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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 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;
import jalview.ext.so.SequenceOntology;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
@@
-319,13
+320,18
@@
public class Jalview
* @j2sIgnore
*/
{
* @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("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;
{
System.setProperty("java.awt.headless", "true");
headless = true;
@@
-557,7
+563,12
@@
public class Jalview
}.start();
}
}.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;
String file = null, data = null;
FileFormatI format = null;