X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=0c1180825aaedfee2eb552963089e72a87565ed5;hb=cb8e52fbbc5f725e3f7f48c672cdddb0690bd978;hp=fe48283085a702013fab5c85f74bf41535a7819b;hpb=9d2408483e451285fd555c3cd6e0273977acbaa7;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index fe48283..0c11808 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,8 +20,6 @@
  */
 package jalview.bin;
 
-import java.util.Locale;
-
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileOutputStream;
@@ -39,6 +37,7 @@ import java.security.PermissionCollection;
 import java.security.Permissions;
 import java.security.Policy;
 import java.util.HashMap;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Vector;
 import java.util.logging.ConsoleHandler;
@@ -319,6 +318,9 @@ public class Jalview
       }
       // anything else!
 
+      // allow https handshakes to download intermediate certs if necessary
+      System.setProperty("com.sun.security.enableAIAcaIssuers", "true");
+
       final String jabawsUrl = aparser.getValue("jabaws");
       if (jabawsUrl != null)
       {
@@ -363,9 +365,10 @@ public class Jalview
     }
     System.setProperty("http.agent",
             "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
+
     try
     {
-      Cache.initLogger();
+      Console.initLogger();
     } catch (NoClassDefFoundError error)
     {
       error.printStackTrace();
@@ -399,13 +402,13 @@ public class Jalview
         JalviewTaskbar.setTaskbar(this);
       } catch (Exception e)
       {
-        Cache.log.info("Cannot set Taskbar");
-        Cache.log.error(e.getMessage());
+        Console.info("Cannot set Taskbar");
+        Console.error(e.getMessage());
         // e.printStackTrace();
       } catch (Throwable t)
       {
-        Cache.log.info("Cannot set Taskbar");
-        Cache.log.error(t.getMessage());
+        Console.info("Cannot set Taskbar");
+        Console.error(t.getMessage());
         // t.printStackTrace();
       }
 
@@ -441,7 +444,7 @@ public class Jalview
           {
             // Start the desktop questionnaire prompter with the specified
             // questionnaire
-            Cache.log.debug("Starting questionnaire url at " + url);
+            Console.debug("Starting questionnaire url at " + url);
             desktop.checkForQuestionnaire(url);
             System.out.println("CMD questionnaire[-" + url
                     + "] executed successfully!");
@@ -456,7 +459,7 @@ public class Jalview
               // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
               // //
               String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
-              Cache.log.debug(
+              Console.debug(
                       "Starting questionnaire with default url: " + defurl);
               desktop.checkForQuestionnaire(defurl);
             }
@@ -784,12 +787,11 @@ public class Jalview
      * @j2sIgnore
      */
     {
-      file = jalview.bin.Cache.getDefault("STARTUP_FILE",
-              jalview.bin.Cache.getDefault("www.jalview.org",
-                      "https://www.jalview.org")
+      file = Cache.getDefault("STARTUP_FILE",
+              Cache.getDefault("www.jalview.org", "https://www.jalview.org")
                       + "/examples/exampleFile_2_7.jvp");
-      if (file.equals(
-              "http://www.jalview.org/examples/exampleFile_2_3.jar") || file.equals(
+      if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
+              || file.equals(
                       "http://www.jalview.org/examples/exampleFile_2_7.jar"))
       {
         file.replace("http:", "https:");
@@ -872,62 +874,62 @@ public class Jalview
       lafSet = setCrossPlatformLookAndFeel();
       if (!lafSet)
       {
-        Cache.log.error("Could not set requested laf=" + laf);
+        Console.error("Could not set requested laf=" + laf);
       }
       break;
     case "system":
       lafSet = setSystemLookAndFeel();
       if (!lafSet)
       {
-        Cache.log.error("Could not set requested laf=" + laf);
+        Console.error("Could not set requested laf=" + laf);
       }
       break;
     case "gtk":
       lafSet = setGtkLookAndFeel();
       if (!lafSet)
       {
-        Cache.log.error("Could not set requested laf=" + laf);
+        Console.error("Could not set requested laf=" + laf);
       }
       break;
     case "metal":
       lafSet = setMetalLookAndFeel();
       if (!lafSet)
       {
-        Cache.log.error("Could not set requested laf=" + laf);
+        Console.error("Could not set requested laf=" + laf);
       }
       break;
     case "nimbus":
       lafSet = setNimbusLookAndFeel();
       if (!lafSet)
       {
-        Cache.log.error("Could not set requested laf=" + laf);
+        Console.error("Could not set requested laf=" + laf);
       }
       break;
     case "quaqua":
       lafSet = setQuaquaLookAndFeel();
       if (!lafSet)
       {
-        Cache.log.error("Could not set requested laf=" + laf);
+        Console.error("Could not set requested laf=" + laf);
       }
       break;
     case "vaqua":
       lafSet = setVaquaLookAndFeel();
       if (!lafSet)
       {
-        Cache.log.error("Could not set requested laf=" + laf);
+        Console.error("Could not set requested laf=" + laf);
       }
       break;
     case "mac":
       lafSet = setMacLookAndFeel();
       if (!lafSet)
       {
-        Cache.log.error("Could not set requested laf=" + laf);
+        Console.error("Could not set requested laf=" + laf);
       }
       break;
     case "none":
       break;
     default:
-      Cache.log.error("Requested laf=" + laf + " not implemented");
+      Console.error("Requested laf=" + laf + " not implemented");
     }
     if (!lafSet)
     {
@@ -953,9 +955,9 @@ public class Jalview
       set = true;
     } catch (Exception ex)
     {
-      Cache.log.error("Unexpected Look and Feel Exception");
-      Cache.log.error(ex.getMessage());
-      Cache.log.debug(Cache.getStackTraceString(ex));
+      Console.error("Unexpected Look and Feel Exception");
+      Console.error(ex.getMessage());
+      Console.debug(Cache.getStackTraceString(ex));
     }
     return set;
   }
@@ -969,9 +971,9 @@ public class Jalview
       set = true;
     } catch (Exception ex)
     {
-      Cache.log.error("Unexpected Look and Feel Exception");
-      Cache.log.error(ex.getMessage());
-      Cache.log.debug(Cache.getStackTraceString(ex));
+      Console.error("Unexpected Look and Feel Exception");
+      Console.error(ex.getMessage());
+      Console.debug(Cache.getStackTraceString(ex));
     }
     return set;
   }
@@ -987,7 +989,8 @@ public class Jalview
         if (info.getName() != null && nameStartsWith
                 ? info.getName().toLowerCase(Locale.ROOT)
                         .startsWith(name.toLowerCase(Locale.ROOT))
-                : info.getName().toLowerCase(Locale.ROOT).equals(name.toLowerCase(Locale.ROOT)))
+                : info.getName().toLowerCase(Locale.ROOT)
+                        .equals(name.toLowerCase(Locale.ROOT)))
         {
           className = info.getClassName();
           break;
@@ -997,9 +1000,9 @@ public class Jalview
       set = true;
     } catch (Exception ex)
     {
-      Cache.log.error("Unexpected Look and Feel Exception");
-      Cache.log.error(ex.getMessage());
-      Cache.log.debug(Cache.getStackTraceString(ex));
+      Console.error("Unexpected Look and Feel Exception");
+      Console.error(ex.getMessage());
+      Console.debug(Cache.getStackTraceString(ex));
     }
     return set;
   }
@@ -1109,17 +1112,16 @@ public class Jalview
               @Override
               public void run()
               {
-                Cache.log.debug(
-                        "Initialising googletracker for usage stats.");
+                Console.debug("Initialising googletracker for usage stats.");
                 Cache.initGoogleTracker();
-                Cache.log.debug("Tracking enabled.");
+                Console.debug("Tracking enabled.");
               }
             }, new Runnable()
             {
               @Override
               public void run()
               {
-                Cache.log.debug("Not enabling Google Tracking.");
+                Console.debug("Not enabling Google Tracking.");
               }
             }, null, true);
     desktop.addDialogThread(prompter);