Merge branch 'kjvdh/features/PhylogenyViewer_tabbedsupport' into merge/2_11_2/kjvdh...

[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 9f11064..6caf563 100644 (file)
--- a/src/jalview/ws/jws1/Discoverer.java
+++ b/src/jalview/ws/jws1/Discoverer.java
@@ -21,6 +21,7 @@
 package jalview.ws.jws1;
 
 import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.gui.JvOptionPane;
 import jalview.util.MessageManager;
 
@@ -99,7 +100,7 @@ public class Discoverer implements Runnable
       // timeout
     } catch (Exception ex)
     {
-      Cache.error(
+      Console.error(
               "Serious!  Service location failed\nfor URL :" + WsURL + "\n",
               ex);
 
@@ -145,21 +146,21 @@ public class Discoverer implements Runnable
           }
           else
           {
-            Cache.info("Ignoring duplicate url in DISCOVERY_URLS list");
+            Console.info("Ignoring duplicate url in DISCOVERY_URLS list");
           }
         } catch (Exception ex)
         {
-          Cache.warn("Problem whilst trying to make a URL from '"
-                          + ((url != null) ? url : "<null>") + "'");
-          Cache.warn(
+          Console.warn("Problem whilst trying to make a URL from '"
+                  + ((url != null) ? url : "<null>") + "'");
+          Console.warn(
                   "This was probably due to a malformed comma separated list"
                           + " in the DISCOVERY_URLS entry of $(HOME)/.jalview_properties)");
-          Cache.debug("Exception was ", ex);
+          Console.debug("Exception was ", ex);
         }
       }
     } catch (Exception ex)
     {
-      Cache.warn(
+      Console.warn(
               "Error parsing comma separated list of urls in DISCOVERY_URLS.",
               ex);
     }
@@ -175,18 +176,17 @@ public class Discoverer implements Runnable
    */
   static public void doDiscovery()
   {
-    Cache.debug("(Re)-Initialising the discovery URL list.");
+    Console.debug("(Re)-Initialising the discovery URL list.");
     try
     {
-      reallyDiscoverServices = Cache
-              .getDefault("DISCOVERY_START", false);
+      reallyDiscoverServices = Cache.getDefault("DISCOVERY_START", false);
       if (reallyDiscoverServices)
       {
         ServiceURLList = getDiscoveryURLS();
       }
       else
       {
-        Cache.debug("Setting default services");
+        Console.debug("Setting default services");
         services = new Hashtable<>();
         // Muscle, Clustal and JPred.
         ServiceHandle[] defServices = { new ServiceHandle("MsaWS",
@@ -237,7 +237,7 @@ public class Discoverer implements Runnable
     ServiceHandles shs = null;
     try
     {
-      Cache.debug("Discovering services using " + location);
+      Console.debug("Discovering services using " + location);
       shs = locateWebService(location).getServices();
     } catch (org.apache.axis.AxisFault f)
     {
@@ -255,13 +255,13 @@ public class Discoverer implements Runnable
       }
       else
       {
-        Cache.warn("No Discovery service at " + location);
-        Cache.debug("Axis Fault", f);
+        Console.warn("No Discovery service at " + location);
+        Console.debug("Axis Fault", f);
       }
     } catch (Exception e)
     {
-      Cache.warn("No Discovery service at " + location);
-      Cache.debug("Discovery Service General Exception", e);
+      Console.warn("No Discovery service at " + location);
+      Console.debug("Discovery Service General Exception", e);
     }
     if ((shs != null) && shs.getServices().length > 0)
     {
@@ -291,9 +291,9 @@ public class Discoverer implements Runnable
     {
       if (!cat.contains(sh[i]))
       {
-        Cache.debug("A " + sh[i].getAbstractName()
-                + " service called " + sh[i].getName() + " exists at "
-                + sh[i].getEndpointURL() + "\n");
+        Console.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<>());
@@ -313,15 +313,15 @@ public class Discoverer implements Runnable
               disc_serv = new java.net.URL(sh[i].getEndpointURL());
               if (!ServiceURLList.contains(disc_serv))
               {
-                Cache.debug(
+                Console.debug(
                         "Adding new discovery service at " + disc_serv);
                 ServiceURLList.add(disc_serv);
                 seenNewDiscovery = true;
               }
             } catch (Exception e)
             {
-              Cache.debug("Ignoring bad discovery service URL "
-                              + sh[i].getEndpointURL(), e);
+              Console.debug("Ignoring bad discovery service URL "
+                      + sh[i].getEndpointURL(), e);
             }
           }
         }
@@ -338,21 +338,19 @@ public class Discoverer implements Runnable
     int s_url = 0;
     if (ServiceURLList == null)
     {
-      Cache.debug("No service endpoints to use for service discovery.");
+      Console.debug("No service endpoints to use for service discovery.");
       return;
     }
     while (s_url < ServiceURLList.size())
     {
-      if ((sh = getServices(
-              ServiceURLList.get(s_url))) != null)
+      if ((sh = getServices(ServiceURLList.get(s_url))) != null)
       {
 
         buildServiceLists(sh, cat, sscat);
       }
       else
       {
-        Cache.warn("No services at "
-                + (ServiceURLList.get(s_url))
+        Console.warn("No services at " + (ServiceURLList.get(s_url))
                 + " - check DISCOVERY_URLS property in .jalview_properties");
       }
       s_url++;
@@ -376,7 +374,7 @@ public class Discoverer implements Runnable
   public void run()
   {
     final Discoverer discoverer = this;
-    Thread discoverThread = new Thread()
+    Thread discoverThread = new Thread() // no function?
     {
       @Override
       public void run()
@@ -403,8 +401,7 @@ public class Discoverer implements Runnable
       serviceClientBindings.put("SecStrPred", new JPredClient());
       serviceClientBindings.put("SeqSearch", new SeqSearchWSClient());
     }
-    WS1Client instance = serviceClientBindings
-            .get(sh.getAbstractName());
+    WS1Client instance = serviceClientBindings.get(sh.getAbstractName());
     if (instance == null)
     {
       System.err.println(