/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
import java.awt.event.ActionListener;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
-import java.io.Closeable;
import java.net.ConnectException;
import java.net.URL;
import java.util.ArrayList;
import jalview.gui.JalviewChangeSupport;
import jalview.gui.JvSwingUtils;
import jalview.ws.WSMenuEntryProviderI;
-import jalview.ws.jws2.Jws2Discoverer.Jws2Instance;
-import jalview.ws.params.ParamDatastoreI;
-import compbio.data.msa.MsaWS;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import compbio.data.msa.JABAService;
import compbio.metadata.Option;
import compbio.metadata.Preset;
-import compbio.metadata.PresetManager;
-import compbio.metadata.RunnerConfig;
import compbio.ws.client.Jws2Client;
import compbio.ws.client.Services;
* @param srv
* @param service2
*/
- synchronized void addService(String jwsservers, Services srv,
- MsaWS service2)
+ synchronized void addService(String jwsservers, Jws2Instance service)
{
if (services == null)
{
services = new Vector<Jws2Instance>();
}
System.out.println("Discovered service: " + jwsservers + " "
- + srv.toString());
- Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(),
- service2);
+ + service.toString());
+// Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(),
+// service2);
services.add(service);
// retrieve the presets and parameter set and cache now
service.hasParameters();
}
- public class Jws2Instance
- {
- public String hosturl;
-
- public String serviceType;
-
- public MsaWS service;
-
- public Jws2Instance(String hosturl, String serviceType, MsaWS service)
- {
- super();
- this.hosturl = hosturl;
- this.serviceType = serviceType;
- this.service = service;
- }
-
- PresetManager presets = null;
-
- public JabaParamStore paramStore = null;
-
- /**
- * non thread safe - gets the presets for this service (blocks whilst it
- * calls the service to get the preset set)
- *
- * @return service presets or null if exceptions were raised.
- */
- public PresetManager getPresets()
- {
- if (presets == null)
- {
- try
- {
- presets = service.getPresets();
- } catch (Exception ex)
- {
- System.err
- .println("Exception when retrieving presets for service "
- + serviceType + " at " + hosturl);
- }
- }
- return presets;
- }
-
- public String getHost()
- {
- return hosturl;
- /*
- * try { URL serviceurl = new URL(hosturl); if (serviceurl.getPort()!=80)
- * { return serviceurl.getHost()+":"+serviceurl.getPort(); } return
- * serviceurl.getHost(); } catch (Exception e) {
- * System.err.println("Failed to parse service URL '" + hosturl +
- * "' as a valid URL!"); } return null;
- */
- }
-
- /**
- * @return short description of what the service will do
- */
- public String getActionText()
- {
- return "Align with " + serviceType;
- }
-
- /**
- * non-thread safe - blocks whilst accessing service to get complete set of
- * available options and parameters
- *
- * @return
- */
- public RunnerConfig getRunnerConfig()
- {
- return service.getRunnerOptions();
- }
-
- @Override
- protected void finalize() throws Throwable
- {
- if (service != null)
- {
- try
- {
- Closeable svc = (Closeable) service;
- service = null;
- svc.close();
- } catch (Exception e)
- {
- }
- ;
- }
- super.finalize();
- }
-
- public ParamDatastoreI getParamStore()
- {
- if (paramStore == null)
- {
- try
- {
- paramStore = new JabaParamStore(this,
- (Desktop.instance != null ? Desktop
- .getUserParameterStore() : null));
- } catch (Exception ex)
- {
- }
-
- }
- return paramStore;
- }
-
- public String getUri()
- {
- // this is only valid for Jaba 1.0 - this formula might have to change!
- return hosturl
- + (hosturl.lastIndexOf("/") == (hosturl.length() - 1) ? ""
- : "/") + serviceType;
- }
-
- private boolean hasParams = false, lookedForParams = false;
-
- public boolean hasParameters()
- {
- if (!lookedForParams)
- {
- lookedForParams = true;
- try
- {
- hasParams = (getRunnerConfig().getArguments().size() > 0);
- } catch (Exception e)
- {
-
- }
- }
- return hasParams;
- }
- };
-
/**
* holds list of services.
*/
protected Vector<Jws2Instance> services;
-
+ /**
+ * attach all available web services to the appropriate submenu in the given JMenu
+ */
public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
{
// dynamically regenerate service list.
- final JMenu jws2al = wsmenu; // new JMenu("JABAWS Alignment");
- jws2al.addMenuListener(new MenuListener()
- {
- // TODO: future: add menu listener to parent menu - so submenus are
- // populated *before* they are selected.
- @Override
- public void menuSelected(MenuEvent e)
- {
- populateWSMenuEntry(jws2al, alignFrame);
- }
-
- @Override
- public void menuDeselected(MenuEvent e)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void menuCanceled(MenuEvent e)
- {
- // TODO Auto-generated method stub
-
- }
-
- });
- wsmenu.add(jws2al);
-
+ populateWSMenuEntry(wsmenu, alignFrame, null);
}
- private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame)
+ private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame, String typeFilter)
{
if (running || services == null || services.size() == 0)
{
jalview.util.QuickSort.sort(sortbytype, orderedsvcs);
for (final Jws2Instance service : orderedsvcs)
{
- atpoint = jws2al;
+ atpoint = JvSwingUtils.findOrCreateMenu(jws2al,service.action);
String type = service.serviceType;
if (byhost)
{
// hostLabels.addElement(host + (bytype ?
// service.serviceType+service.getActionText() : ""));
}
- msacl.attachWSMenuEntry(atpoint, service, alignFrame);
+
+ service.attachWSMenuEntry(atpoint, alignFrame);
/*
* JMenuItem sitem = new JMenuItem(service.serviceType);
* sitem.setToolTipText("Hosted at " + service.hosturl);
public static void main(String[] args)
{
+ if (args.length>0)
+ {
+ testUrls = new Vector<String>();
+ for (String url:args)
+ {
+ testUrls.add(url);
+ };
+ }
Thread runner = getDiscoverer().startDiscoverer(
new PropertyChangeListener()
{
}
}
+ private static Vector<String> testUrls=null;
public static Vector<String> getServiceUrls()
{
+ if (testUrls!=null)
+ {
+ // return test urls, if there are any, instead of touching cache
+ return testUrls;
+ }
String surls = Cache.getDefault(JWS2HOSTURLS,
"http://www.compbio.dundee.ac.uk/jabaws");
Vector<String> urls = new Vector<String>();
}
return null;
}
-
}
git://source.jalview.org / jalview.git / blobdiff