JAL-1953 2.11.2 with Archeopteryx!

[jalview.git] / src / jalview / bin / Jalview.java

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 0b5fafa..ea61024 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -37,6 +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;
@@ -48,6 +49,7 @@ import javax.swing.UIManager.LookAndFeelInfo;
 
 import com.threerings.getdown.util.LaunchUtil;
 
+//import edu.stanford.ejalbert.launching.IBrowserLaunching;
 import groovy.lang.Binding;
 import groovy.util.GroovyScriptEngine;
 import jalview.ext.so.SequenceOntology;
@@ -74,6 +76,9 @@ import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.jws2.Jws2Discoverer;
 
+import groovy.lang.Binding;
+import groovy.util.GroovyScriptEngine;
+
 /**
  * Main class for Jalview Application <br>
  * <br>
@@ -94,6 +99,10 @@ public class Jalview
   static
   {
     Platform.getURLCommandArguments();
+    Platform.addJ2SDirectDatabaseCall("https://www.jalview.org");
+    Platform.addJ2SDirectDatabaseCall("http://www.jalview.org");
+    Platform.addJ2SDirectDatabaseCall("http://www.compbio.dundee.ac.uk");
+    Platform.addJ2SDirectDatabaseCall("https://www.compbio.dundee.ac.uk");
   }
 
   /*
@@ -182,7 +191,7 @@ public class Jalview
             running--;
           }
         }
-      }).start();
+      }, "FeatureFetcher").start();
     }
 
     public synchronized boolean allFinished()
@@ -317,6 +326,9 @@ 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)
       {
@@ -361,9 +373,10 @@ public class Jalview
     }
     System.setProperty("http.agent",
             "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
+
     try
     {
-      Cache.initLogger();
+      Console.initLogger();
     } catch (NoClassDefFoundError error)
     {
       error.printStackTrace();
@@ -397,13 +410,13 @@ 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();
       }
 
@@ -439,7 +452,7 @@ 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!");
@@ -454,7 +467,7 @@ 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);
             }
@@ -466,12 +479,17 @@ public class Jalview
                   .println("CMD [-noquestionnaire] executed successfully!");
         }
 
-        if (!aparser.contains("nonews"))
+        if (!aparser.contains("nonews")
+                || Cache.getProperty("NONEWS") == null)
         {
           desktop.checkForNews();
         }
 
-        BioJsHTMLOutput.updateBioJS();
+        if (!aparser.contains("nohtmltemplates")
+                || Cache.getProperty("NOHTMLTEMPLATES") == null)
+        {
+          BioJsHTMLOutput.updateBioJS();
+        }
       }
     }
 
@@ -782,12 +800,11 @@ 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:");
@@ -870,62 +887,62 @@ 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)
     {
@@ -951,9 +968,9 @@ 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;
   }
@@ -967,9 +984,9 @@ 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;
   }
@@ -983,9 +1000,10 @@ public class Jalview
       for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
       {
         if (info.getName() != null && nameStartsWith
-                ? info.getName().toLowerCase()
-                        .startsWith(name.toLowerCase())
-                : info.getName().toLowerCase().equals(name.toLowerCase()))
+                ? info.getName().toLowerCase(Locale.ROOT)
+                        .startsWith(name.toLowerCase(Locale.ROOT))
+                : info.getName().toLowerCase(Locale.ROOT)
+                        .equals(name.toLowerCase(Locale.ROOT)))
         {
           className = info.getClassName();
           break;
@@ -995,9 +1013,9 @@ 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;
   }
@@ -1042,7 +1060,7 @@ public class Jalview
     System.setProperty("apple.laf.useScreenMenuBar", "true");
     set = setQuaquaLookAndFeel();
     if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
-            .toLowerCase().contains("quaqua"))
+            .toLowerCase(Locale.ROOT).contains("quaqua"))
     {
       set = setVaquaLookAndFeel();
     }
@@ -1107,17 +1125,17 @@ public class Jalview
               @Override
               public void run()
               {
-                Cache.log.debug(
+                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);