-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
*/
package jalview.ws.jws2;
+import jalview.api.AlignCalcWorkerI;
+import jalview.bin.Cache;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvSwingUtils;
+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.JCheckBoxMenuItem;
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.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.WsParamSetI;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
/**
- * @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);
+ .getRegisteredWorkersOfClass(clientClass);
+ JabawsAlignCalcWorker worker;
if (clnts == null || clnts.size() == 0)
{
if (!processParams(sh, editParams))
{
return;
}
+ try {
+ worker = (JabawsAlignCalcWorker) (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("Implementation error",x);
+ }
alignFrame
.getViewport()
.getCalcManager()
.registerWorker(
- new AAConsClient(sh, alignFrame, preset, paramset));
+ worker);
+ alignFrame.getViewport().getCalcManager().startWorker(worker);
+
}
else
{
- AAConsClient worker = (AAConsClient) clnts.get(0);
+ worker = (JabawsAlignCalcWorker) 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(calcName + " Defaults");
+ 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("Edit settings and run ...");
+ annotservice
+ .setToolTipText("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("Run " + calcName + "with preset");
- aacons.addActionListener(new ActionListener()
+ for (final WsParamSetI preset : presets)
{
- public void actionPerformed(ActionEvent e)
+ 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()
{
- new SequenceAnnotationWSClient(service, alignFrame, null, true);
+ public void actionPerformed(ActionEvent e)
+ {
+ new SequenceAnnotationWSClient(service, alignFrame, preset,
+ false);
+ }
+
+ });
+ presetlist.add(methodR);
+ }
+ wsmenu.add(presetlist);
+ }
+
+ }
+ else
+ {
+ annotservice = new JMenuItem("View documentation");
+ if (service.docUrl != null)
+ {
+ annotservice.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ Desktop.instance.showUrl(service.docUrl);
}
});
- wsmenu.add(aacons);
- List<WsParamSetI> presets = service.getParamStore().getPresets();
- if (presets != null && presets.size() > 0)
- {
- JMenu presetlist = new JMenu("Run " + calcName + "with preset");
+ annotservice.setToolTipText("<html>"
+ + JvSwingUtils.wrapTooltip("View <a href=\""
+ + service.docUrl + "\">" + service.docUrl + "</a>")
+ + "</html>");
+ wsmenu.add(annotservice);
+ }
+ }
+ }
- for (final WsParamSetI preset : presets)
+
+ private boolean registerAAConWSInstance(final JMenu wsmenu,
+ final Jws2Instance service, final AlignFrame alignFrame)
+ {
+ final AlignAnalysisUIText aaui = service.getAlignAnalysisUI(); // null ; // AlignAnalysisUIText.aaConGUI.get(service.serviceType.toString());
+ if (aaui==null)
+ {
+ // not an instantaneous calculation GUI type service
+ return false;
+ }
+ // create the instaneous calculation GUI bits and update state if existing GUI elements already present
+
+ JCheckBoxMenuItem _aaConEnabled = null;
+ for (int i = 0; i < wsmenu.getItemCount(); i++)
+ {
+ JMenuItem item = wsmenu.getItem(i);
+ if (item instanceof JCheckBoxMenuItem
+ && item.getText().equals(aaui.getAAconToggle()))
+ {
+ _aaConEnabled = (JCheckBoxMenuItem) item;
+ }
+ }
+ // is there an aaCon worker already present - if so, set it to use the
+ // given service handle
+ {
+ List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
+ .getCalcManager()
+ .getRegisteredWorkersOfClass(aaui.getClient());
+ if (aaconClient != null && aaconClient.size() > 0)
+ {
+ JabawsAlignCalcWorker worker = (JabawsAlignCalcWorker) aaconClient.get(0);
+ if (!worker.service.hosturl.equals(service.hosturl))
+ {
+ // javax.swing.SwingUtilities.invokeLater(new Runnable()
{
- 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()
+ // @Override
+ // public void run()
{
- public void actionPerformed(ActionEvent e)
- {
- new SequenceAnnotationWSClient(service, alignFrame, preset,
- false);
- }
-
- });
- presetlist.add(methodR);
+ removeCurrentAAConWorkerFor(aaui, alignFrame);
+ buildCurrentAAConWorkerFor(aaui, alignFrame, service);
+ }
+ }// );
+ }
+ }
+ }
+
+ // is there a service already registered ? there shouldn't be if we are
+ // being called correctly
+ if (_aaConEnabled == null)
+ {
+ final JCheckBoxMenuItem aaConEnabled = new JCheckBoxMenuItem(
+ aaui.getAAconToggle());
+ wsmenu.addMenuListener(new MenuListener()
+ {
+
+ @Override
+ public void menuSelected(MenuEvent arg0)
+ {
+ // TODO: refactor to the implementing class.
+ wsmenu.setEnabled((alignFrame.getViewport().getAlignment()
+ .isNucleotide() ? aaui.isNa() : aaui.isPr()));
+ List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
+ .getCalcManager()
+ .getRegisteredWorkersOfClass(aaui.getClient());
+ if (aaconClient != null && aaconClient.size() > 0)
+ {
+ aaConEnabled.setSelected(true);
+ }
+ else
+ {
+ aaConEnabled.setSelected(false);
}
- wsmenu.add(presetlist);
}
+
+ @Override
+ public void menuDeselected(MenuEvent arg0)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void menuCanceled(MenuEvent arg0)
+ {
+ // TODO Auto-generated method stub
+
+ }
+ });
+ aaConEnabled.setToolTipText("<html><p>"
+ + JvSwingUtils.wrapTooltip(aaui.getAAconToggleTooltip() + "</p>")
+ + "</html>");
+ aaConEnabled.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
+ .getCalcManager()
+ .getRegisteredWorkersOfClass(aaui.getClient());
+ if (aaconClient != null && aaconClient.size() > 0)
+ {
+ removeCurrentAAConWorkerFor(aaui, alignFrame);
+ }
+ else
+ {
+ buildCurrentAAConWorkerFor(aaui, alignFrame);
+
+ }
+ }
+
+ });
+ wsmenu.add(aaConEnabled);
+ JMenuItem modifyParams = new JMenuItem(aaui.getAAeditSettings());
+ modifyParams.setToolTipText("<html><p>"
+ + JvSwingUtils.wrapTooltip(aaui.getAAeditSettingsTooltip() + "</p>")
+ + "</html>");
+ modifyParams.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ showAAConAnnotationSettingsFor(aaui, alignFrame);
+ }
+ });
+ wsmenu.add(modifyParams);
+
+ }
+ return true;
+ }
+
+ private static void showAAConAnnotationSettingsFor(final AlignAnalysisUIText aaui, AlignFrame alignFrame)
+ {
+ /*
+ * preferred settings Whether AACon is automatically recalculated Which
+ * AACon server to use What parameters to use
+ */
+ // could actually do a class search for this too
+ AAConSettings fave = (AAConSettings) alignFrame.getViewport()
+ .getCalcIdSettingsFor(aaui.getCalcId());
+ if (fave == null)
+ {
+ fave = createDefaultAAConSettings(aaui);
+ }
+ new SequenceAnnotationWSClient(fave, alignFrame, true);
+
+ }
+
+ private static void buildCurrentAAConWorkerFor(final AlignAnalysisUIText aaui, AlignFrame alignFrame)
+ {
+ buildCurrentAAConWorkerFor(aaui, alignFrame, null);
+ }
+
+ private static void buildCurrentAAConWorkerFor(final AlignAnalysisUIText aaui, AlignFrame alignFrame,
+ Jws2Instance service)
+ {
+ /*
+ * preferred settings Whether AACon is automatically recalculated Which
+ * AACon server to use What parameters to use
+ */
+ AAConSettings fave = (AAConSettings) alignFrame.getViewport()
+ .getCalcIdSettingsFor(aaui.getCalcId());
+ if (fave == null)
+ {
+ fave = createDefaultAAConSettings(aaui, service);
+ }
+ else
+ {
+ if (service != null
+ && !fave.getService().hosturl.equals(service.hosturl))
+ {
+ Cache.log.debug("Changing AACon service to " + service.hosturl
+ + " from " + fave.getService().hosturl);
+ fave.setService(service);
}
+ }
+ new SequenceAnnotationWSClient(fave, alignFrame, false);
+ }
+ private static AAConSettings createDefaultAAConSettings(AlignAnalysisUIText aaui)
+ {
+ return createDefaultAAConSettings(aaui, null);
+ }
+
+ private static AAConSettings createDefaultAAConSettings(AlignAnalysisUIText aaui,
+ Jws2Instance service)
+ {
+ if (service != null)
+ {
+ if (!service.serviceType.toString().equals(
+ compbio.ws.client.Services.AAConWS.toString()))
+ {
+ Cache.log
+ .warn("Ignoring invalid preferred service for AACon calculations (service type was "
+ + service.serviceType + ")");
+ service = null;
+ }
+ else
+ {
+ // check service is actually in the list of currently avaialable
+ // services
+ if (!Jws2Discoverer.getDiscoverer().getServices().contains(service))
+ {
+ // it isn't ..
+ service = null;
+ }
+ }
}
+ if (service == null)
+ {
+ // get the default service for AACon
+ service = Jws2Discoverer.getDiscoverer().getPreferredServiceFor(null,
+ aaui.getServiceType());
+ }
+ if (service == null)
+ {
+ // TODO raise dialog box explaining error, and/or open the JABA
+ // preferences menu.
+ throw new Error("No AACon service found.");
+ }
+ return new AAConSettings(true, service, null, null);
+ }
+
+ private static void removeCurrentAAConWorkerFor(AlignAnalysisUIText aaui, AlignFrame alignFrame)
+ {
+ alignFrame.getViewport().getCalcManager()
+ .removeRegisteredWorkersOfClass(aaui.getClient());
}
}
git://source.jalview.org / jalview.git / blobdiff