JAL-3609 HiDPI scale setting done via system prop in getdown or halview.bin.Launcher

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 86499c8..a571ce9 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,27 +20,6 @@
  */
 package jalview.bin;
 
-import jalview.ext.so.SequenceOntology;
-import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.gui.PromptUserConfig;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.BioJsHTMLOutput;
-import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
-import jalview.io.FileFormatException;
-import jalview.io.FileFormatI;
-import jalview.io.FileLoader;
-import jalview.io.HtmlSvgOutput;
-import jalview.io.IdentifyFile;
-import jalview.io.NewickFile;
-import jalview.io.gff.SequenceOntologyFactory;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.ws.jws2.Jws2Discoverer;
-
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileOutputStream;
@@ -68,6 +47,26 @@ import com.threerings.getdown.util.LaunchUtil;
 
 import groovy.lang.Binding;
 import groovy.util.GroovyScriptEngine;
+import jalview.ext.so.SequenceOntology;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.PromptUserConfig;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.BioJsHTMLOutput;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormatI;
+import jalview.io.FileLoader;
+import jalview.io.HtmlSvgOutput;
+import jalview.io.IdentifyFile;
+import jalview.io.NewickFile;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.jws2.Jws2Discoverer;
 
 /**
  * Main class for Jalview Application <br>
@@ -107,7 +106,7 @@ public class Jalview
         perms.add(new AllPermission());
         return (perms);
       }
-    
+
       @Override
       public void refresh()
       {
@@ -124,8 +123,8 @@ public class Jalview
   class FeatureFetcher
   {
     /*
-     * TODO: generalise to track all jalview events to orchestrate batch
-     * processing events.
+     * TODO: generalise to track all jalview events to orchestrate batch processing
+     * events.
      */
 
     private int queued = 0;
@@ -199,29 +198,29 @@ public class Jalview
     System.setSecurityManager(null);
     System.out
             .println("Java version: " + System.getProperty("java.version"));
+    System.out.println("Java Home: " + System.getProperty("java.home"));
     System.out.println(System.getProperty("os.arch") + " "
             + System.getProperty("os.name") + " "
             + System.getProperty("os.version"));
+    String val = System.getProperty("sys.install4jVersion");
+    if (val != null)
+    {
+      System.out.println("Install4j version: " + val);
+    }
+    val = System.getProperty("installer_template_version");
+    if (val != null)
+    {
+      System.out.println("Install4j template version: " + val);
+    }
+    val = System.getProperty("launcher_version");
+    if (val != null)
+    {
+      System.out.println("Launcher version: " + val);
+    }
+
     // report Jalview version
     Cache.loadBuildProperties(true);
 
-    String appdirString = System.getProperty("getdownappdir");
-    if (appdirString != null && appdirString.length() > 0)
-    {
-      final File appdir = new File(appdirString);
-      new Thread()
-      {
-        @Override
-        public void run()
-        {
-          LaunchUtil.upgradeGetdown(
-                  new File(appdir, "getdown-launcher-old.jar"),
-                  new File(appdir, "getdown-launcher.jar"),
-                  new File(appdir, "getdown-launcher-new.jar"));
-        }
-      }.start();
-
-    }
     ArgsParser aparser = new ArgsParser(args);
     boolean headless = false;
 
@@ -325,8 +324,9 @@ public class Jalview
                   "Failed to set QuaQua look and feel: " + e.toString());
         }
       }
-      if (lookAndFeel == null || !(lookAndFeel.getClass()
-              .isAssignableFrom(UIManager.getLookAndFeel().getClass()))
+      if (lookAndFeel == null
+              || !(lookAndFeel.getClass().isAssignableFrom(
+                      UIManager.getLookAndFeel().getClass()))
               || !UIManager.getLookAndFeel().getClass().toString()
                       .toLowerCase().contains("quaqua"))
       {
@@ -344,16 +344,17 @@ public class Jalview
     }
 
     /*
-     * configure 'full' SO model if preferences say to, 
-     * else use the default (SO Lite)
+     * configure 'full' SO model if preferences say to, else use the default (SO
+     * Lite)
      */
-    if (Cache.getDefault("USE_FULL_SO", false))
+    if (Cache.getDefault("USE_FULL_SO", true))
     {
       SequenceOntologyFactory.setInstance(new SequenceOntology());
     }
 
     if (!headless)
     {
+
       desktop = new Desktop();
       desktop.setInBatchMode(true); // indicate we are starting up
 
@@ -422,6 +423,25 @@ public class Jalview
       BioJsHTMLOutput.updateBioJS();
     }
 
+    // Move any new getdown-launcher-new.jar into place over old
+    // getdown-launcher.jar
+    String appdirString = System.getProperty("getdownappdir");
+    if (appdirString != null && appdirString.length() > 0)
+    {
+      final File appdir = new File(appdirString);
+      new Thread()
+      {
+        @Override
+        public void run()
+        {
+          LaunchUtil.upgradeGetdown(
+                  new File(appdir, "getdown-launcher-old.jar"),
+                  new File(appdir, "getdown-launcher.jar"),
+                  new File(appdir, "getdown-launcher-new.jar"));
+        }
+      }.start();
+    }
+
     String file = null, data = null;
     FileFormatI format = null;
     DataSourceType protocol = null;
@@ -487,9 +507,8 @@ public class Jalview
         {
           data.replaceAll("%20", " ");
 
-          ColourSchemeI cs = ColourSchemeProperty
-                  .getColourScheme(af.getViewport(),
-                          af.getViewport().getAlignment(), data);
+          ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
+                  af.getViewport(), af.getViewport().getAlignment(), data);
 
           if (cs != null)
           {