/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws1;
-import java.util.*;
+import jalview.bin.Cache;
+import jalview.gui.JvOptionPane;
+import jalview.util.MessageManager;
-import javax.swing.*;
+import java.net.URL;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
-import ext.vamsas.*;
+import ext.vamsas.IRegistry;
+import ext.vamsas.IRegistryServiceLocator;
+import ext.vamsas.RegistryServiceSoapBindingStub;
+import ext.vamsas.ServiceHandle;
+import ext.vamsas.ServiceHandles;
public class Discoverer implements Runnable
{
// timeout
} catch (Exception ex)
{
- jalview.bin.Cache.log
- .error("Serious! Service location failed\nfor URL :" + WsURL
- + "\n", ex);
+ Cache.error(
+ "Serious! Service location failed\nfor URL :" + WsURL + "\n",
+ ex);
return null;
}
static private java.net.URL RootServiceURL = null;
- static public Vector ServiceURLList = null;
+ static public Vector<URL> ServiceURLList = null;
static private boolean reallyDiscoverServices = true;
- public static java.util.Hashtable services = null; // vectors of services
-
+ public static java.util.Hashtable<String, Vector<ServiceHandle>> services = null;
// stored by
// abstractServiceType
// string
- public static java.util.Vector serviceList = null; // flat list of services
+ public static java.util.Vector<ServiceHandle> serviceList = null;
- static private Vector getDiscoveryURLS()
+ static private Vector<URL> getDiscoveryURLS()
{
- Vector urls = new Vector();
- String RootServiceURLs = jalview.bin.Cache
- .getDefault("DISCOVERY_URLS",
- "http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry");
+ Vector<URL> urls = new Vector<>();
+ String RootServiceURLs = Cache.getDefault("DISCOVERY_URLS",
+ "http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry");
try
{
}
else
{
- jalview.bin.Cache.log
- .info("Ignoring duplicate url in DISCOVERY_URLS list");
+ Cache.info("Ignoring duplicate url in DISCOVERY_URLS list");
}
} catch (Exception ex)
{
- jalview.bin.Cache.log
- .warn("Problem whilst trying to make a URL from '"
+ Cache.warn("Problem whilst trying to make a URL from '"
+ ((url != null) ? url : "<null>") + "'");
- jalview.bin.Cache.log
- .warn("This was probably due to a malformed comma separated list"
+ Cache.warn(
+ "This was probably due to a malformed comma separated list"
+ " in the DISCOVERY_URLS entry of $(HOME)/.jalview_properties)");
- jalview.bin.Cache.log.debug("Exception was ", ex);
+ Cache.debug("Exception was ", ex);
}
}
} catch (Exception ex)
{
- jalview.bin.Cache.log
- .warn("Error parsing comma separated list of urls in DISCOVERY_URLS.",
- ex);
+ Cache.warn(
+ "Error parsing comma separated list of urls in DISCOVERY_URLS.",
+ ex);
}
if (urls.size() > 0)
{
*/
static public void doDiscovery()
{
- jalview.bin.Cache.log
- .debug("(Re)-Initialising the discovery URL list.");
+ Cache.debug("(Re)-Initialising the discovery URL list.");
try
{
- reallyDiscoverServices = jalview.bin.Cache.getDefault(
- "DISCOVERY_START", false);
+ reallyDiscoverServices = Cache
+ .getDefault("DISCOVERY_START", false);
if (reallyDiscoverServices)
{
ServiceURLList = getDiscoveryURLS();
}
else
{
- jalview.bin.Cache.log.debug("Setting default services");
- services = new Hashtable();
+ Cache.debug("Setting default services");
+ services = new Hashtable<>();
// Muscle, Clustal and JPred.
- ServiceHandle[] defServices =
- {
- new ServiceHandle(
- "MsaWS",
- "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment "
- + "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.",
- "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS",
- "Muscle Multiple Protein Sequence Alignment"),
- new ServiceHandle(
- "MsaWS",
+ ServiceHandle[] defServices = { new ServiceHandle("MsaWS",
+ "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment "
+ + "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.",
+ "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS",
+ MessageManager.getString(
+ "label.muscle_multiple_protein_sequence_alignment")),
+ new ServiceHandle("MsaWS",
"Katoh, K., K. Kuma, K., Toh, H., and Miyata, T. (2005) "
+ "\"MAFFT version 5: improvement in accuracy of multiple sequence alignment.\""
+ " Nucleic Acids Research, 33 511-518",
"http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS",
- "MAFFT Multiple Sequence Alignment"),
- new ServiceHandle(
- "MsaWS",
+ MessageManager.getString(
+ "label.mafft_multiple_sequence_alignment")),
+ new ServiceHandle("MsaWS",
"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"
+ " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."
+ " Nucleic Acids Research, 22 4673-4680",
"http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS",
- "ClustalW Multiple Sequence Alignment"),
- new ServiceHandle(
- "SecStrPred",
- "Cole C., Barber J. D., Barton G.J (2008) "
- + "The Jpred 3 secondary structure prediction server "
- + "Nucleic Acids Research, 36 W197-W201",
+ MessageManager.getString(
+ "label.clustalw_multiple_sequence_alignment")),
+ new ServiceHandle("SecStrPred",
+ "Drozdetskiy A, Cole C, Procter J & Barton GJ. (2015)\nJPred4: a protein secondary structure prediction server"
+ + "\nNucleic Acids Research, Web Server issue (first published 15th April 2015)"
+ + "\ndoi://10.1093/nar/gkv332",
"http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred",
- "JNet Secondary Structure Prediction") };
- services = new Hashtable();
- serviceList = new Vector();
+ "JPred Secondary Structure Prediction") };
+ services = new Hashtable<>();
+ serviceList = new Vector<>();
buildServiceLists(defServices, serviceList, services);
}
} catch (Exception e)
{
- System.err
- .println("jalview.rootRegistry is not a proper url!\nWas set to "
+ System.err.println(
+ "jalview.rootRegistry is not a proper url!\nWas set to "
+ RootServiceURL + "\n" + e);
}
ServiceHandles shs = null;
try
{
- jalview.bin.Cache.log.debug("Discovering services using " + location);
+ Cache.debug("Discovering services using " + location);
shs = locateWebService(location).getServices();
} catch (org.apache.axis.AxisFault f)
{
{
if (jalview.gui.Desktop.desktop != null)
{
- JOptionPane
- .showMessageDialog(
- jalview.gui.Desktop.desktop,
- "Please set up your proxy settings in the 'Connections' tab of the Preferences window",
- "Proxy Authorization Failed",
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showMessageDialog(jalview.gui.Desktop.desktop,
+ MessageManager.getString("label.set_proxy_settings"),
+ MessageManager
+ .getString("label.proxy_authorization_failed"),
+ JvOptionPane.WARNING_MESSAGE);
}
}
else
{
- jalview.bin.Cache.log.warn("No Discovery service at " + location);
- jalview.bin.Cache.log.debug("Axis Fault", f);
+ Cache.warn("No Discovery service at " + location);
+ Cache.debug("Axis Fault", f);
}
} catch (Exception e)
{
- jalview.bin.Cache.log.warn("No Discovery service at " + location);
- jalview.bin.Cache.log.debug("Discovery Service General Exception", e);
+ Cache.warn("No Discovery service at " + location);
+ Cache.debug("Discovery Service General Exception", e);
}
if ((shs != null) && shs.getServices().length > 0)
{
* Hashtable
* @return boolean
*/
- static private boolean buildServiceLists(ServiceHandle[] sh, Vector cat,
- Hashtable sscat)
+ static private boolean buildServiceLists(ServiceHandle[] sh,
+ Vector<ServiceHandle> cat,
+ Hashtable<String, Vector<ServiceHandle>> sscat)
{
boolean seenNewDiscovery = false;
for (int i = 0, j = sh.length; i < j; i++)
{
if (!cat.contains(sh[i]))
{
- jalview.bin.Cache.log.debug("A " + sh[i].getAbstractName()
+ Cache.debug("A " + sh[i].getAbstractName()
+ " service called " + sh[i].getName() + " exists at "
+ sh[i].getEndpointURL() + "\n");
if (!sscat.containsKey(sh[i].getAbstractName()))
{
- sscat.put(sh[i].getAbstractName(), cat = new Vector());
+ sscat.put(sh[i].getAbstractName(), cat = new Vector<>());
}
else
{
- cat = (Vector) sscat.get(sh[i].getAbstractName());
+ cat = sscat.get(sh[i].getAbstractName());
}
cat.add(sh[i]);
if (sh[i].getAbstractName().equals("Registry"))
disc_serv = new java.net.URL(sh[i].getEndpointURL());
if (!ServiceURLList.contains(disc_serv))
{
- jalview.bin.Cache.log
- .debug("Adding new discovery service at "
- + disc_serv);
+ Cache.debug(
+ "Adding new discovery service at " + disc_serv);
ServiceURLList.add(disc_serv);
seenNewDiscovery = true;
}
} catch (Exception e)
{
- jalview.bin.Cache.log.debug(
- "Ignoring bad discovery service URL "
+ Cache.debug("Ignoring bad discovery service URL "
+ sh[i].getEndpointURL(), e);
}
}
public void discoverServices()
{
- Hashtable sscat = new Hashtable();
- Vector cat = new Vector();
+ Hashtable<String, Vector<ServiceHandle>> sscat = new Hashtable<>();
+ Vector<ServiceHandle> cat = new Vector<>();
ServiceHandle sh[] = null;
int s_url = 0;
if (ServiceURLList == null)
{
- jalview.bin.Cache.log
- .debug("No service endpoints to use for service discovery.");
+ Cache.debug("No service endpoints to use for service discovery.");
return;
}
while (s_url < ServiceURLList.size())
{
- if ((sh = getServices((java.net.URL) ServiceURLList.get(s_url))) != null)
+ if ((sh = getServices(
+ ServiceURLList.get(s_url))) != null)
{
buildServiceLists(sh, cat, sscat);
}
else
{
- jalview.bin.Cache.log
- .warn("No services at "
- + ((java.net.URL) ServiceURLList.get(s_url))
- + " - check DISCOVERY_URLS property in .jalview_properties");
+ Cache.warn("No services at "
+ + (ServiceURLList.get(s_url))
+ + " - check DISCOVERY_URLS property in .jalview_properties");
}
s_url++;
}
// so no need to access original discovery thread.
// Curent decision is to change properties then notify listeners with old
// and new values.
- Hashtable oldServices = services;
+ Hashtable<String, Vector<ServiceHandle>> oldServices = services;
// Vector oldServicelist = serviceList;
services = sscat;
serviceList = cat;
/**
* creates a new thread to call discoverServices()
*/
+ @Override
public void run()
{
final Discoverer discoverer = this;
Thread discoverThread = new Thread()
{
+ @Override
public void run()
{
- discoverer.doDiscovery();
+ Discoverer.doDiscovery();
discoverer.discoverServices();
}
};
/**
* binding service abstract name to handler class
*/
- private static Hashtable serviceClientBindings;
+ private static Hashtable<String, WS1Client> serviceClientBindings;
public static WS1Client getServiceClient(ServiceHandle sh)
{
if (serviceClientBindings == null)
{
// get a list from Config or create below
- serviceClientBindings = new Hashtable();
+ serviceClientBindings = new Hashtable<>();
serviceClientBindings.put("MsaWS", new MsaWSClient());
serviceClientBindings.put("SecStrPred", new JPredClient());
serviceClientBindings.put("SeqSearch", new SeqSearchWSClient());
}
- WS1Client instance = (WS1Client) serviceClientBindings.get(sh
- .getAbstractName());
+ WS1Client instance = serviceClientBindings
+ .get(sh.getAbstractName());
if (instance == null)
{
- System.err
- .println("WARNING - POSSIBLE IMPLEMENTATION ERROR - cannot find WSClient implementation for "
+ System.err.println(
+ "WARNING - POSSIBLE IMPLEMENTATION ERROR - cannot find WSClient implementation for "
+ sh.getAbstractName());
}
else
git://source.jalview.org / jalview.git / blobdiff