JAL-629 Added 'Type' to args and argvalues

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index cf73c81..8bc3e1b 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -68,6 +68,7 @@ import groovy.lang.Binding;
 import groovy.util.GroovyScriptEngine;
 import jalview.bin.argparser.Arg;
 import jalview.bin.argparser.Arg.Opt;
+import jalview.bin.argparser.Arg.Type;
 import jalview.bin.argparser.ArgParser;
 import jalview.bin.argparser.BootstrapArgs;
 import jalview.ext.so.SequenceOntology;
@@ -473,7 +474,7 @@ public class Jalview
     if (bootstrapArgs.contains(Arg.ARGFILE))
     {
       argparser = ArgParser.parseArgFiles(
-              bootstrapArgs.getList(Arg.ARGFILE),
+              bootstrapArgs.getValueList(Arg.ARGFILE),
               bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS),
               bootstrapArgs);
     }
@@ -491,9 +492,11 @@ public class Jalview
      * @j2sIgnore
      */
     {
-      if (bootstrapArgs.contains(Arg.HELP))
+      if (bootstrapArgs.containsType(Type.HELP))
       {
-        System.out.println(Arg.usage());
+        System.out.println("##### HERE");
+        System.out
+                .println(Arg.usage(bootstrapArgs.getArgsOfType(Type.HELP)));
         Jalview.exit(null, 0);
       }
       if (aparser.contains("help") || aparser.contains("h"))
@@ -547,7 +550,7 @@ public class Jalview
     List<String> setprops = new ArrayList<>();
     if (bootstrapArgs.contains(Arg.SETPROP))
     {
-      setprops = bootstrapArgs.getList(Arg.SETPROP);
+      setprops = bootstrapArgs.getValueList(Arg.SETPROP);
     }
     else
     {