Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_optio...

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 73227d3..fd1783a 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -45,11 +45,15 @@ import java.util.logging.ConsoleHandler;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
+import javax.swing.SwingUtilities;
 import javax.swing.UIManager;
 import javax.swing.UIManager.LookAndFeelInfo;
 
+import com.formdev.flatlaf.FlatLightLaf;
+import com.formdev.flatlaf.util.SystemInfo;
 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;
@@ -96,6 +100,10 @@ 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");
   }
 
   /*
@@ -319,6 +327,9 @@ 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 +374,10 @@ 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 +411,13 @@ 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 +453,7 @@ 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 +468,7 @@ 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);
             }
@@ -468,12 +480,17 @@ 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();
+        }
       }
     }
 
@@ -784,12 +801,11 @@ 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:");
@@ -872,69 +888,69 @@ 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 "flat":
       lafSet = setFlatLookAndFeel();
       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)
     {
@@ -960,9 +976,9 @@ 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;
   }
@@ -976,9 +992,9 @@ 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;
   }
@@ -994,7 +1010,8 @@ 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;
@@ -1004,9 +1021,9 @@ 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;
   }
@@ -1035,8 +1052,34 @@ public class Jalview
             "com.formdev.flatlaf.FlatLightLaf", false);
     if (set)
     {
+      if (Platform.isMac())
+      {
+        System.setProperty("apple.laf.useScreenMenuBar", "true");
+        System.setProperty("apple.awt.application.name",
+                ChannelProperties.getProperty("app_name"));
+        System.setProperty("apple.awt.application.appearance", "system");
+        if (SystemInfo.isMacFullWindowContentSupported
+                && Desktop.desktop != null)
+        {
+          Desktop.desktop.getRootPane()
+                  .putClientProperty("apple.awt.fullWindowContent", true);
+          Desktop.desktop.getRootPane()
+                  .putClientProperty("apple.awt.transparentTitleBar", true);
+        }
+
+        SwingUtilities.invokeLater(() -> {
+          FlatLightLaf.setup();
+        });
+      }
+
       UIManager.put("TabbedPane.showTabSeparators", true);
       UIManager.put("TabbedPane.tabSeparatorsFullHeight", true);
+      UIManager.put("TabbedPane.tabsOverlapBorder", true);
+      // UIManager.put("TabbedPane.hasFullBorder", true);
+      UIManager.put("TabbedPane.tabLayoutPolicy", "scroll");
+      UIManager.put("TabbedPane.scrollButtonsPolicy", "asNeeded");
+      UIManager.put("TabbedPane.smoothScrolling", true);
+      UIManager.put("TabbedPane.tabWidthMode", "compact");
       UIManager.put("TabbedPane.selectedBackground", Color.white);
     }
     return set;
@@ -1129,17 +1172,17 @@ 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);