Merge branch 'releases/Release_2_11_3_Branch'

[jalview.git] / src / jalview / ws / jws2 / Jws2Discoverer.java

diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java
index 516a719..2e4631f 100644 (file)
--- a/src/jalview/ws/jws2/Jws2Discoverer.java
+++ b/src/jalview/ws/jws2/Jws2Discoverer.java
@@ -21,6 +21,7 @@
 package jalview.ws.jws2;
 
 import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.JvSwingUtils;
@@ -164,7 +165,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       {
         try
         {
-          Cache.log.debug(
+          Console.debug(
                   "Waiting around for old discovery thread to finish.");
           // wait around until old discoverer dies
           Thread.sleep(100);
@@ -173,7 +174,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
         }
       }
       aborted = false;
-      Cache.log.debug("Old discovery thread has finished.");
+      Console.debug("Old discovery thread has finished.");
     }
     running = true;
 
@@ -194,7 +195,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
               .loadClass("compbio.ws.client.Jws2Client");
     } catch (ClassNotFoundException e)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Not enabling JABA Webservices : client jar is not available."
                       + "\nPlease check that your webstart JNLP file is up to date!");
       running = false;
@@ -258,7 +259,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       }
       if (aborted)
       {
-        Cache.log.debug(
+        Console.debug(
                 "Aborting " + qrys.size() + " JABAWS discovery threads.");
         for (JabaWsServerQuery squery : qrys)
         {
@@ -313,7 +314,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     {
       services = new Vector<>();
     }
-    System.out.println(
+    jalview.bin.Console.outPrintln(
             "Discovered service: " + jwsservers + " " + service.toString());
     // Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(),
     // service2);
@@ -491,8 +492,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       ArrayList<Jws2Instance> hostservices = hosts.get(service.getHost());
       if (hostservices == null)
       {
-        hosts.put(service.getHost(),
-                hostservices = new ArrayList<>());
+        hosts.put(service.getHost(), hostservices = new ArrayList<>());
         hostlist.add(service.getHost());
       }
       hostservices.add(service);
@@ -600,12 +600,14 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
               {
                 if (getDiscoverer().services != null)
                 {
-                  System.out.println("Changesupport: There are now "
-                          + getDiscoverer().services.size() + " services");
+                  jalview.bin.Console
+                          .outPrintln("Changesupport: There are now "
+                                  + getDiscoverer().services.size()
+                                  + " services");
                   int i = 1;
                   for (Jws2Instance instance : getDiscoverer().services)
                   {
-                    System.out.println("Service " + i++ + " "
+                    jalview.bin.Console.outPrintln("Service " + i++ + " "
                             + instance.getClass() + "@" + instance.getHost()
                             + ": " + instance.getActionText());
                   }
@@ -711,23 +713,23 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
           }
           else
           {
-            Cache.log.warn("Ignoring duplicate url " + url + " in "
+            Console.warn("Ignoring duplicate url " + url + " in "
                     + JWS2HOSTURLS + " list");
           }
         } catch (MalformedURLException ex)
         {
-          Cache.log.warn("Problem whilst trying to make a URL from '"
+          Console.warn("Problem whilst trying to make a URL from '"
                   + ((url != null) ? url : "<null>") + "'");
-          Cache.log.warn(
+          Console.warn(
                   "This was probably due to a malformed comma separated list"
                           + " in the " + JWS2HOSTURLS
                           + " entry of $(HOME)/.jalview_properties)");
-          Cache.log.debug("Exception was ", ex);
+          Console.debug("Exception was ", ex);
         }
       }
     } catch (Exception ex)
     {
-      Cache.log.warn("Error parsing comma separated list of urls in "
+      Console.warn("Error parsing comma separated list of urls in "
               + JWS2HOSTURLS + " preference.", ex);
     }
     return urls;
@@ -735,8 +737,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
 
   public Vector<Jws2Instance> getServices()
   {
-    return (services == null) ? new Vector<>()
-            : new Vector<>(services);
+    return (services == null) ? new Vector<>() : new Vector<>(services);
   }
 
   /**