-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * 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.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-
-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.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.
*/
AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
{
super(alignFrame, preset, null);
- if (sh.serviceType.toLowerCase().contains("aaconws"))
+ 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)
+ {
+ // 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)
{
- // Build an AACons client
- if (alignFrame.getViewport().getAlignment().isNucleotide())
- {
- JOptionPane
- .showMessageDialog(
- Desktop.desktop,
- "AACons can only be used\nfor amino acid alignments.\nSorry about that!",
- "Wrong type of sequences!",
- JOptionPane.WARNING_MESSAGE);
- return;
+ Class clientClass = aaui.getClient();
+
+ // 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;
}
- alignFrame
- .getViewport()
- .getCalcManager()
- .registerWorker(
- new AAConsClient(sh, alignFrame, 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();
}
if (!processParams(sh, editParams, true))
+ {
return;
+ }
// 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"))
+ {
+ // build IUPred style client. take sequences, returns annotation per
+ // sequence.
+ if (!processParams(sh, editParams))
+ {
+ return;
+ }
+
+ alignFrame
+ .getViewport()
+ .getCalcManager()
+ .startWorker(
+ new AADisorderClient(sh, alignFrame, preset, paramset));
+ }
+ }
+
+ public SequenceAnnotationWSClient(AAConSettings fave,
+ AlignFrame alignFrame, boolean b)
+ {
+ super(alignFrame, fave.getPreset(), fave.getJobArgset());
+ initSequenceAnnotationWSClient(fave.getService(), alignFrame,
+ fave.getPreset(), b);
}
/*
public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
final AlignFrame alignFrame)
{
- if (service.serviceType.toLowerCase().contains("aaconws"))
+ if (registerAAConWSInstance(wsmenu, service, alignFrame))
+ {
+ // Alignment dependent analysis calculation WS gui
+ return;
+ }
+ boolean hasparams = service.hasParameters();
+ // Assume name ends in WS
+ String calcName = service.serviceType.substring(0,
+ service.serviceType.length() - 2);
+
+ JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage(
+ "label.calcname_with_default_settings",
+ new String[] { calcName }));
+ annotservice.addActionListener(new ActionListener()
{
- boolean hasparams = service.hasParameters();
- String calcName = "AACons";
- JMenuItem aacons = new JMenuItem("AACons Defaults");
- aacons.addActionListener(new ActionListener()
+
+ @Override
+ public void actionPerformed(ActionEvent e)
{
+ new SequenceAnnotationWSClient(service, alignFrame, null, false);
+ }
+ });
+ wsmenu.add(annotservice);
+ if (hasparams)
+ {
+ // only add these menu options if the service has user-modifiable
+ // arguments
+ annotservice = new JMenuItem(
+ MessageManager.getString("label.edit_settings_and_run"));
+ annotservice
+ .setToolTipText(MessageManager
+ .getString("label.view_and_change_parameters_before_running_calculation"));
- @Override
+ annotservice.addActionListener(new ActionListener()
+ {
public void actionPerformed(ActionEvent e)
{
- new SequenceAnnotationWSClient(service, alignFrame, null, false);
+ new SequenceAnnotationWSClient(service, alignFrame, null, true);
}
});
- wsmenu.add(aacons);
- if (hasparams)
+ wsmenu.add(annotservice);
+ List<WsParamSetI> presets = service.getParamStore().getPresets();
+ if (presets != null && presets.size() > 0)
{
- // only add these menu options if the service has user-modifiable
- // arguments
- aacons = new JMenuItem("Edit settings and run ...");
- aacons.setToolTipText("View and change the parameters before alignment.");
+ JMenu presetlist = new JMenu(MessageManager.formatMessage(
+ "label.run_with_preset", new String[] { calcName }));
- aacons.addActionListener(new ActionListener()
+ for (final WsParamSetI preset : presets)
{
- public void actionPerformed(ActionEvent e)
+ final JMenuItem methodR = new JMenuItem(preset.getName());
+ 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()
{
- new SequenceAnnotationWSClient(service, alignFrame, null, true);
- }
- });
- wsmenu.add(aacons);
- List<WsParamSetI> presets = service.getParamStore().getPresets();
- if (presets != null && presets.size() > 0)
+ public void actionPerformed(ActionEvent e)
+ {
+ new SequenceAnnotationWSClient(service, alignFrame, preset,
+ false);
+ }
+
+ });
+ presetlist.add(methodR);
+ }
+ wsmenu.add(presetlist);
+ }
+
+ }
+ else
+ {
+ annotservice = new JMenuItem(
+ MessageManager.getString("label.view_documentation"));
+ if (service.docUrl != null)
+ {
+ annotservice.addActionListener(new ActionListener()
{
- JMenu presetlist = new JMenu("Run " + calcName + "with preset");
- for (final WsParamSetI preset : presets)
+ @Override
+ public void actionPerformed(ActionEvent arg0)
{
- 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.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- new SequenceAnnotationWSClient(service, alignFrame, preset,
- false);
- }
-
- });
- presetlist.add(methodR);
+ Desktop.instance.showUrl(service.docUrl);
}
- wsmenu.add(presetlist);
- }
+ });
+ annotservice.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.formatMessage("label.view_service_doc_url",
+ new String[] { service.docUrl, service.docUrl })));
+ wsmenu.add(annotservice);
}
-
}
}
}
git://source.jalview.org / jalview.git / blobdiff