JAL-1807 explicit imports (jalview.ws.*)

[jalview.git] / src / jalview / ws / jws1 / Discoverer.java

diff --git a/src/jalview/ws/jws1/Discoverer.java b/src/jalview/ws/jws1/Discoverer.java
index 4ee1f87..60bbd95 100644 (file)
--- a/src/jalview/ws/jws1/Discoverer.java
+++ b/src/jalview/ws/jws1/Discoverer.java
@@ -20,13 +20,21 @@
  */
 package jalview.ws.jws1;
 
+import jalview.bin.Cache;
+import jalview.gui.Desktop;
 import jalview.util.MessageManager;
 
-import java.util.*;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
 
-import javax.swing.*;
+import javax.swing.JOptionPane;
 
-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
 {
@@ -92,7 +100,7 @@ public class Discoverer implements Runnable
       // timeout
     } catch (Exception ex)
     {
-      jalview.bin.Cache.log
+      Cache.log
               .error("Serious!  Service location failed\nfor URL :" + WsURL
                       + "\n", ex);
 
@@ -121,7 +129,7 @@ public class Discoverer implements Runnable
   static private Vector getDiscoveryURLS()
   {
     Vector urls = new Vector();
-    String RootServiceURLs = jalview.bin.Cache
+    String RootServiceURLs = Cache
             .getDefault("DISCOVERY_URLS",
                     "http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry");
 
@@ -140,23 +148,23 @@ public class Discoverer implements Runnable
           }
           else
           {
-            jalview.bin.Cache.log
+            Cache.log
                     .info("Ignoring duplicate url in DISCOVERY_URLS list");
           }
         } catch (Exception ex)
         {
-          jalview.bin.Cache.log
+          Cache.log
                   .warn("Problem whilst trying to make a URL from '"
                           + ((url != null) ? url : "<null>") + "'");
-          jalview.bin.Cache.log
+          Cache.log
                   .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.log.debug("Exception was ", ex);
         }
       }
     } catch (Exception ex)
     {
-      jalview.bin.Cache.log
+      Cache.log
               .warn("Error parsing comma separated list of urls in DISCOVERY_URLS.",
                       ex);
     }
@@ -172,11 +180,11 @@ public class Discoverer implements Runnable
    */
   static public void doDiscovery()
   {
-    jalview.bin.Cache.log
+    Cache.log
             .debug("(Re)-Initialising the discovery URL list.");
     try
     {
-      reallyDiscoverServices = jalview.bin.Cache.getDefault(
+      reallyDiscoverServices = Cache.getDefault(
               "DISCOVERY_START", false);
       if (reallyDiscoverServices)
       {
@@ -184,7 +192,7 @@ public class Discoverer implements Runnable
       }
       else
       {
-        jalview.bin.Cache.log.debug("Setting default services");
+        Cache.log.debug("Setting default services");
         services = new Hashtable();
         // Muscle, Clustal and JPred.
         ServiceHandle[] defServices =
@@ -211,9 +219,9 @@ public class Discoverer implements Runnable
                     MessageManager.getString("label.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",
+                    "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();
@@ -238,32 +246,30 @@ public class Discoverer implements Runnable
     ServiceHandles shs = null;
     try
     {
-      jalview.bin.Cache.log.debug("Discovering services using " + location);
+      Cache.log.debug("Discovering services using " + location);
       shs = locateWebService(location).getServices();
     } catch (org.apache.axis.AxisFault f)
     {
       // JBPNote - should do this a better way!
       if (f.getFaultReason().indexOf("(407)") > -1)
       {
-        if (jalview.gui.Desktop.desktop != null)
+        if (Desktop.desktop != null)
         {
-          JOptionPane
-                  .showMessageDialog(
-                          jalview.gui.Desktop.desktop,
-                          MessageManager.getString("label.set_proxy_settings"),
-                          MessageManager.getString("label.proxy_authorization_failed"),
-                          JOptionPane.WARNING_MESSAGE);
+          JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+                  .getString("label.set_proxy_settings"), MessageManager
+                  .getString("label.proxy_authorization_failed"),
+                  JOptionPane.WARNING_MESSAGE);
         }
       }
       else
       {
-        jalview.bin.Cache.log.warn("No Discovery service at " + location);
-        jalview.bin.Cache.log.debug("Axis Fault", f);
+        Cache.log.warn("No Discovery service at " + location);
+        Cache.log.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.log.warn("No Discovery service at " + location);
+      Cache.log.debug("Discovery Service General Exception", e);
     }
     if ((shs != null) && shs.getServices().length > 0)
     {
@@ -292,7 +298,7 @@ public class Discoverer implements Runnable
     {
       if (!cat.contains(sh[i]))
       {
-        jalview.bin.Cache.log.debug("A " + sh[i].getAbstractName()
+        Cache.log.debug("A " + sh[i].getAbstractName()
                 + " service called " + sh[i].getName() + " exists at "
                 + sh[i].getEndpointURL() + "\n");
         if (!sscat.containsKey(sh[i].getAbstractName()))
@@ -314,7 +320,7 @@ public class Discoverer implements Runnable
               disc_serv = new java.net.URL(sh[i].getEndpointURL());
               if (!ServiceURLList.contains(disc_serv))
               {
-                jalview.bin.Cache.log
+                Cache.log
                         .debug("Adding new discovery service at "
                                 + disc_serv);
                 ServiceURLList.add(disc_serv);
@@ -322,7 +328,7 @@ public class Discoverer implements Runnable
               }
             } catch (Exception e)
             {
-              jalview.bin.Cache.log.debug(
+              Cache.log.debug(
                       "Ignoring bad discovery service URL "
                               + sh[i].getEndpointURL(), e);
             }
@@ -341,7 +347,7 @@ public class Discoverer implements Runnable
     int s_url = 0;
     if (ServiceURLList == null)
     {
-      jalview.bin.Cache.log
+      Cache.log
               .debug("No service endpoints to use for service discovery.");
       return;
     }
@@ -354,9 +360,9 @@ public class Discoverer implements Runnable
       }
       else
       {
-        jalview.bin.Cache.log
+        Cache.log
                 .warn("No services at "
-                        + ((java.net.URL) ServiceURLList.get(s_url))
+                        + (ServiceURLList.get(s_url))
                         + " - check DISCOVERY_URLS property in .jalview_properties");
       }
       s_url++;