import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.HashMap;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
import java.util.StringTokenizer;
import java.util.Vector;
// dynamically regenerate service list.
populateWSMenuEntry(wsmenu, alignFrame, null);
}
-
+ private boolean isRecalculable(String action) {
+ return (action!=null && action.equalsIgnoreCase("conservation"));
+ }
private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame, String typeFilter)
{
if (running || services == null || services.size() == 0)
* for moment we keep them separate.
*/
JMenu atpoint;
- MsaWSClient msacl = new MsaWSClient();
- Vector hostLabels = new Vector();
+ List<Jws2Instance> enumerableServices=new ArrayList<Jws2Instance>();
//jws2al.removeAll();
- Hashtable<String,String> lasthostFor = new Hashtable<String,String>();
+ Map<String, Jws2Instance> preferredHosts=new HashMap<String,Jws2Instance>();
+ Map<String, List<Jws2Instance>> alternates = new HashMap<String, List<Jws2Instance>>();
+ for (Jws2Instance service : services.toArray(new Jws2Instance[0]))
+ {
+ if (!isRecalculable(service.action)) {
+ // add 'one shot' services to be displayed using the classic menu structure
+ enumerableServices.add(service);
+ } else {
+ if (!preferredHosts.containsKey(service.serviceType))
+ {
+ Jws2Instance preferredInstance = getPreferredServiceFor(alignFrame,
+ service.serviceType);
+ if (preferredInstance != null)
+ {
+ preferredHosts.put(service.serviceType, preferredInstance);
+ }
+ else
+ {
+ preferredHosts.put(service.serviceType, service);
+ }
+ }
+ List<Jws2Instance> ph=alternates.get(service.serviceType);
+ if (preferredHosts.get(service.serviceType)!=service)
+ {
+ if (ph==null)
+ {
+ ph=new ArrayList<Jws2Instance>();
+ }
+ ph.add(service);
+ alternates.put(service.serviceType, ph);
+ }
+ }
+
+ }
+
+ // create GUI element for classic services
+ addEnumeratedServices(jws2al, alignFrame, enumerableServices);
+ // and the instantaneous services
+ for (final Jws2Instance service : preferredHosts.values())
+ {
+ atpoint = JvSwingUtils.findOrCreateMenu(jws2al,service.action);
+ JMenuItem hitm;
+ if (atpoint.getItemCount()>1) {
+ // previous service of this type already present
+ atpoint.addSeparator();
+ }
+ atpoint.add(hitm = new JMenuItem(service.getHost()));
+ hitm.setForeground(Color.blue);
+ hitm.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ Desktop.showUrl(service.getHost());
+ }
+ });
+ hitm.setToolTipText(JvSwingUtils
+ .wrapTooltip("Opens the JABAWS server's homepage in web browser"));
+
+ service.attachWSMenuEntry(atpoint, alignFrame);
+ if (alternates.containsKey(service.serviceType))
+ {
+ atpoint.add(hitm=new JMenu("Switch server"));
+ hitm.setToolTipText(JvSwingUtils.wrapTooltip("Choose a server for running this service"));
+ for (final Jws2Instance sv:alternates.get(service.serviceType))
+ {
+ JMenuItem itm;
+ hitm.add(itm=new JMenuItem(sv.getHost()));
+ itm.setForeground(Color.blue);
+ itm.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ new Thread(new Runnable() {
+ public void run() {
+ setPreferredServiceFor(alignFrame, sv.serviceType, sv.action, sv);
+ changeSupport.firePropertyChange("services", new Vector(), services);
+ };
+ }).start();
+
+ }
+ });
+ }
+ /*hitm.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ new Thread(new Runnable() {
+ @Override
+ public void run()
+ {
+ new SetPreferredServer(alignFrame, service.serviceType, service.action);
+ }
+ }).start();
+ }
+ });*/
+ }
+ }
+ }
+ /**
+ * add services using the Java 2.5/2.6/2.7 system which optionally creates submenus to index by host and service program type
+ */
+ private void addEnumeratedServices(final JMenu jws2al, final AlignFrame alignFrame, List<Jws2Instance> enumerableServices)
+ {
+ boolean byhost = Cache.getDefault("WSMENU_BYHOST", false), bytype = Cache
+ .getDefault("WSMENU_BYTYPE", false);
+ /**
+ * eventually, JWS2 services will appear under the same align/etc submenus.
+ * for moment we keep them separate.
+ */
+ JMenu atpoint;
+ MsaWSClient msacl = new MsaWSClient();
+ Vector hostLabels = new Vector();
+ Hashtable<String,String> lasthostFor = new Hashtable<String,String>();
Hashtable<String, ArrayList<Jws2Instance>> hosts = new Hashtable<String, ArrayList<Jws2Instance>>();
ArrayList<String> hostlist=new ArrayList<String>();
- for (Jws2Instance service : services)
+ for (Jws2Instance service : enumerableServices)
{
ArrayList<Jws2Instance> hostservices = hosts.get(service.getHost());
if (hostservices == null)
*/
}
}
-
}
-
public static void main(String[] args)
{
if (args.length>0)
}
return match;
}
+
+ Map<String, Map<String, String>> preferredServiceMap = new HashMap<String, Map<String, String>>();
+;
+
+ /**
+ * get current preferred service of the given type, or global default
+ * @param af null or a specific alignFrame
+ * @param serviceType Jws2Instance.serviceType for service
+ * @return null if no service of this type is available, the preferred service for the serviceType and af if specified and if defined.
+ */
+ public Jws2Instance getPreferredServiceFor(AlignFrame af,
+ String serviceType)
+ {
+ String serviceurl = null;
+ synchronized (preferredServiceMap)
+ {
+ String afid = (af == null) ? "" : af.getViewport().getSequenceSetId();
+ Map<String, String> prefmap = preferredServiceMap.get(afid);
+ if (afid.length() > 0 && prefmap == null)
+ {
+ // recover global setting, if any
+ prefmap = preferredServiceMap.get("");
+ }
+ if (prefmap != null)
+ {
+ serviceurl = prefmap.get(serviceType);
+ }
+
+ }
+ Jws2Instance response = null;
+ for (Jws2Instance svc : services)
+ {
+ if (svc.serviceType.equals(serviceType))
+ {
+ if (serviceurl == null || serviceurl.equals(svc.getHost()))
+ {
+ response = svc;
+ break;
+ }
+ }
+ }
+ return response;
+ }
+
+ public void setPreferredServiceFor(AlignFrame af, String serviceType,
+ String serviceAction, Jws2Instance selectedServer)
+ {
+ String afid = (af == null) ? "" : af.getViewport().getSequenceSetId();
+ if (preferredServiceMap == null)
+ {
+ preferredServiceMap = new HashMap<String, Map<String, String>>();
+ }
+ Map<String, String> prefmap = preferredServiceMap.get(afid);
+ if (prefmap == null)
+ {
+ prefmap = new HashMap<String, String>();
+ preferredServiceMap.put(afid, prefmap);
+ }
+ prefmap.put(serviceType, selectedServer.getHost());
+ prefmap.put(serviceAction, selectedServer.getHost());
+ }
+
+ public void setPreferredServiceFor(String serviceType,
+ String serviceAction, Jws2Instance selectedServer)
+ {
+ setPreferredServiceFor(null, serviceType, serviceAction, selectedServer);
+ }
}
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.ws.params.WsParamSetI;
/**
- * @author jimp
+ * @author jprocter
*
*/
-public class SequenceAnnotationWSClient extends Jws2Client
+public class SequenceAnnotationWSClient extends Jws2Client
{
public static final String AAConsCalcId = "jabaws2.AACons";
super(alignFrame, preset, null);
initSequenceAnnotationWSClient(sh, alignFrame, preset, editParams);
}
-
+
public void initSequenceAnnotationWSClient(final Jws2Instance sh,
AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
{
.getViewport()
.getCalcManager()
.registerWorker(
- worker = new AAConsClient(sh, alignFrame, this.preset,
- paramset));
+ worker = new AAConsClient(sh, alignFrame,
+ this.preset, paramset));
alignFrame.getViewport().getCalcManager().startWorker(worker);
}
AlignFrame alignFrame, boolean b)
{
super(alignFrame, fave.getPreset(), fave.getJobArgset());
- initSequenceAnnotationWSClient(fave.getService(), alignFrame, fave.getPreset(), b);
+ initSequenceAnnotationWSClient(fave.getService(), alignFrame,
+ fave.getPreset(), b);
}
/*
AAeditSettings = "Change AACons Settings...",
AAeditSettingsTooltip = "Modify settings for AACons calculations.";
- private SequenceAnnotationWSClient preferredAAConsClient = null;
-
// private final enableAAConsCalculation(final AlignFrame alignFrame, )
private void registerAAConsWSInstance(final JMenu wsmenu,
final Jws2Instance service, final AlignFrame alignFrame)
_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 ?
+ // is there a service already registered ? there shouldn't be if we are
+ // being called correctly
if (_aaConsEnabled == null)
{
final JCheckBoxMenuItem aaConsEnabled = new JCheckBoxMenuItem(
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
+ * 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)
+ 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
+ * 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)
+ AAConsSettings fave = (AAConsSettings) alignFrame.getViewport()
+ .getCalcIdSettingsFor(AAConsCalcId);
+ if (fave == null)
{
- fave = createDefaultAAConsSettings();
+ 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()
{
- Jws2Instance service=null;
- // set sensible defaults
- for (Jws2Instance sv: Jws2Discoverer.getDiscoverer().getServices()) {
- if (sv.serviceType.toString().equals(compbio.ws.client.Services.AAConWS.toString()))
+ 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
{
- service = sv;
- break;
+ // 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)
+ 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.
+ // 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);
git://source.jalview.org / jalview.git / commitdiff