+ public static void cleanupFiles(String[] filenames)
+ {
+ for (String filename : filenames)
+ {
+ File file = new File(filename);
+ if (file.exists())
+ {
+ file.delete();
+ }
+ }
+ }
+
+ @Test(
+ groups = "Functional",
+ dataProvider = "allLinkedIdsData",
+ singleThreaded = true)
+ public void allLinkedIdsTest(String cmdLine, String[] filenames,
+ String[] nonfilenames)
+ {
+ String[] args = (cmdLine + " --gui").split("\\s+");
+ callJalviewMain(args);
+ Commands cmds = Jalview.getInstance().getCommands();
+ Assert.assertNotNull(cmds);
+ for (String filename : filenames)
+ {
+ Assert.assertTrue(new File(filename).exists(),
+ "File '" + filename + "' was not created");
+ }
+ cleanupFiles(filenames);
+ if (nonfilenames != null)
+ {
+ for (String nonfilename : nonfilenames)
+ {
+ File nonfile = new File(nonfilename);
+ Assert.assertFalse(nonfile.exists(),
+ "File " + nonfilename + " exists when it shouldn't!");
+ }
+ }
+ }
+
+ @DataProvider(name = "allLinkedIdsData")
+ public Object[][] allLinkedIdsData()
+ {
+ 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", }, },
+ //
+ };
+ }
+