JAL-4059 fix that boolean for non-value query string args

[jalview.git] / src / jalview / bin / argparser / BootstrapArgs.java

diff --git a/src/jalview/bin/argparser/BootstrapArgs.java b/src/jalview/bin/argparser/BootstrapArgs.java
index a989206..5c21d03 100644 (file)
--- a/src/jalview/bin/argparser/BootstrapArgs.java
+++ b/src/jalview/bin/argparser/BootstrapArgs.java
@@ -214,6 +214,13 @@ public class BootstrapArgs
         }
       }
     }
+
+    // if in an argfile, remove it from the hashset so it can be re-used in
+    // another argfile
+    if (inArgFile != null)
+    {
+      argFiles.remove(inArgFile);
+    }
   }
 
   public boolean contains(Arg a)
@@ -292,7 +299,7 @@ public class BootstrapArgs
   private void add(Arg a, Type t, String s)
   {
     List<Map.Entry<Type, String>> l = getOrCreateList(a);
-    if (a.hasOption(Opt.MULTI) || l.size() == 0)
+    if (a.hasOption(Opt.MULTIVALUE) || l.size() == 0)
     {
       l.add(entry(t, s));
     }
@@ -301,7 +308,7 @@ public class BootstrapArgs
   private void addAll(Arg a, Type t, List<String> al)
   {
     List<Map.Entry<Type, String>> l = getOrCreateList(a);
-    if (a.hasOption(Opt.MULTI))
+    if (a.hasOption(Opt.MULTIVALUE))
     {
       for (String s : al)
       {
@@ -384,7 +391,7 @@ public class BootstrapArgs
     }
     else if (this.contains(Arg.HEADLESS))
     {
-      // --headless, --noheadless specified => use value
+      // --headless has been specified on the command line => headless
       isHeadless = this.getBoolean(Arg.HEADLESS);
     }
     else if (this.argsHaveOption(Opt.OUTPUTFILE))