JAL-3949 An attempt at converting to Log4j 2 -- no output achieved!

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index b5ec365..1ae1014 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,6 +20,8 @@
  */
 package jalview.bin;
 
+import java.util.Locale;
+
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileOutputStream;
@@ -68,6 +70,7 @@ import jalview.io.NewickFile;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
+import jalview.util.ChannelProperties;
 import jalview.util.HttpUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -316,6 +319,9 @@ 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)
       {
@@ -452,7 +458,7 @@ 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);
@@ -727,17 +733,37 @@ public class Jalview
             af.createEPS(outputFile);
             continue;
           }
-
-          af.saveAlignment(file, format);
-          if (af.isSaveAlignmentSuccessful())
+          FileFormatI outFormat = null;
+          try
           {
-            System.out.println("Written alignment in " + format
-                    + " format to " + file);
+            outFormat = FileFormats.getInstance().forName(outputFormat);
+          } catch (Exception formatP)
+          {
+            System.out.println("Couldn't parse " + outFormat
+                    + " as a valid Jalview format string.");
           }
-          else
+          if (outFormat != null)
           {
-            System.out.println("Error writing file " + file + " in "
-                    + format + " format!!");
+            if (!outFormat.isWritable())
+            {
+              System.out.println(
+                      "This version of Jalview does not support alignment export as "
+                              + outputFormat);
+            }
+            else
+            {
+              af.saveAlignment(file, outFormat);
+              if (af.isSaveAlignmentSuccessful())
+              {
+                System.out.println("Written alignment in "
+                        + outFormat.getName() + " format to " + file);
+              }
+              else
+              {
+                System.out.println("Error writing file " + file + " in "
+                        + outFormat.getName() + " format!!");
+              }
+            }
           }
 
         }
@@ -761,14 +787,18 @@ 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");
       }
@@ -958,9 +988,9 @@ 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;
@@ -1013,11 +1043,11 @@ public class Jalview
   {
     boolean set = false;
     System.setProperty("com.apple.mrj.application.apple.menu.about.name",
-            "Jalview");
+            ChannelProperties.getProperty("app_name"));
     System.setProperty("apple.laf.useScreenMenuBar", "true");
     set = setQuaquaLookAndFeel();
     if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
-            .toLowerCase().contains("quaqua"))
+            .toLowerCase(Locale.ROOT).contains("quaqua"))
     {
       set = setVaquaLookAndFeel();
     }
@@ -1062,7 +1092,9 @@ public class Jalview
                     + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
                     + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
                     + "-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"
-                    + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\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 https://www.jalview.org for description of Features and Annotations file~\n\n");
   }
 
   private static void startUsageStats(final Desktop desktop)