X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FDiscoverer.java;h=9f11064170c63b9e58c9a64bdee2ff87dfce7a78;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=c40145279b83469dbec3f6801353b22aad089821;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/src/jalview/ws/jws1/Discoverer.java b/src/jalview/ws/jws1/Discoverer.java
index c401452..9f11064 100644
--- a/src/jalview/ws/jws1/Discoverer.java
+++ b/src/jalview/ws/jws1/Discoverer.java
@@ -1,27 +1,39 @@
 /*
- * 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
 {
@@ -87,9 +99,9 @@ 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;
     }
@@ -101,24 +113,22 @@ public class Discoverer implements Runnable
 
   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
     {
@@ -135,25 +145,23 @@ public class Discoverer implements Runnable
           }
           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)
     {
@@ -167,59 +175,55 @@ public class Discoverer implements Runnable
    */
   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);
     }
 
@@ -233,7 +237,7 @@ public class Discoverer implements Runnable
     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)
     {
@@ -242,23 +246,22 @@ public class Discoverer implements Runnable
       {
         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)
     {
@@ -279,24 +282,25 @@ public class Discoverer implements Runnable
    *          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"))
@@ -309,16 +313,14 @@ public class Discoverer implements Runnable
               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);
             }
           }
@@ -330,29 +332,28 @@ public class Discoverer implements Runnable
 
   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++;
     }
@@ -361,7 +362,7 @@ public class Discoverer implements Runnable
     // 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;
@@ -371,14 +372,16 @@ public class Discoverer implements Runnable
   /**
    * 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();
       }
     };
@@ -388,24 +391,24 @@ public class Discoverer implements Runnable
   /**
    * 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