import jalview.jbgui.*;
import jalview.schemes.*;
import jalview.ws.*;
+import jalview.ws.jws1.Discoverer;
+import jalview.ws.jws2.Jws2Discoverer;
/**
* DOCUMENT ME!
/* Set up intrinsic listeners for dynamically generated GUI bits. */
private void addServiceListeners()
{
- final java.beans.PropertyChangeListener thisListener;
+ final java.beans.PropertyChangeListener thisListener, thatListener;
// Do this once to get current state
BuildWebServiceMenu();
Desktop.discoverer
// System.out.println("Discoverer property change.");
if (evt.getPropertyName().equals("services"))
{
- // System.out.println("Rebuilding web service menu");
- BuildWebServiceMenu();
+ SwingUtilities.invokeLater(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ System.err
+ .println("Change support JWS1: build services again.");
+ BuildWebServiceMenu();
+ }
+
+ });
}
}
});
-
+ jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+ .addPropertyChangeListener(
+ thatListener = new java.beans.PropertyChangeListener()
+ {
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ System.err
+ .println("Change support JWS2: build services again.");
+ BuildWebServiceMenu();
+ }
+ });
addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
public void internalFrameClosed(
{
// System.out.println("deregistering discoverer listener");
Desktop.discoverer.removePropertyChangeListener(thisListener);
+ jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+ .removePropertyChangeListener(thatListener);
closeMenuItem_actionPerformed(true);
};
});
annotationPanelMenuItem.setState(av.showAnnotation);
viewBoxesMenuItem.setSelected(av.showBoxes);
viewTextMenuItem.setSelected(av.showText);
- showUnconservedMenuItem.setSelected(av.showUnconserved);
+ showNonconservedMenuItem.setSelected(av.showUnconserved);
showGroupConsensus.setSelected(av.showGroupConsensus);
showGroupConservation.setSelected(av.showGroupConservation);
showConsensusHistogram.setSelected(av.showConsensusHistogram);
if (viewport.hasHiddenColumns)
{
hiddenColumns = new Vector();
- int hiddenOffset = viewport.getSelectionGroup().getStartRes();
+ int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
+ .getSelectionGroup().getEndRes();
for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
.size(); i++)
{
int[] region = (int[]) viewport.getColumnSelection()
.getHiddenColumns().elementAt(i);
-
- hiddenColumns.addElement(new int[]
- { region[0] - hiddenOffset, region[1] - hiddenOffset });
+ if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
+ {
+ hiddenColumns.addElement(new int[]
+ { region[0] - hiddenOffset, region[1] - hiddenOffset });
+ }
}
}
return tp;
}
+ private boolean buildingMenu = false;
+
/**
* Generates menu items and listener event actions for web service clients
*
*/
public void BuildWebServiceMenu()
{
- // TODO: add support for context dependent disabling of services based on
- // alignment and current selection
- // TODO: add additional serviceHandle parameter to specify abstract handler
- // class independently of AbstractName
- // TODO: add in rediscovery GUI function to restart discoverer
- // TODO: group services by location as well as function and/or introduce
- // object broker mechanism.
- if ((Discoverer.services != null) && (Discoverer.services.size() > 0))
- {
- // TODO: refactor to allow list of AbstractName/Handler bindings to be
- // stored or retrieved from elsewhere
- Vector msaws = (Vector) Discoverer.services.get("MsaWS");
- Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
- Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
- // TODO: move GUI generation code onto service implementation - so a
- // client instance attaches itself to the GUI with method call like
- // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
- // alignframe)
+ while (buildingMenu)
+ {
+ try
+ {
+ System.err.println("Waiting for building menu to finish.");
+ Thread.sleep(10);
+ } catch (Exception e)
+ {
+ }
+ ;
+ }
+ buildingMenu = true;
+ try
+ {
+ System.err
+ .println("Building ws menu again " + Thread.currentThread());
+ // TODO: add support for context dependent disabling of services based on
+ // alignment and current selection
+ // TODO: add additional serviceHandle parameter to specify abstract
+ // handler
+ // class independently of AbstractName
+ // TODO: add in rediscovery GUI function to restart discoverer
+ // TODO: group services by location as well as function and/or introduce
+ // object broker mechanism.
Vector wsmenu = new Vector();
final IProgressIndicator af = this;
- if (msaws != null)
+ if ((Discoverer.services != null) && (Discoverer.services.size() > 0))
{
- // Add any Multiple Sequence Alignment Services
- final JMenu msawsmenu = new JMenu("Alignment");
- for (int i = 0, j = msaws.size(); i < j; i++)
+ // TODO: refactor to allow list of AbstractName/Handler bindings to be
+ // stored or retrieved from elsewhere
+ Vector msaws = (Vector) Discoverer.services.get("MsaWS");
+ Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
+ Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
+ // TODO: move GUI generation code onto service implementation - so a
+ // client instance attaches itself to the GUI with method call like
+ // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
+ // alignframe)
+ if (msaws != null)
{
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
- .get(i);
- jalview.ws.WSClient impl = jalview.ws.Discoverer
- .getServiceClient(sh);
- impl.attachWSMenuEntry(msawsmenu, this);
+ // Add any Multiple Sequence Alignment Services
+ final JMenu msawsmenu = new JMenu("Alignment");
+ for (int i = 0, j = msaws.size(); i < j; i++)
+ {
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
+ .get(i);
+ jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
+ .getServiceClient(sh);
+ impl.attachWSMenuEntry(msawsmenu, this);
+ }
+ wsmenu.add(msawsmenu);
+ }
+ if (secstrpr != null)
+ {
+ // Add any secondary structure prediction services
+ final JMenu secstrmenu = new JMenu(
+ "Secondary Structure Prediction");
+ for (int i = 0, j = secstrpr.size(); i < j; i++)
+ {
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
+ .get(i);
+ jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
+ .getServiceClient(sh);
+ impl.attachWSMenuEntry(secstrmenu, this);
+ }
+ wsmenu.add(secstrmenu);
+ }
+ if (seqsrch != null)
+ {
+ // Add any sequence search services
+ final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
+ for (int i = 0, j = seqsrch.size(); i < j; i++)
+ {
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
+ .elementAt(i);
+ jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
+ .getServiceClient(sh);
+ impl.attachWSMenuEntry(seqsrchmenu, this);
+ }
+ wsmenu.add(seqsrchmenu);
}
- wsmenu.add(msawsmenu);
}
- if (secstrpr != null)
+
+ // TODO: move into separate menu builder class.
{
- // Add any secondary structure prediction services
- final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
- for (int i = 0, j = secstrpr.size(); i < j; i++)
+ Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
+ if (jws2servs != null)
{
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
- .get(i);
- jalview.ws.WSClient impl = jalview.ws.Discoverer
- .getServiceClient(sh);
- impl.attachWSMenuEntry(secstrmenu, this);
+ if (jws2servs.hasServices())
+ {
+ JMenu jws2men = new JMenu("Jalview 2 Services");
+ jws2servs.attachWSMenuEntry(jws2men, this);
+ wsmenu.add(jws2men);
+ }
+ else
+ {
+ if (!jws2servs.isRunning())
+ {
+ new Thread(jws2servs).start();
+ }
+ }
}
- wsmenu.add(secstrmenu);
}
- if (seqsrch != null)
+ resetWebServiceMenu();
+ // finally, add the whole shebang onto the webservices menu
+ if (wsmenu.size() > 0)
{
- // Add any sequence search services
- final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
- for (int i = 0, j = seqsrch.size(); i < j; i++)
+ for (int i = 0, j = wsmenu.size(); i < j; i++)
{
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
- .elementAt(i);
- jalview.ws.WSClient impl = jalview.ws.Discoverer
- .getServiceClient(sh);
- impl.attachWSMenuEntry(seqsrchmenu, this);
+ webService.add((JMenu) wsmenu.get(i));
}
- wsmenu.add(seqsrchmenu);
}
- // finally, add the whole shebang onto the webservices menu
- resetWebServiceMenu();
- for (int i = 0, j = wsmenu.size(); i < j; i++)
+ else
{
- webService.add((JMenu) wsmenu.get(i));
+ this.webService.add(this.webServiceNoServices);
}
- }
- else
+ } catch (Exception e)
{
- resetWebServiceMenu();
- this.webService.add(this.webServiceNoServices);
}
+ ;
+ buildingMenu = false;
}
/**
*/
protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
{
- viewport.setShowUnconserved(showUnconservedMenuItem.getState());
+ viewport.setShowUnconserved(showNonconservedMenuItem.getState());
alignPanel.paintAlignment(true);
}
// set view properties for each group
for (int g = 0; g < gps.length; g++)
{
- gps[g].setShowunconserved(viewport.getShowUnconserved());
+ gps[g].setShowNonconserved(viewport.getShowUnconserved());
gps[g].setIncludeAllConsSymbols(viewport
.isIncludeAllConsensusSymbols());
viewport.alignment.addGroup(gps[g]);
git://source.jalview.org / jalview.git / blobdiff