From: jprocter Date: Tue, 7 Aug 2012 15:46:35 +0000 (+0100) Subject: JAL-1137 JAL-975 simpler menu for the AACon service - allows user to switch calculati... X-Git-Tag: Jalview_2_9~399 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9975647d6dbd89ecc08d3f6dab4adefc71afc297;p=jalview.git JAL-1137 JAL-975 simpler menu for the AACon service - allows user to switch calculation to different servers for an alignment view. --- diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java index 96a6f6b..a727485 100644 --- a/src/jalview/ws/jws2/Jws2Discoverer.java +++ b/src/jalview/ws/jws2/Jws2Discoverer.java @@ -32,9 +32,11 @@ import java.beans.PropertyChangeListener; 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; @@ -266,7 +268,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI // 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) @@ -280,13 +284,130 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI * for moment we keep them separate. */ JMenu atpoint; - MsaWSClient msacl = new MsaWSClient(); - Vector hostLabels = new Vector(); + List enumerableServices=new ArrayList(); //jws2al.removeAll(); - Hashtable lasthostFor = new Hashtable(); + Map preferredHosts=new HashMap(); + Map> alternates = new HashMap>(); + 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 ph=alternates.get(service.serviceType); + if (preferredHosts.get(service.serviceType)!=service) + { + if (ph==null) + { + ph=new ArrayList(); + } + 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 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 lasthostFor = new Hashtable(); Hashtable> hosts = new Hashtable>(); ArrayList hostlist=new ArrayList(); - for (Jws2Instance service : services) + for (Jws2Instance service : enumerableServices) { ArrayList hostservices = hosts.get(service.getHost()); if (hostservices == null) @@ -378,9 +499,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI */ } } - } - public static void main(String[] args) { if (args.length>0) @@ -732,4 +851,71 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } return match; } + + Map> preferredServiceMap = new HashMap>(); +; + + /** + * 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 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>(); + } + Map prefmap = preferredServiceMap.get(afid); + if (prefmap == null) + { + prefmap = new HashMap(); + 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); + } } diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java index e629503..d72681d 100644 --- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java +++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java @@ -19,6 +19,7 @@ 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; @@ -29,10 +30,10 @@ 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"; @@ -51,7 +52,7 @@ public class SequenceAnnotationWSClient extends Jws2Client super(alignFrame, preset, null); initSequenceAnnotationWSClient(sh, alignFrame, preset, editParams); } - + public void initSequenceAnnotationWSClient(final Jws2Instance sh, AlignFrame alignFrame, WsParamSetI preset, boolean editParams) { @@ -82,8 +83,8 @@ public class SequenceAnnotationWSClient extends Jws2Client .getViewport() .getCalcManager() .registerWorker( - worker = new AAConsClient(sh, alignFrame, this.preset, - paramset)); + worker = new AAConsClient(sh, alignFrame, + this.preset, paramset)); alignFrame.getViewport().getCalcManager().startWorker(worker); } @@ -129,7 +130,8 @@ public class SequenceAnnotationWSClient extends Jws2Client AlignFrame alignFrame, boolean b) { super(alignFrame, fave.getPreset(), fave.getJobArgset()); - initSequenceAnnotationWSClient(fave.getService(), alignFrame, fave.getPreset(), b); + initSequenceAnnotationWSClient(fave.getService(), alignFrame, + fave.getPreset(), b); } /* @@ -213,8 +215,6 @@ public class SequenceAnnotationWSClient extends Jws2Client 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) @@ -230,8 +230,32 @@ public class SequenceAnnotationWSClient extends Jws2Client _aaConsEnabled = (JCheckBoxMenuItem) item; } } + // is there an aaCons worker already present - if so, set it to use the + // given service handle + { + List 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( @@ -312,56 +336,101 @@ public class SequenceAnnotationWSClient extends Jws2Client 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);