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

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

diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java
index 0a8b8d3..f08e678 100644 (file)
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -453,7 +453,7 @@ public class ArgParser
         {
           if (linkedId == null)
           {
-            if (a.hasOption(Opt.OUTPUT) && a.hasOption(Opt.ALLOWALL)
+            if (a.hasOption(Opt.OUTPUTFILE) && a.hasOption(Opt.ALLOWALL)
                     && val.startsWith(MATCHALLLINKEDIDS))
             {
               // --output=*.ext is shorthand for --all --output {basename}.ext
@@ -464,7 +464,7 @@ public class ArgParser
               val = LINKEDIDDIRNAME + File.separator + LINKEDIDBASENAME
                       + val.substring(MATCHALLLINKEDIDS.length());
             }
-            else if (a.hasOption(Opt.OUTPUT) && a.hasOption(Opt.ALLOWALL)
+            else if (a.hasOption(Opt.OUTPUTFILE) && a.hasOption(Opt.ALLOWALL)
                     && val.startsWith(MATCHOPENEDLINKEDIDS))
             {
               // --output=open*.ext is shorthand for --opened --output