+ return new Object[][] {
+ //
+ /*
+ */
+ { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
+ new String[]
+ { "test/jalview/bin/argparser/testfiles/test1.stk",
+ "test/jalview/bin/argparser/testfiles/test2.stk",
+ "test/jalview/bin/argparser/testfiles/test3.stk", },
+ null },
+ { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
+ new String[]
+ { "test/jalview/bin/argparser/testfiles/test1.png",
+ "test/jalview/bin/argparser/testfiles/test2.png",
+ "test/jalview/bin/argparser/testfiles/test3.png", },
+ null },
+ { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
+ new String[]
+ { "test/jalview/bin/argparser/testfiles/test1.stk",
+ "test/jalview/bin/argparser/testfiles/test2.stk",
+ "test/jalview/bin/argparser/testfiles/test3.stk", },
+ new String[]
+ { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
+ { "--gui --open=test/jalview/bin/argparser/**/*.fa --all --output={dirname}/{basename}.stk --close",
+ new String[]
+ { "test/jalview/bin/argparser/testfiles/test1.stk",
+ "test/jalview/bin/argparser/testfiles/test2.stk",
+ "test/jalview/bin/argparser/testfiles/test3.stk",
+ "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
+ null },
+ { "--gui --open=test/jalview/bin/argparser/**/*.fa --output=*.stk --close",
+ new String[]
+ { "test/jalview/bin/argparser/testfiles/test1.stk",
+ "test/jalview/bin/argparser/testfiles/test2.stk",
+ "test/jalview/bin/argparser/testfiles/test3.stk",
+ "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
+ null },
+ { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*.stk --close",
+ new String[]
+ { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
+ new String[]
+ { "test/jalview/bin/argparser/testfiles/test1.stk",
+ "test/jalview/bin/argparser/testfiles/test2.stk",
+ "test/jalview/bin/argparser/testfiles/test3.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
+ { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.stk --close",
+ new String[]
+ { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
+ new String[]
+ { "test/jalview/bin/argparser/testfiles/test1.stk",
+ "test/jalview/bin/argparser/testfiles/test2.stk",
+ "test/jalview/bin/argparser/testfiles/test3.stk",
+ "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
+ { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --opened --output={dirname}/{basename}.stk --close",
+ new String[]
+ { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
+ new String[]
+ { "test/jalview/bin/argparser/testfiles/test1.stk",
+ "test/jalview/bin/argparser/testfiles/test2.stk",
+ "test/jalview/bin/argparser/testfiles/test3.stk",
+ "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
+ { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output open*.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.aln --close",
+ new String[]
+ { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test1.aln",
+ "test/jalview/bin/argparser/testfiles/dir2/test2.aln",
+ "test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
+ new String[]
+ { "test/jalview/bin/argparser/testfiles/test1.stk",
+ "test/jalview/bin/argparser/testfiles/test2.stk",
+ "test/jalview/bin/argparser/testfiles/test3.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
+ "test/jalview/bin/argparser/testfiles/test1.aln",
+ "test/jalview/bin/argparser/testfiles/test2.aln",
+ "test/jalview/bin/argparser/testfiles/test3.aln",
+ "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
+ "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
+ //
+ };