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;
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)
{
{
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;
if (service == null)
{
// get the default service for AACon
- service = Jws2Discoverer.getDiscoverer().getPreferredServiceFor(null,
+ service = PreferredServiceRegistry.getRegistry().getPreferredServiceFor(null,
aaui.getServiceType());
}
if (service == null)
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;
@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<ServiceWithParameters> enumerableServices = new ArrayList<>();
- // jws2al.removeAll();
- Map<String, ServiceWithParameters> preferredHosts = new HashMap<>();
- Map<String, List<ServiceWithParameters>> 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<ServiceWithParameters> 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<Jws2Instance>(), 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<ServiceWithParameters> 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<String> hostLabels = new ArrayList<>();
- Hashtable<String, String> lasthostFor = new Hashtable<>();
- Hashtable<String, ArrayList<ServiceWithParameters>> hosts = new Hashtable<>();
- ArrayList<String> hostlist = new ArrayList<>();
- for (ServiceWithParameters service : enumerableServices)
- {
- ArrayList<ServiceWithParameters> 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<String> urls = new HashSet<>();
- urls.addAll(Arrays.asList(serviceURLs));
- ServiceWithParameters match = null;
- List<ServiceWithParameters> 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<String, Map<String, String>> 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<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(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<String, String> 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)
--- /dev/null
+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<ServiceWithParameters> ourServices = new ArrayList();
+
+ /**
+ * forget about any known services
+ */
+ public void clearServices()
+ {
+ ourServices.clear();
+ }
+
+ public void populateWSMenuEntry(List<ServiceWithParameters> 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<ServiceWithParameters> enumerableServices = new ArrayList<>();
+ // jws2al.removeAll();
+ Map<String, ServiceWithParameters> preferredHosts = new HashMap<>();
+ Map<String, List<ServiceWithParameters>> 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<ServiceWithParameters> 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<ServiceWithParameters>(), 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<ServiceWithParameters> 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<String> hostLabels = new ArrayList<>();
+ Hashtable<String, String> lasthostFor = new Hashtable<>();
+ Hashtable<String, ArrayList<ServiceWithParameters>> hosts = new Hashtable<>();
+ ArrayList<String> hostlist = new ArrayList<>();
+ for (ServiceWithParameters service : enumerableServices)
+ {
+ ArrayList<ServiceWithParameters> 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<String> 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<String, Map<String, String>> 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<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(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<String, String> 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);
+ }
+
+}
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;
{
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);
{
SlivkaAnnotationServiceInstance serviceInstance = new SlivkaAnnotationServiceInstance(
slivkaClient, service, false);
+
SequenceAnnotationWSClient client = new SequenceAnnotationWSClient();
client.attachWSMenuEntry(disorderMenu, serviceInstance, alignFrame);
disorderMenu.addSeparator();
conservationMenu.addSeparator();
}
+ private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
+ this);
+
@Override
public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
{
slivkaMenu.add(conservationMenu);
try
{
+ List<ServiceWithParameters> 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);
git://source.jalview.org / jalview.git / commitdiff