X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=2e4631fb2426f6852d80b616a7edf77b6b4e3593;hb=bc1a3842b31a35a7794f4afec4911ad421c7c3e4;hp=5319eab2979525105e2281d0772b40466db34363;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java
index 5319eab..2e4631f 100644
--- 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);
@@ -173,12 +174,12 @@ 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;
 
     // first set up exclusion list if needed
-    final Set<String> ignoredServices = new HashSet<String>();
+    final Set<String> ignoredServices = new HashSet<>();
     for (String ignored : Cache
             .getDefault("IGNORED_JABAWS_SERVICETYPES", "").split("\\|"))
     {
@@ -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;
@@ -217,9 +218,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     {
       validServiceUrls.removeAllElements();
     }
-    ArrayList<String> svctypes = new ArrayList<String>();
+    ArrayList<String> svctypes = new ArrayList<>();
 
-    List<JabaWsServerQuery> qrys = new ArrayList<JabaWsServerQuery>();
+    List<JabaWsServerQuery> qrys = new ArrayList<>();
     for (final String jwsserver : getServiceUrls())
     {
       JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsserver);
@@ -249,7 +250,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       } catch (Exception e)
       {
       }
-      ;
       for (JabaWsServerQuery squery : qrys)
       {
         if (squery.isRunning())
@@ -259,7 +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)
         {
@@ -285,7 +285,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
                   + svctypes.indexOf(svc.serviceType);
         }
         jalview.util.QuickSort.sort(spos, svcs);
-        services = new Vector<Jws2Instance>();
+        services = new Vector<>();
         for (Jws2Instance svc : svcs)
         {
           if (!ignoredServices.contains(svc.serviceType))
@@ -312,9 +312,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   {
     if (services == null)
     {
-      services = new Vector<Jws2Instance>();
+      services = new Vector<>();
     }
-    System.out.println(
+    jalview.bin.Console.outPrintln(
             "Discovered service: " + jwsservers + " " + service.toString());
     // Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(),
     // service2);
@@ -329,7 +329,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     service.hasParameters();
     if (validServiceUrls == null)
     {
-      validServiceUrls = new Vector<String>();
+      validServiceUrls = new Vector<>();
     }
     validServiceUrls.add(jwsservers);
   }
@@ -363,10 +363,10 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
      * for moment we keep them separate.
      */
     JMenu atpoint;
-    List<Jws2Instance> enumerableServices = new ArrayList<Jws2Instance>();
+    List<Jws2Instance> enumerableServices = new ArrayList<>();
     // jws2al.removeAll();
-    Map<String, Jws2Instance> preferredHosts = new HashMap<String, Jws2Instance>();
-    Map<String, List<Jws2Instance>> alternates = new HashMap<String, List<Jws2Instance>>();
+    Map<String, Jws2Instance> preferredHosts = new HashMap<>();
+    Map<String, List<Jws2Instance>> alternates = new HashMap<>();
     for (Jws2Instance service : services.toArray(new Jws2Instance[0]))
     {
       if (!isRecalculable(service.action))
@@ -395,7 +395,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
         {
           if (ph == null)
           {
-            ph = new ArrayList<Jws2Instance>();
+            ph = new ArrayList<>();
           }
           ph.add(service);
           alternates.put(service.serviceType, ph);
@@ -457,7 +457,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
                           sv.action, sv);
                   changeSupport.firePropertyChange("services",
                           new Vector<Jws2Instance>(), services);
-                };
+                }
               }).start();
 
             }
@@ -483,17 +483,16 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
      */
     JMenu atpoint;
 
-    List<String> hostLabels = new ArrayList<String>();
-    Hashtable<String, String> lasthostFor = new Hashtable<String, String>();
-    Hashtable<String, ArrayList<Jws2Instance>> hosts = new Hashtable<String, ArrayList<Jws2Instance>>();
-    ArrayList<String> hostlist = new ArrayList<String>();
+    List<String> hostLabels = new ArrayList<>();
+    Hashtable<String, String> lasthostFor = new Hashtable<>();
+    Hashtable<String, ArrayList<Jws2Instance>> hosts = new Hashtable<>();
+    ArrayList<String> hostlist = new ArrayList<>();
     for (Jws2Instance service : enumerableServices)
     {
       ArrayList<Jws2Instance> hostservices = hosts.get(service.getHost());
       if (hostservices == null)
       {
-        hosts.put(service.getHost(),
-                hostservices = new ArrayList<Jws2Instance>());
+        hosts.put(service.getHost(), hostservices = new ArrayList<>());
         hostlist.add(service.getHost());
       }
       hostservices.add(service);
@@ -577,16 +576,20 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     }
   }
 
+  /**
+   * 
+   * @param args
+   * @j2sIgnore
+   */
   public static void main(String[] args)
   {
     if (args.length > 0)
     {
-      testUrls = new ArrayList<String>();
+      testUrls = new ArrayList<>();
       for (String url : args)
       {
         testUrls.add(url);
       }
-      ;
     }
     Thread runner = getDiscoverer()
             .startDiscoverer(new PropertyChangeListener()
@@ -597,12 +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());
                   }
@@ -618,7 +623,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       } catch (InterruptedException e)
       {
       }
-      ;
     }
     try
     {
@@ -685,7 +689,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       // return test urls, if there are any, instead of touching cache
       return testUrls;
     }
-    List<String> urls = new ArrayList<String>();
+    List<String> urls = new ArrayList<>();
 
     if (this.preferredUrl != null)
     {
@@ -709,23 +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;
@@ -733,8 +737,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
 
   public Vector<Jws2Instance> getServices()
   {
-    return (services == null) ? new Vector<Jws2Instance>()
-            : new Vector<Jws2Instance>(services);
+    return (services == null) ? new Vector<>() : new Vector<>(services);
   }
 
   /**
@@ -839,7 +842,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   {
     if (urlsWithoutServices == null)
     {
-      urlsWithoutServices = new Vector<String>();
+      urlsWithoutServices = new Vector<>();
     }
 
     if ((invalidServiceUrls == null
@@ -859,7 +862,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   {
     if (invalidServiceUrls == null)
     {
-      invalidServiceUrls = new Vector<String>();
+      invalidServiceUrls = new Vector<>();
     }
     if (!invalidServiceUrls.contains(jwsservers))
     {
@@ -947,7 +950,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
    */
   public Jws2Instance getPreferredServiceFor(String[] serviceURLs)
   {
-    HashSet<String> urls = new HashSet<String>();
+    HashSet<String> urls = new HashSet<>();
     urls.addAll(Arrays.asList(serviceURLs));
     Jws2Instance match = null;
     if (services != null)
@@ -974,7 +977,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     return match;
   }
 
-  Map<String, Map<String, String>> preferredServiceMap = new HashMap<String, Map<String, String>>();;
+  Map<String, Map<String, String>> preferredServiceMap = new HashMap<>();
 
   /**
    * get current preferred service of the given type, or global default
@@ -1026,12 +1029,12 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     String afid = (af == null) ? "" : af.getViewport().getSequenceSetId();
     if (preferredServiceMap == null)
     {
-      preferredServiceMap = new HashMap<String, Map<String, String>>();
+      preferredServiceMap = new HashMap<>();
     }
     Map<String, String> prefmap = preferredServiceMap.get(afid);
     if (prefmap == null)
     {
-      prefmap = new HashMap<String, String>();
+      prefmap = new HashMap<>();
       preferredServiceMap.put(afid, prefmap);
     }
     prefmap.put(serviceType, selectedServer.getHost());