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.bin.Cache;
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.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
/**
- * @author jimp
+ * @author jprocter
*
*/
-public class SequenceAnnotationWSClient extends Jws2Client
+public class SequenceAnnotationWSClient extends Jws2Client
{
+ public static final String AAConsCalcId = "jabaws2.AACons";
+
/**
* initialise a client so its attachWSMenuEntry method can be called.
*/
AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
{
super(alignFrame, preset, null);
+ 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);
+ 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 AACons style client - take alignment, return annotation for columns
+ // Build an AACons style client - take alignment, return annotation for
+ // columns
List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
.getCalcManager()
{
return;
}
+ AAConsClient worker;
alignFrame
.getViewport()
.getCalcManager()
.registerWorker(
- new AAConsClient(sh, alignFrame, preset, paramset));
+ worker = new AAConsClient(sh, alignFrame,
+ this.preset, paramset));
+ alignFrame.getViewport().getCalcManager().startWorker(worker);
+
}
else
{
}
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.
+ // build IUPred style client. take sequences, returns annotation per
+ // sequence.
if (!processParams(sh, editParams))
{
return;
}
+ public SequenceAnnotationWSClient(AAConsSettings fave,
+ AlignFrame alignFrame, boolean b)
+ {
+ super(alignFrame, fave.getPreset(), fave.getJobArgset());
+ initSequenceAnnotationWSClient(fave.getService(), alignFrame,
+ fave.getPreset(), b);
+ }
+
/*
* (non-Javadoc)
*
public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
final AlignFrame alignFrame)
{
+ if (service.serviceType.equals(compbio.ws.client.Services.AAConWS
+ .toString()))
+ {
+ registerAAConsWSInstance(wsmenu, service, alignFrame);
+ return;
+ }
boolean hasparams = service.hasParameters();
// Assume name ends in WS
- String calcName = service.serviceType.substring(0,service.serviceType.length()-2);
+ String calcName = service.serviceType.substring(0,
+ service.serviceType.length() - 2);
JMenuItem aacons = new JMenuItem(calcName + " Defaults");
aacons.addActionListener(new ActionListener()
}
}
+
+ 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 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 an aaCons worker already present - if so, set it to use the
+ // given service handle
+ {
+ List<AlignCalcWorkerI> aaconsClient = alignFrame.getViewport()
+ .getCalcManager()
+ .getRegisteredWorkersOfClass(AAConsClient.class);
+ if (aaconsClient != null && aaconsClient.size() > 0)
+ {
+ AAConsClient worker = (AAConsClient) aaconsClient.get(0);
+ if (!worker.service.hosturl.equals(service.hosturl))
+ {
+ // javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ // @Override
+ // public void run()
+ {
+ removeCurrentAAConsWorkerFor(alignFrame);
+ buildCurrentAAConsWorkerFor(alignFrame, service);
+ }
+ }//);
+ }
+ }
+ }
+
+ // is there a service already registered ? there shouldn't be if we are
+ // being called correctly
+ if (_aaConsEnabled == null)
+ {
+ final JCheckBoxMenuItem aaConsEnabled = new JCheckBoxMenuItem(
+ AAconsToggle);
+ wsmenu.addMenuListener(new MenuListener()
+ {
+
+ @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)
+ {
+ // 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)
+ {
+ removeCurrentAAConsWorkerFor(alignFrame);
+ }
+ 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
+ */
+ // could actually do a class search for this too
+ AAConsSettings fave = (AAConsSettings) alignFrame.getViewport()
+ .getCalcIdSettingsFor(AAConsCalcId);
+ if (fave == null)
+ {
+ fave = createDefaultAAConsSettings();
+ }
+ new SequenceAnnotationWSClient(fave, alignFrame, true);
+
+ }
+
+ private static void buildCurrentAAConsWorkerFor(AlignFrame alignFrame)
+ {
+ buildCurrentAAConsWorkerFor(alignFrame, null);
+ }
+
+ private static void buildCurrentAAConsWorkerFor(AlignFrame alignFrame,
+ Jws2Instance service)
+ {
+ /*
+ * preferred settings Whether AACons is automatically recalculated Which
+ * AACons server to use What parameters to use
+ */
+ AAConsSettings fave = (AAConsSettings) alignFrame.getViewport()
+ .getCalcIdSettingsFor(AAConsCalcId);
+ if (fave == null)
+ {
+ fave = createDefaultAAConsSettings(service);
+ }
+ else
+ {
+ if (service != null
+ && !fave.getService().hosturl.equals(service.hosturl))
+ {
+ Cache.log.debug("Changing AACons service to " + service.hosturl
+ + " from " + fave.getService().hosturl);
+ fave.setService(service);
+ }
+ }
+ new SequenceAnnotationWSClient(fave, alignFrame, false);
+ }
+
+ private static AAConsSettings createDefaultAAConsSettings()
+ {
+ return createDefaultAAConsSettings(null);
+ }
+
+ private static AAConsSettings createDefaultAAConsSettings(
+ Jws2Instance service)
+ {
+ if (service != null)
+ {
+ if (!service.serviceType.toString().equals(
+ compbio.ws.client.Services.AAConWS.toString()))
+ {
+ Cache.log
+ .warn("Ignoring invalid preferred service for AACons 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 AACons
+ service = Jws2Discoverer.getDiscoverer().getPreferredServiceFor(null,
+ compbio.ws.client.Services.AAConWS.toString());
+ /*
+ * for (Jws2Instance sv : Jws2Discoverer.getDiscoverer().getServices()) {
+ * if (sv.serviceType.toString().equals(
+ * compbio.ws.client.Services.AAConWS.toString())) { service = sv; break;
+ * } }
+ */
+ }
+ 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