From: Jim Procter Date: Thu, 3 Oct 2019 15:21:08 +0000 (+0100) Subject: JAL-3070 alignment analysis service worker UI and settings management refactored... X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=8775e0baba5a310900582fc0eb0d277937f6c0f7 JAL-3070 alignment analysis service worker UI and settings management refactored from Jws2/JABAWS specific classes --- diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index c2e3eb3..afd00bd 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -99,7 +99,7 @@ import jalview.viewmodel.seqfeatures.FeatureRendererModel; import jalview.viewmodel.seqfeatures.FeatureRendererSettings; import jalview.viewmodel.seqfeatures.FeaturesDisplayed; import jalview.ws.api.ServiceWithParameters; -import jalview.ws.jws2.Jws2Discoverer; +import jalview.ws.jws2.PreferredServiceRegistry; import jalview.ws.jws2.dm.AAConSettings; import jalview.ws.params.ArgumentI; import jalview.ws.params.AutoCalcSetting; @@ -2413,7 +2413,7 @@ public class Jalview2XML if (calcIdParam.getVersion().equals("1.0")) { final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]); - ServiceWithParameters service = Jws2Discoverer.getDiscoverer() + ServiceWithParameters service = PreferredServiceRegistry.getRegistry() .getPreferredServiceFor(calcIds); if (service != null) { diff --git a/src/jalview/ws/jws2/Jws2ClientFactory.java b/src/jalview/ws/jws2/Jws2ClientFactory.java index 2a38b85..c724c45 100644 --- a/src/jalview/ws/jws2/Jws2ClientFactory.java +++ b/src/jalview/ws/jws2/Jws2ClientFactory.java @@ -238,19 +238,20 @@ public class Jws2ClientFactory { if (service != null) { - if (!service.getServiceType() - .equals(compbio.ws.client.Services.AAConWS.toString())) - { - Cache.log.warn( - "Ignoring invalid preferred service for AACon calculations (service type was " - + service.getServiceType() + ")"); - service = null; - } - else + // if (!service.getServiceType() + // .equals(compbio.ws.client.Services.AAConWS.toString())) + // { + // Cache.log.warn( + // "Ignoring invalid preferred service for AACon calculations (service + // type was " + // + service.getServiceType() + ")"); + // service = null; + // } + // else { // check service is actually in the list of currently avaialable // services - if (!Jws2Discoverer.getDiscoverer().getServices().contains(service)) + if (!PreferredServiceRegistry.getRegistry().contains(service)) { // it isn't .. service = null; @@ -260,7 +261,7 @@ public class Jws2ClientFactory if (service == null) { // get the default service for AACon - service = Jws2Discoverer.getDiscoverer().getPreferredServiceFor(null, + service = PreferredServiceRegistry.getRegistry().getPreferredServiceFor(null, aaui.getServiceType()); } if (service == null) diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java index 49f3195..d11174e 100644 --- a/src/jalview/ws/jws2/Jws2Discoverer.java +++ b/src/jalview/ws/jws2/Jws2Discoverer.java @@ -22,35 +22,25 @@ package jalview.ws.jws2; import jalview.bin.Cache; import jalview.gui.AlignFrame; -import jalview.gui.Desktop; -import jalview.gui.JvSwingUtils; import jalview.util.MessageManager; import jalview.ws.WSMenuEntryProviderI; import jalview.ws.api.ServiceWithParameters; import jalview.ws.jws2.jabaws2.Jws2Instance; import jalview.ws.params.ParamDatastoreI; -import java.awt.Color; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; import java.beans.PropertyChangeSupport; import java.net.MalformedURLException; 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.Set; import java.util.StringTokenizer; import java.util.Vector; import javax.swing.JMenu; -import javax.swing.JMenuItem; import compbio.ws.client.Services; @@ -342,358 +332,21 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI @Override public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame) { - // 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) { return; } - - /** - * eventually, JWS2 services will appear under the same align/etc submenus. - * for moment we keep them separate. - */ - JMenu atpoint; - List enumerableServices = new ArrayList<>(); - // jws2al.removeAll(); - Map preferredHosts = new HashMap<>(); - Map> alternates = new HashMap<>(); - for (ServiceWithParameters service : getServices()) - { - // TODO: check this behaves with refactored serviceType to getName - if (!isRecalculable(service.getName())) - { - // add 'one shot' services to be displayed using the classic menu - // structure - enumerableServices.add(service); - } - else - { - if (!preferredHosts.containsKey(service.getName())) - { - ServiceWithParameters preferredInstance = getPreferredServiceFor( - alignFrame, service.getName()); - if (preferredInstance != null) - { - preferredHosts.put(service.getName(), preferredInstance); - } - else - { - preferredHosts.put(service.getName(), service); - } - } - List ph = alternates.get(service.getName()); - if (preferredHosts.get(service.getName()) != service) - { - if (ph == null) - { - ph = new ArrayList<>(); - } - ph.add(service); - alternates.put(service.getName(), ph); - } - } - - } - - // create GUI element for classic services - addEnumeratedServices(jws2al, alignFrame, enumerableServices); - // and the instantaneous services - for (final ServiceWithParameters service : preferredHosts.values()) - { - atpoint = JvSwingUtils.findOrCreateMenu(jws2al, - service.getServiceType()); - JMenuItem hitm; - if (atpoint.getItemCount() > 1) - { - // previous service of this type already present - atpoint.addSeparator(); - } - atpoint.add(hitm = new JMenuItem(service.getHostURL())); - hitm.setForeground(Color.blue); - hitm.addActionListener(new ActionListener() - { - - @Override - public void actionPerformed(ActionEvent e) - { - Desktop.showUrl(service.getHostURL()); - } - }); - hitm.setToolTipText(JvSwingUtils.wrapTooltip(false, - MessageManager.getString("label.open_jabaws_web_page"))); - - service.attachWSMenuEntry(atpoint, alignFrame); - if (alternates.containsKey(service.getName())) - { - atpoint.add(hitm = new JMenu( - MessageManager.getString("label.switch_server"))); - hitm.setToolTipText(JvSwingUtils.wrapTooltip(false, - MessageManager.getString("label.choose_jabaws_server"))); - for (final ServiceWithParameters sv : alternates.get(service.getName())) - { - JMenuItem itm; - hitm.add(itm = new JMenuItem(sv.getHostURL())); - itm.setForeground(Color.blue); - itm.addActionListener(new ActionListener() - { - - @Override - public void actionPerformed(ActionEvent arg0) - { - new Thread(new Runnable() - { - @Override - public void run() - { - setPreferredServiceFor(alignFrame, sv.getName(), - sv.getServiceType(), sv); - changeSupport.firePropertyChange("services", - new Vector(), services); - }; - }).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; - - List hostLabels = new ArrayList<>(); - Hashtable lasthostFor = new Hashtable<>(); - Hashtable> hosts = new Hashtable<>(); - ArrayList hostlist = new ArrayList<>(); - for (ServiceWithParameters service : enumerableServices) - { - ArrayList hostservices = hosts - .get(service.getHostURL()); - if (hostservices == null) - { - hosts.put(service.getHostURL(), - hostservices = new ArrayList<>()); - hostlist.add(service.getHostURL()); - } - hostservices.add(service); - } - // now add hosts in order of the given array - for (String host : hostlist) - { - Jws2Instance orderedsvcs[] = hosts.get(host) - .toArray(new Jws2Instance[1]); - String sortbytype[] = new String[orderedsvcs.length]; - for (int i = 0; i < sortbytype.length; i++) - { - sortbytype[i] = orderedsvcs[i].getName(); - } - jalview.util.QuickSort.sort(sortbytype, orderedsvcs); - for (final Jws2Instance service : orderedsvcs) - { - atpoint = JvSwingUtils.findOrCreateMenu(jws2al, - service.getAction()); - String type = service.getName(); - if (byhost) - { - atpoint = JvSwingUtils.findOrCreateMenu(atpoint, host); - if (atpoint.getToolTipText() == null) - { - atpoint.setToolTipText(MessageManager - .formatMessage("label.services_at", new String[] - { host })); - } - } - if (bytype) - { - atpoint = JvSwingUtils.findOrCreateMenu(atpoint, type); - if (atpoint.getToolTipText() == null) - { - atpoint.setToolTipText(service.getActionText()); - } - } - if (!byhost && !hostLabels.contains( - host + service.getName() + service.getActionText())) - // !hostLabels.contains(host + (bytype ? - // service.serviceType+service.getActionText() : ""))) - { - // add a marker indicating where this service is hosted - // relies on services from the same host being listed in a - // contiguous - // group - JMenuItem hitm; - if (hostLabels.contains(host)) - { - atpoint.addSeparator(); - } - else - { - hostLabels.add(host); - } - if (lasthostFor.get(service.getAction()) == null - || !lasthostFor.get(service.getAction()).equals(host)) - { - atpoint.add(hitm = new JMenuItem(host)); - hitm.setForeground(Color.blue); - hitm.addActionListener(new ActionListener() - { - - @Override - public void actionPerformed(ActionEvent e) - { - Desktop.showUrl(service.getHostURL()); - } - }); - hitm.setToolTipText( - JvSwingUtils.wrapTooltip(true, MessageManager - .getString("label.open_jabaws_web_page"))); - lasthostFor.put(service.getAction(), host); - } - hostLabels.add( - host + service.getName() + service.getActionText()); - } - - service.attachWSMenuEntry(atpoint, alignFrame); - } - } - } - - /** - * pick the user's preferred service based on a set of URLs (jaba server - * locations) and service URIs (specifying version and service interface - * class) - * - * @param serviceURL - * @return null or best match for given uri/ls. - */ - public ServiceWithParameters getPreferredServiceFor(String[] serviceURLs) - { - HashSet urls = new HashSet<>(); - urls.addAll(Arrays.asList(serviceURLs)); - ServiceWithParameters match = null; - List ourServices = getServices(); - - if (ourServices != null) - { - for (ServiceWithParameters svc : ourServices) - { - // TODO getNameURI Should return a versioned URI for the service, but - // doesn't as of 2.11 - if (urls.contains(svc.getNameURI())) - { - if (match == null) - { - // for moment we always pick service from server ordered first in - // user's preferences - match = svc; - } - if (urls.contains(svc.getUri())) - { - // stop and return - we've matched type URI and URI for service - // endpoint - return svc; - } - } - } - } - return match; - } - - Map> preferredServiceMap = new HashMap<>(); - - /** - * get current preferred endpoint of the given Jabaws service, or global - * default - * - * @param af - * null or a specific alignFrame - * @param serviceName - * Jws2Instance.getName() 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 ServiceWithParameters getPreferredServiceFor(AlignFrame af, - String serviceName) - { - 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(serviceName); - } - - } - ServiceWithParameters response = null; - for (ServiceWithParameters svc : getServices()) - { - if (svc.getName().equals(serviceName)) - { - if (serviceurl == null || serviceurl.equals(svc.getHostURL())) - { - response = svc; - break; - } - } - } - return response; - } - - public void setPreferredServiceFor(AlignFrame af, String serviceName, - String serviceAction, ServiceWithParameters selectedServer) - { - // TODO: pull out and generalise for the selectedServer's attributes - 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(serviceName, selectedServer.getHostURL()); - prefmap.put(serviceAction, selectedServer.getHostURL()); + // dynamically regenerate service list. + populateWSMenuEntry(wsmenu, alignFrame, null); } - public void setPreferredServiceFor(String serviceType, - String serviceAction, ServiceWithParameters selectedServer) + private void populateWSMenuEntry(JMenu jws2al, + final AlignFrame alignFrame, String typeFilter) { - setPreferredServiceFor(null, serviceType, serviceAction, - selectedServer); + PreferredServiceRegistry.getRegistry().populateWSMenuEntry( + getServices(), + changeSupport, jws2al, + alignFrame, typeFilter); } public static void main(String[] args) diff --git a/src/jalview/ws/jws2/PreferredServiceRegistry.java b/src/jalview/ws/jws2/PreferredServiceRegistry.java new file mode 100644 index 0000000..9e7438c --- /dev/null +++ b/src/jalview/ws/jws2/PreferredServiceRegistry.java @@ -0,0 +1,396 @@ +package jalview.ws.jws2; + +import jalview.bin.Cache; +import jalview.gui.AlignFrame; +import jalview.gui.Desktop; +import jalview.gui.JvSwingUtils; +import jalview.util.MessageManager; +import jalview.ws.api.ServiceWithParameters; + +import java.awt.Color; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.beans.PropertyChangeSupport; +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.Vector; + +import javax.swing.JMenu; +import javax.swing.JMenuItem; + +public class PreferredServiceRegistry +{ + + private static PreferredServiceRegistry us = new PreferredServiceRegistry(); + + public static PreferredServiceRegistry getRegistry() + { + if (us == null) + { + us = new PreferredServiceRegistry(); + } + return us; + } + + List ourServices = new ArrayList(); + + /** + * forget about any known services + */ + public void clearServices() + { + ourServices.clear(); + } + + public void populateWSMenuEntry(List services, + PropertyChangeSupport changeSupport, + JMenu jws2al, final AlignFrame alignFrame, String typeFilter) + { + /** + * eventually, JWS2 services will appear under the same align/etc submenus. + * for moment we keep them separate. + */ + JMenu atpoint; + List enumerableServices = new ArrayList<>(); + // jws2al.removeAll(); + Map preferredHosts = new HashMap<>(); + Map> alternates = new HashMap<>(); + for (ServiceWithParameters service : services) + { + ourServices.add(service); + // TODO: check this behaves with refactored serviceType to getName + if (!service.isInteractiveUpdate()) + { + // add 'one shot' services to be displayed using the classic menu + // structure + enumerableServices.add(service); + } + else + { + if (!preferredHosts.containsKey(service.getName())) + { + ServiceWithParameters preferredInstance = getPreferredServiceFor( + alignFrame, service.getName()); + if (preferredInstance != null) + { + preferredHosts.put(service.getName(), preferredInstance); + } + else + { + preferredHosts.put(service.getName(), service); + } + } + List ph = alternates.get(service.getName()); + if (preferredHosts.get(service.getName()) != service) + { + if (ph == null) + { + ph = new ArrayList<>(); + } + ph.add(service); + alternates.put(service.getName(), ph); + } + } + + } + + // create GUI element for classic services + addEnumeratedServices(jws2al, alignFrame, enumerableServices); + // and the instantaneous services + for (final ServiceWithParameters service : preferredHosts.values()) + { + atpoint = JvSwingUtils.findOrCreateMenu(jws2al, + service.getServiceType()); + JMenuItem hitm; + if (atpoint.getItemCount() > 1) + { + // previous service of this type already present + atpoint.addSeparator(); + } + atpoint.add(hitm = new JMenuItem(service.getHostURL())); + hitm.setForeground(Color.blue); + hitm.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + Desktop.showUrl(service.getHostURL()); + } + }); + hitm.setToolTipText(JvSwingUtils.wrapTooltip(false, + MessageManager.getString("label.open_jabaws_web_page"))); + + service.attachWSMenuEntry(atpoint, alignFrame); + if (alternates.containsKey(service.getName())) + { + atpoint.add(hitm = new JMenu( + MessageManager.getString("label.switch_server"))); + hitm.setToolTipText(JvSwingUtils.wrapTooltip(false, + MessageManager.getString("label.choose_jabaws_server"))); + for (final ServiceWithParameters sv : alternates + .get(service.getName())) + { + JMenuItem itm; + hitm.add(itm = new JMenuItem(sv.getHostURL())); + itm.setForeground(Color.blue); + itm.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent arg0) + { + new Thread(new Runnable() + { + @Override + public void run() + { + setPreferredServiceFor(alignFrame, sv.getName(), + sv.getServiceType(), sv); + changeSupport.firePropertyChange("services", + new Vector(), services); + }; + }).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; + + List hostLabels = new ArrayList<>(); + Hashtable lasthostFor = new Hashtable<>(); + Hashtable> hosts = new Hashtable<>(); + ArrayList hostlist = new ArrayList<>(); + for (ServiceWithParameters service : enumerableServices) + { + ArrayList hostservices = hosts + .get(service.getHostURL()); + if (hostservices == null) + { + hosts.put(service.getHostURL(), hostservices = new ArrayList<>()); + hostlist.add(service.getHostURL()); + } + hostservices.add(service); + } + // now add hosts in order of the given array + for (String host : hostlist) + { + ServiceWithParameters orderedsvcs[] = hosts.get(host) + .toArray(new ServiceWithParameters[1]); + String sortbytype[] = new String[orderedsvcs.length]; + for (int i = 0; i < sortbytype.length; i++) + { + sortbytype[i] = orderedsvcs[i].getName(); + } + jalview.util.QuickSort.sort(sortbytype, orderedsvcs); + for (final ServiceWithParameters service : orderedsvcs) + { + atpoint = JvSwingUtils.findOrCreateMenu(jws2al, + service.getAction()); + String type = service.getName(); + if (byhost) + { + atpoint = JvSwingUtils.findOrCreateMenu(atpoint, host); + if (atpoint.getToolTipText() == null) + { + atpoint.setToolTipText(MessageManager + .formatMessage("label.services_at", new String[] + { host })); + } + } + if (bytype) + { + atpoint = JvSwingUtils.findOrCreateMenu(atpoint, type); + if (atpoint.getToolTipText() == null) + { + atpoint.setToolTipText(service.getActionText()); + } + } + if (!byhost && !hostLabels.contains( + host + service.getName() + service.getActionText())) + // !hostLabels.contains(host + (bytype ? + // service.serviceType+service.getActionText() : ""))) + { + // add a marker indicating where this service is hosted + // relies on services from the same host being listed in a + // contiguous + // group + JMenuItem hitm; + if (hostLabels.contains(host)) + { + atpoint.addSeparator(); + } + else + { + hostLabels.add(host); + } + if (lasthostFor.get(service.getAction()) == null + || !lasthostFor.get(service.getAction()).equals(host)) + { + atpoint.add(hitm = new JMenuItem(host)); + hitm.setForeground(Color.blue); + hitm.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + Desktop.showUrl(service.getHostURL()); + } + }); + hitm.setToolTipText( + JvSwingUtils.wrapTooltip(true, MessageManager + .getString("label.open_jabaws_web_page"))); + lasthostFor.put(service.getAction(), host); + } + hostLabels + .add(host + service.getName() + service.getActionText()); + } + + service.attachWSMenuEntry(atpoint, alignFrame); + } + } + } + + /** + * pick the user's preferred service based on a set of URLs (jaba server + * locations) and service URIs (specifying version and service interface + * class) + * + * @param serviceURL + * @return null or best match for given uri/ls. + */ + public ServiceWithParameters getPreferredServiceFor(String[] serviceURLs) + { + HashSet urls = new HashSet<>(); + urls.addAll(Arrays.asList(serviceURLs)); + ServiceWithParameters match = null; + + if (ourServices != null) + { + for (ServiceWithParameters svc : ourServices) + { + // TODO getNameURI Should return a versioned URI for the service, but + // doesn't as of 2.11 + if (urls.contains(svc.getNameURI())) + { + if (match == null) + { + // for moment we always pick service from server ordered first in + // user's preferences + match = svc; + } + if (urls.contains(svc.getUri())) + { + // stop and return - we've matched type URI and URI for service + // endpoint + return svc; + } + } + } + } + return match; + } + + Map> preferredServiceMap = new HashMap<>(); + + /** + * get current preferred endpoint of the given Jabaws service, or global + * default + * + * @param af + * null or a specific alignFrame + * @param serviceName + * ServiceWithParameters.getName() 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 ServiceWithParameters getPreferredServiceFor(AlignFrame af, + String serviceName) + { + 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(serviceName); + } + + } + ServiceWithParameters response = null; + for (ServiceWithParameters svc : ourServices) + { + if (svc.getName().equals(serviceName)) + { + if (serviceurl == null || serviceurl.equals(svc.getHostURL())) + { + response = svc; + break; + } + } + } + return response; + } + + public void setPreferredServiceFor(AlignFrame af, String serviceName, + String serviceAction, ServiceWithParameters selectedServer) + { + // TODO: pull out and generalise for the selectedServer's attributes + 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(serviceName, selectedServer.getHostURL()); + prefmap.put(serviceAction, selectedServer.getHostURL()); + } + + public void setPreferredServiceFor(String serviceType, + String serviceAction, ServiceWithParameters selectedServer) + { + setPreferredServiceFor(null, serviceType, serviceAction, + selectedServer); + } + + public boolean contains(ServiceWithParameters service) + { + return ourServices.contains(service); + } + +} diff --git a/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java b/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java index 993d8ed8..1531e2d 100644 --- a/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java +++ b/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java @@ -2,12 +2,17 @@ package jalview.ws.slivkaws; import jalview.gui.AlignFrame; import jalview.ws.WSMenuEntryProviderI; +import jalview.ws.api.ServiceWithParameters; import jalview.ws.jws2.MsaWSClient; +import jalview.ws.jws2.PreferredServiceRegistry; import jalview.ws.jws2.SequenceAnnotationWSClient; +import java.beans.PropertyChangeSupport; import java.io.IOError; import java.io.IOException; import java.net.URISyntaxException; +import java.util.ArrayList; +import java.util.List; import javax.swing.JMenu; @@ -24,7 +29,7 @@ public class SlivkaWSDiscoverer implements Runnable, WSMenuEntryProviderI { try { - slivkaClient = new SlivkaClient("gjb-www-1.cluster.lifesci.dundee.ac.uk", 3203); + slivkaClient = new SlivkaClient("localhost", 4954); } catch (URISyntaxException e) { throw new RuntimeException(e); @@ -55,6 +60,7 @@ public class SlivkaWSDiscoverer implements Runnable, WSMenuEntryProviderI { SlivkaAnnotationServiceInstance serviceInstance = new SlivkaAnnotationServiceInstance( slivkaClient, service, false); + SequenceAnnotationWSClient client = new SequenceAnnotationWSClient(); client.attachWSMenuEntry(disorderMenu, serviceInstance, alignFrame); disorderMenu.addSeparator(); @@ -70,6 +76,9 @@ public class SlivkaWSDiscoverer implements Runnable, WSMenuEntryProviderI conservationMenu.addSeparator(); } + private PropertyChangeSupport changeSupport = new PropertyChangeSupport( + this); + @Override public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame) { @@ -84,27 +93,36 @@ public class SlivkaWSDiscoverer implements Runnable, WSMenuEntryProviderI slivkaMenu.add(conservationMenu); try { + List instances = new ArrayList<>(); for (SlivkaService service : slivkaClient.getServices()) { for (String classifier : service.classifiers) { if (classifier.contains("Multiple sequence alignment")) { - addMsaServiceClient(alignmentMenu, service, alignFrame); + instances.add( + new SlivkaMsaServiceInstance(slivkaClient, service)); + // addMsaServiceClient(alignmentMenu, service, alignFrame); } else if (classifier.contains("Protein sequence analysis")) { - addDisorderServiceClient(disorderMenu, service, alignFrame); + instances.add(new SlivkaAnnotationServiceInstance(slivkaClient, + service, false)); + // addDisorderServiceClient(disorderMenu, service, alignFrame); } else if (classifier .contains("Sequence alignment analysis (conservation)")) { - addConservationServiceClient(conservationMenu, service, - alignFrame); + instances.add(new SlivkaAnnotationServiceInstance(slivkaClient, + service, true)); + // addConservationServiceClient(conservationMenu, service, + // alignFrame); } } } + PreferredServiceRegistry.getRegistry().populateWSMenuEntry(instances, + changeSupport, slivkaMenu, alignFrame, null); } catch (IOException e) { throw new IOError(e);