X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=b5ec365644b51aed02e29ef698e6ef53e8b466d3;hb=ba1ea2deefe026b1b862de72aed232060dd92c7c;hp=06f3a473fc233057d9fcf6b34147d6752d54ec50;hpb=b9bf3044b32b62771648842169f79ca8e7050c7f;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 06f3a47..b5ec365 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -60,6 +60,7 @@ import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FileFormatException;
 import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
 import jalview.io.FileLoader;
 import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
@@ -67,6 +68,7 @@ import jalview.io.NewickFile;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
+import jalview.util.HttpUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.jws2.Jws2Discoverer;
@@ -286,17 +288,6 @@ public class Jalview
     ArgsParser aparser = new ArgsParser(args);
     boolean headless = false;
 
-    if (aparser.contains("help") || aparser.contains("h"))
-    {
-      showUsage();
-      System.exit(0);
-    }
-    if (aparser.contains("nodisplay") || aparser.contains("nogui")
-            || aparser.contains("headless"))
-    {
-      System.setProperty("java.awt.headless", "true");
-      headless = true;
-    }
     String usrPropsFile = aparser.getValue("props");
     Cache.loadProperties(usrPropsFile); // must do this before
     if (usrPropsFile != null)
@@ -396,6 +387,7 @@ public class Jalview
 
     if (!headless)
     {
+      Desktop.nosplash = aparser.contains("nosplash");
       desktop = new Desktop();
       desktop.setInBatchMode(true); // indicate we are starting up
 
@@ -414,6 +406,9 @@ public class Jalview
         // t.printStackTrace();
       }
 
+      // set Proxy settings before all the internet calls
+      Cache.setProxyPropertiesFromPreferences();
+
       desktop.setVisible(true);
 
       if (!Platform.isJS())
@@ -423,7 +418,10 @@ public class Jalview
        * @j2sIgnore
        */
       {
-        desktop.startServiceDiscovery();
+        if (!aparser.contains("nowebservicediscovery"))
+        {
+          desktop.startServiceDiscovery();
+        }
         if (!aparser.contains("nousagestats"))
         {
           startUsageStats(desktop);
@@ -531,8 +529,7 @@ public class Jalview
        * @j2sIgnore
        */
       {
-        if (!file.startsWith("http://") && !file.startsWith("https://"))
-        // BH 2019 added https check for Java
+        if (!HttpUtils.startsWithHttpOrHttps(file))
         {
           if (!(new File(file)).exists())
           {
@@ -776,12 +773,7 @@ public class Jalview
         Cache.removeProperty("STARTUP_FILE");
       }
 
-      protocol = DataSourceType.FILE;
-
-      if (file.indexOf("http:") > -1)
-      {
-        protocol = DataSourceType.URL;
-      }
+      protocol = AppletFormatAdapter.checkProtocol(file);
 
       if (file.endsWith(".jar"))
       {