*/
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 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 compbio.metadata.Argument;
-
-import jalview.api.AlignCalcWorkerI;
-import jalview.datamodel.AlignmentView;
-import jalview.gui.AlignFrame;
-import jalview.gui.JvSwingUtils;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.WsParamSetI;
+import javax.swing.JOptionPane;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
/**
- * @author jimp
+ * @author jprocter
*
*/
public class SequenceAnnotationWSClient extends Jws2Client
{
+ public static final String AAConCalcId = "jabaws2.AACon";
+
/**
* initialise a client so its attachWSMenuEntry method can be called.
*/
AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
{
super(alignFrame, preset, null);
- List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
- .getCalcManager()
- .getRegisteredWorkersOfClass(AAConsClient.class);
- if (clnts == null || clnts.size() == 0)
+ initSequenceAnnotationWSClient(sh, alignFrame, preset, editParams);
+ }
+
+ public void initSequenceAnnotationWSClient(final Jws2Instance sh,
+ AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
+ {
+ 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;
+
+ }
+ if (sh.action.toLowerCase().contains("conservation"))
+ {
+ // Build an AACon style client - take alignment, return annotation for
+ // columns
+
+ List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
+ .getCalcManager()
+ .getRegisteredWorkersOfClass(AAConClient.class);
+ if (clnts == null || clnts.size() == 0)
+ {
+ if (!processParams(sh, editParams))
+ {
+ return;
+ }
+ AAConClient worker;
+ alignFrame
+ .getViewport()
+ .getCalcManager()
+ .registerWorker(
+ worker = new AAConClient(sh, alignFrame,
+ this.preset, paramset));
+ alignFrame.getViewport().getCalcManager().startWorker(worker);
+
+ }
+ else
+ {
+ AAConClient worker = (AAConClient) clnts.get(0);
+ if (editParams)
+ {
+ paramset = worker.getArguments();
+ preset = worker.getPreset();
+ }
+
+ 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(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()
- .registerWorker(
- new AAConsClient(sh, alignFrame, preset, paramset));
+ .startWorker(
+ new AADisorderClient(sh, alignFrame, preset, paramset));
}
- else
- {
- AAConsClient worker = (AAConsClient) clnts.get(0);
- if (editParams)
- {
- paramset = worker.getArguments();
- preset = worker.getPreset();
- }
- 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);
+ }
- }
+ 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 (service.serviceType.equals(compbio.ws.client.Services.AAConWS
+ .toString()))
+ {
+ registerAAConWSInstance(wsmenu, service, alignFrame);
+ 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";
- System.out.println("Making an aacons client!");
- 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");
+
+ 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.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ new SequenceAnnotationWSClient(service, alignFrame, preset,
+ false);
+ }
+
+ });
+ presetlist.add(methodR);
+ }
+ wsmenu.add(presetlist);
+ }
- aacons.addActionListener(new ActionListener()
+ }
+ else
+ {
+ annotservice = new JMenuItem("View documentation");
+ if (service.docUrl != null)
+ {
+ annotservice.addActionListener(new ActionListener()
{
- public void actionPerformed(ActionEvent e)
+
+ @Override
+ public void actionPerformed(ActionEvent arg0)
{
- new SequenceAnnotationWSClient(service, alignFrame, null, true);
+ 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);
+ }
+ }
+ }
+
+ private final String AAconToggle = "AACon Calculations",
+ AAconToggleTooltip = "When checked, AACon calculations are updated automatically.",
+ AAeditSettings = "Change AACon Settings...",
+ AAeditSettingsTooltip = "Modify settings for AACon calculations.";
- for (final WsParamSetI preset : presets)
+ private void registerAAConWSInstance(final JMenu wsmenu,
+ final Jws2Instance service, final AlignFrame alignFrame)
+ {
+ // register this in the AACon settings set
+ JCheckBoxMenuItem _aaConEnabled = null;
+ for (int i = 0; i < wsmenu.getItemCount(); i++)
+ {
+ JMenuItem item = wsmenu.getItem(i);
+ if (item instanceof JCheckBoxMenuItem
+ && item.getText().equals(AAconToggle))
+ {
+ _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(AAConClient.class);
+ if (aaconClient != null && aaconClient.size() > 0)
+ {
+ AAConClient worker = (AAConClient) 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(alignFrame);
+ buildCurrentAAConWorkerFor(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(
+ AAconToggle);
+ wsmenu.addMenuListener(new MenuListener()
+ {
+
+ @Override
+ public void menuSelected(MenuEvent arg0)
+ {
+ wsmenu.setEnabled(!alignFrame.getViewport().getAlignment()
+ .isNucleotide());
+ List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
+ .getCalcManager()
+ .getRegisteredWorkersOfClass(AAConClient.class);
+ if (aaconClient != null && aaconClient.size() > 0)
+ {
+ aaConEnabled.setSelected(true);
+ }
+ else
+ {
+ aaConEnabled.setSelected(false);
+ }
+ }
+
+ @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(AAconToggleTooltip + "</p>")
+ + "</html>");
+ aaConEnabled.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
+ .getCalcManager()
+ .getRegisteredWorkersOfClass(AAConClient.class);
+ if (aaconClient != null && aaconClient.size() > 0)
+ {
+ removeCurrentAAConWorkerFor(alignFrame);
}
- wsmenu.add(presetlist);
+ else
+ {
+ buildCurrentAAConWorkerFor(alignFrame);
+
+ }
+ }
+
+ });
+ wsmenu.add(aaConEnabled);
+ JMenuItem modifyParams = new JMenuItem(AAeditSettings);
+ modifyParams.setToolTipText("<html><p>"
+ + JvSwingUtils.wrapTooltip(AAeditSettingsTooltip + "</p>")
+ + "</html>");
+ modifyParams.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ showAAConAnnotationSettingsFor(alignFrame);
}
+ });
+ wsmenu.add(modifyParams);
+
+ }
+ }
+
+ private static void showAAConAnnotationSettingsFor(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(AAConCalcId);
+ if (fave == null)
+ {
+ fave = createDefaultAAConSettings();
+ }
+ new SequenceAnnotationWSClient(fave, alignFrame, true);
+
+ }
+
+ private static void buildCurrentAAConWorkerFor(AlignFrame alignFrame)
+ {
+ buildCurrentAAConWorkerFor(alignFrame, null);
+ }
+
+ private static void buildCurrentAAConWorkerFor(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(AAConCalcId);
+ if (fave == null)
+ {
+ fave = createDefaultAAConSettings(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()
+ {
+ return createDefaultAAConSettings(null);
+ }
+ private static AAConSettings createDefaultAAConSettings(
+ 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,
+ compbio.ws.client.Services.AAConWS.toString());
}
+ 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(AlignFrame alignFrame)
+ {
+ alignFrame.getViewport().getCalcManager()
+ .removeRegisteredWorkersOfClass(AAConClient.class);
}
}
git://source.jalview.org / jalview.git / blobdiff