Merge branch 'develop' into JAL-3416_different_look_and_feel_on_linux

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index a1a6846..73227d3 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -38,6 +38,7 @@ 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;
@@ -454,7 +455,7 @@ public class Jalview
               // String defurl =
               // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
               // //
-              String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
+              String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
               Cache.log.debug(
                       "Starting questionnaire with default url: " + defurl);
               desktop.checkForQuestionnaire(defurl);
@@ -783,14 +784,18 @@ public class Jalview
      * @j2sIgnore
      */
     {
-      file = Cache.getDefault("STARTUP_FILE",
-              Cache.getDefault("www.jalview.org", "http://www.jalview.org")
-                      + "/examples/exampleFile_2_7.jar");
+      file = jalview.bin.Cache.getDefault("STARTUP_FILE",
+              jalview.bin.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"))
+              "http://www.jalview.org/examples/exampleFile_2_3.jar") || file.equals(
+                      "http://www.jalview.org/examples/exampleFile_2_7.jar"))
       {
+        file.replace("http:", "https:");
         // hardwire upgrade of the startup file
-        file.replace("_2_3.jar", "_2_7.jar");
+        file.replace("_2_3", "_2_7");
+        file.replace("2_7.jar", "2_7.jvp");
         // and remove the stale setting
         Cache.removeProperty("STARTUP_FILE");
       }
@@ -987,9 +992,9 @@ public class Jalview
       for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
       {
         if (info.getName() != null && nameStartsWith
-                ? info.getName().toLowerCase()
-                        .startsWith(name.toLowerCase())
-                : info.getName().equalsIgnoreCase(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;
@@ -1059,7 +1064,7 @@ 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();
     }
@@ -1106,7 +1111,7 @@ public class Jalview
                     + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
                     + "-jvmmempc=PERCENT\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to PERCENT% of total physical memory detected. This defaults to 90 if total physical memory can be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
                     + "-jvmmemmax=MAXMEMORY\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m), gigabytes(g) or if you're lucky enough, terabytes(t). This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
-                    + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
+                    + "\n~Read documentation in Application or visit https://www.jalview.org for description of Features and Annotations file~\n\n");
   }
 
   private static void startUsageStats(final Desktop desktop)