JAL-629 example files from nf-core

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 6f000dd..6238c7d 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -57,6 +57,7 @@ import com.threerings.getdown.util.LaunchUtil;
 //import edu.stanford.ejalbert.launching.IBrowserLaunching;
 import groovy.lang.Binding;
 import groovy.util.GroovyScriptEngine;
+import jalview.bin.ArgParser.Arg;
 import jalview.ext.so.SequenceOntology;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
@@ -319,13 +320,18 @@ public class Jalview
      * @j2sIgnore
      */
     {
+      if (argparser.isSet(Arg.HEADLESS))
+      {
+        headless = argparser.getBool(Arg.HEADLESS);
+      }
+
       if (aparser.contains("help") || aparser.contains("h"))
       {
         showUsage();
         System.exit(0);
       }
-      if (aparser.contains("nodisplay") || aparser.contains("nogui")
-              || aparser.contains("headless"))
+      if (headless || aparser.contains("nodisplay")
+              || aparser.contains("nogui") || aparser.contains("headless"))
       {
         System.setProperty("java.awt.headless", "true");
         headless = true;
@@ -557,7 +563,12 @@ public class Jalview
       }.start();
     }
 
-    Commands.processArgs(argparser, headless);
+    if (argparser.isSet(Arg.HEADLESS))
+      headless = argparser.getBool(Arg.HEADLESS);
+    if (Commands.processArgs(argparser, headless))
+    {
+      System.exit(1);
+    }
 
     String file = null, data = null;
     FileFormatI format = null;