JAL-4121 Store Arg.Opts in bootstrapArgs. Change Opt.OUTPUT to Opt.OUTPUTFILE for...

[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 faa4a43..a6bad24 100644 (file)
--- a/src/jalview/bin/argparser/BootstrapArgs.java
+++ b/src/jalview/bin/argparser/BootstrapArgs.java
@@ -23,6 +23,8 @@ public class BootstrapArgs
 
   private Set<File> argFiles = new HashSet<>();
 
+  private Set<Opt> argsOptions = new HashSet<>();
+
   public static BootstrapArgs getBootstrapArgs(String[] args)
   {
     List<String> argList = new ArrayList<>(Arrays.asList(args));
@@ -111,6 +113,17 @@ public class BootstrapArgs
 
         Arg a = ArgParser.argMap.get(argName);
 
+        if (a != null)
+        {
+          for (Opt opt : a.getOptions())
+          {
+            if (!argsOptions.contains(opt))
+            {
+              argsOptions.add(opt);
+            }
+          }
+        }
+
         if (a == null || !a.hasOption(Opt.BOOTSTRAP))
         {
           // not a valid bootstrap arg
@@ -284,8 +297,17 @@ public class BootstrapArgs
       return false;
     }
     if (bootstrapArgMap.containsKey(a))
+    {
       return Boolean.parseBoolean(get(a));
+    }
     else
+    {
       return a.getDefaultBoolValue();
+    }
+  }
+
+  public boolean argsHaveOption(Opt opt)
+  {
+    return argsOptions.contains(opt);
   }
 }