifyParams.setToolTipText("<html><p>"
- + JvSwingUtils.wrapTooltip(AAeditSettingsTooltip + "</p>")
- + "</html>");
- modifyParams.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent arg0)
- {
- showAAConsAnnotationSettingsFor(alignFrame);
- }
- });
- wsmenu.add(modifyParams);
-
- }
-
- }
-
- private static void showAAConsAnnotationSettingsFor(AlignFrame alignFrame)
- {
- /*
- * preferred settings
- * Whether AACons is automatically recalculated
- * Which AACons server to use
- * What parameters to use
- */
- AAConsSettings fave= alignFrame.getViewport().getPreferredAAConsSettings();
- if (fave==null)
- {
- fave = createDefaultAAConsSettings();
- }
- new SequenceAnnotationWSClient(fave, alignFrame, true);
-
- }
- private static void buildCurrentAAConsWorkerFor(AlignFrame alignFrame)
- {
- /*
- * preferred settings
- * Whether AACons is automatically recalculated
- * Which AACons server to use
- * What parameters to use
- */
- AAConsSettings fave= alignFrame.getViewport().getPreferredAAConsSettings();
- if (fave==null)
- {
- fave = createDefaultAAConsSettings();
- }
- new SequenceAnnotationWSClient(fave, alignFrame, false);
- }
-
- private static AAConsSettings createDefaultAAConsSettings()
- {
- Jws2Instance service=null;
- // set sensible defaults
- for (Jws2Instance sv: Jws2Discoverer.getDiscoverer().getServices()) {
- if (sv.serviceType.toString().equals(compbio.ws.client.Services.AAConWS.toString()))
- {
- service = sv;
- break;
+ });
+ annotservice.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.formatMessage("label.view_service_doc_url",
+ new String[] { service.docUrl, service.docUrl })));
+ wsmenu.add(annotservice);
}
}
- if (service==null)
- {
- // TODO raise dialog box explaining error, and/or open the JABA preferences menu.
- throw new Error("No AACons service found.");
- }
- return new AAConsSettings(true, service, null, null);
- }
-
- private static void removeCurrentAAConsWorkerFor(AlignFrame alignFrame)
- {
- alignFrame.getViewport().getCalcManager()
- .removeRegisteredWorkersOfClass(AAConsClient.class);
- // AAConsClient.removeAAConsAnnotation(alignFrame.alignPanel);
-
}
}
git://source.jalview.org / jalview.git / blobdiff