4 import java.io.IOException;
5 import java.nio.file.Files;
7 import java.util.HashSet;
10 import org.testng.Assert;
11 import org.testng.annotations.AfterClass;
12 import org.testng.annotations.AfterMethod;
13 import org.testng.annotations.BeforeClass;
14 import org.testng.annotations.DataProvider;
15 import org.testng.annotations.Test;
17 import jalview.gui.AlignFrame;
18 import jalview.gui.Desktop;
19 import jalview.gui.JvOptionPane;
20 import jalview.util.ArrayUtils;
22 public class CommandsTest
24 private static final String testfiles = "test/jalview/bin/argparser/testfiles";
26 @BeforeClass(alwaysRun = true)
27 public static void setUpBeforeClass() throws Exception
29 Cache.loadProperties("test/jalview/gui/quitProps.jvprops");
30 Date oneHourFromNow = new Date(
31 System.currentTimeMillis() + 3600 * 1000);
32 Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
35 @AfterClass(alwaysRun = true)
36 public static void resetProps()
38 Cache.loadProperties("test/jalview/testProps.jvprops");
41 @BeforeClass(alwaysRun = true)
42 public void setUpJvOptionPane()
44 JvOptionPane.setInteractiveMode(false);
45 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
48 @AfterMethod(alwaysRun = true)
49 public void tearDown()
51 Desktop.closeDesktop();
54 public static void callJalviewMain(String[] args)
56 if (Jalview.getInstance() != null)
58 Jalview.getInstance().doMain(args);
66 /* --setprops is currently disabled so this test won't work
67 @Test(groups = "Functional")
68 public void setpropsTest()
70 final String MOSTLY_HARMLESS = "MOSTLY_HARMLESS";
71 String cmdLine = "--setprop=" + MOSTLY_HARMLESS + "=Earth";
72 String[] args = cmdLine.split("\\s+");
74 Assert.assertEquals(Cache.getDefault(MOSTLY_HARMLESS, "Magrathea"),
79 @Test(groups = "Functional", dataProvider = "cmdLines")
80 public void commandsOpenTest(String cmdLine, boolean cmdArgs,
81 int numFrames, String[] sequences)
85 String[] args = (cmdLine + " --gui").split("\\s+");
86 callJalviewMain(args);
87 Commands cmds = Jalview.getInstance().getCommands();
88 Assert.assertNotNull(cmds);
89 Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs,
90 "Commands were not provided in the args");
91 Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
92 "Overall command parse and operation is false");
94 Assert.assertEquals(Desktop.getAlignFrames().length, numFrames,
95 "Wrong number of AlignFrames");
97 if (sequences != null)
99 Set<String> openedSequenceNames = new HashSet<>();
100 AlignFrame[] afs = Desktop.getAlignFrames();
101 for (AlignFrame af : afs)
103 openedSequenceNames.addAll(
104 af.getViewport().getAlignment().getSequenceNames());
106 for (String sequence : sequences)
108 Assert.assertTrue(openedSequenceNames.contains(sequence),
109 "Sequence '" + sequence
110 + "' was not found in opened alignment files: "
111 + cmdLine + ".\nOpened sequence names are:\n"
112 + String.join("\n", openedSequenceNames));
117 lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
118 } catch (Exception x)
120 Assert.fail("Unexpected exception during commandsOpenTest", x);
130 { "Functional", "testTask1" },
131 dataProvider = "structureImageOutputFiles")
132 public void structureImageOutputTest(String cmdLine, String[] filenames)
135 cleanupFiles(filenames);
136 String[] args = (cmdLine + " --gui").split("\\s+");
139 callJalviewMain(args);
140 Commands cmds = Jalview.getInstance().getCommands();
141 Assert.assertNotNull(cmds);
142 File lastFile = null;
143 for (String filename : filenames)
145 File file = new File(filename);
146 Assert.assertTrue(file.exists(), "File '" + filename
147 + "' was not created by '" + cmdLine + "'");
148 Assert.assertTrue(file.isFile(), "File '" + filename
149 + "' is not a file from '" + cmdLine + "'");
150 Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
151 + "' has no content from '" + cmdLine + "'");
152 // make sure the successive output files get bigger!
153 if (lastFile != null)
154 Assert.assertTrue(Files.size(file.toPath()) > Files
155 .size(lastFile.toPath()));
157 } catch (Exception x)
159 Assert.fail("Unexpected exception during structureImageOutputTest",
163 cleanupFiles(filenames);
168 @Test(groups = "Functional", dataProvider = "argfileOutputFiles")
169 public void argFilesGlobAndSubstitutionsTest(String cmdLine,
170 String[] filenames) throws IOException
172 cleanupFiles(filenames);
173 String[] args = (cmdLine + " --gui").split("\\s+");
176 callJalviewMain(args);
177 Commands cmds = Jalview.getInstance().getCommands();
178 Assert.assertNotNull(cmds);
179 File lastFile = null;
180 for (String filename : filenames)
182 File file = new File(filename);
183 Assert.assertTrue(file.exists(), "File '" + filename
184 + "' was not created by '" + cmdLine + "'");
185 Assert.assertTrue(file.isFile(), "File '" + filename
186 + "' is not a file from '" + cmdLine + "'");
187 Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
188 + "' has no content from '" + cmdLine + "'");
189 // make sure the successive output files get bigger!
190 if (lastFile != null)
191 Assert.assertTrue(Files.size(file.toPath()) > Files
192 .size(lastFile.toPath()));
194 } catch (Exception x)
197 "Unexpected exception during argFilesGlobAndSubstitutions",
201 cleanupFiles(filenames);
206 @DataProvider(name = "structureImageOutputFiles")
207 public Object[][] structureImageOutputFiles()
209 return new Object[][] {
211 { "--gui --nonews --nosplash --open=./examples/test_fab41.result/sample.a2m "
212 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
213 + "--structureimage=" + testfiles + "/structureimage1.png "
214 + "--open=./examples/test_fab41.result/sample.a2m "
215 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
216 + "--structureimage=" + testfiles
217 + "/structureimage2.png --structureimagescale=1.5"
218 + "--open=./examples/test_fab41.result/sample.a2m "
219 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
220 + "--structureimage=" + testfiles
221 + "/structureimage3.png --structureimagescale=2.0",
223 { testfiles + "/structureimage1.png",
224 testfiles + "/structureimage2.png",
225 testfiles + "/structureimage3.png" } },
226 { "--headless --noquit --open=./examples/test_fab41.result/sample.a2m "
227 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
228 + "--structureimage=" + testfiles + "/structureimage1.png "
229 + "--open=./examples/test_fab41.result/sample.a2m "
230 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
231 + "--structureimage=" + testfiles
232 + "/structureimage2.png --structureimagescale=1.5"
233 + "--open=./examples/test_fab41.result/sample.a2m "
234 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
235 + "--structureimage=" + testfiles
236 + "/structureimage3.png --structureimagescale=2.0",
238 { testfiles + "/structureimage1.png",
239 testfiles + "/structureimage2.png",
240 testfiles + "/structureimage3.png" } },
248 @DataProvider(name = "argfileOutputFiles")
249 public Object[][] argfileOutputFiles()
251 return new Object[][] {
253 { "--gui --argfile=" + testfiles + "/**/*.txt", new String[]
254 { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
255 testfiles + "/dir3/subdir/test0.png" } },
256 { "--gui --argfile=" + testfiles + "/**/argfile.txt", new String[]
257 { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
258 { "--gui --argfile=" + testfiles + "/dir*/argfile.txt", new String[]
259 { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
260 { "--gui --initsubstitutions --append examples/uniref50.fa --image "
261 + testfiles + "/{basename}.png",
263 { testfiles + "/uniref50.png" } },
264 { "--gui --append examples/uniref50.fa --nosubstitutions --image "
265 + testfiles + "/{basename}.png",
267 { testfiles + "/{basename}.png" } }
273 @DataProvider(name = "cmdLines")
274 public Object[][] cmdLines()
276 String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN",
277 "FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" };
278 String[] t1 = new String[] { "TEST1" };
279 String[] t2 = new String[] { "TEST2" };
280 String[] t3 = new String[] { "TEST3" };
281 return new Object[][] {
284 { "--append=examples/uniref50.fa", true, 1, someUniref50Seqs },
285 { "--append examples/uniref50.fa", true, 1, someUniref50Seqs },
286 { "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs },
287 // NOTE we cannot use shell expansion in tests, so list all files!
288 { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
290 { "--append=[new]examples/uniref50*.fa", true, 2,
292 { "--open=examples/uniref50*.fa", true, 2, someUniref50Seqs },
293 { "examples/uniref50.fa", true, 1, someUniref50Seqs },
294 { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
295 ArrayUtils.concatArrays(someUniref50Seqs, t1) },
296 { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
297 { "--gui --argfile=" + testfiles + "/argfile0.txt", true, 1,
298 ArrayUtils.concatArrays(t1, t3) },
299 { "--gui --argfile=" + testfiles + "/argfile*.txt", true, 5,
300 ArrayUtils.concatArrays(t1, t2, t3) },
301 { "--gui --argfile=" + testfiles + "/argfile.autocounter", true, 3,
302 ArrayUtils.concatArrays(t1, t2) } };
306 public static boolean lookForSequenceName(String sequenceName)
308 AlignFrame[] afs = Desktop.getAlignFrames();
309 for (AlignFrame af : afs)
311 for (String name : af.getViewport().getAlignment().getSequenceNames())
313 if (sequenceName.equals(name))
322 public static void cleanupFiles(String[] filenames)
324 for (String filename : filenames)
326 File file = new File(filename);
334 private final String deleteDir = "test/deleteAfter";
337 groups = "Functional",
338 dataProvider = "allLinkedIdsData",
339 singleThreaded = true)
340 public void allLinkedIdsTest(String cmdLine, String[] filenames,
341 String[] nonfilenames)
343 String[] args = (cmdLine + " --gui").split("\\s+");
344 callJalviewMain(args);
345 Commands cmds = Jalview.getInstance().getCommands();
346 Assert.assertNotNull(cmds);
347 for (String filename : filenames)
349 Assert.assertTrue(new File(filename).exists(),
350 "File '" + filename + "' was not created");
352 cleanupFiles(filenames);
353 if (nonfilenames != null)
355 for (String nonfilename : nonfilenames)
357 File nonfile = new File(nonfilename);
358 Assert.assertFalse(nonfile.exists(),
359 "File " + nonfilename + " exists when it shouldn't!");
363 File deleteDirF = new File(deleteDir);
364 if (deleteDirF.exists())
370 @DataProvider(name = "allLinkedIdsData")
371 public Object[][] allLinkedIdsData()
373 return new Object[][] {
375 { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
377 { "test/jalview/bin/argparser/testfiles/test1.stk",
378 "test/jalview/bin/argparser/testfiles/test2.stk",
379 "test/jalview/bin/argparser/testfiles/test3.stk", },
381 { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
383 { "test/jalview/bin/argparser/testfiles/test1.png",
384 "test/jalview/bin/argparser/testfiles/test2.png",
385 "test/jalview/bin/argparser/testfiles/test3.png", },
387 { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
389 { "test/jalview/bin/argparser/testfiles/test1.stk",
390 "test/jalview/bin/argparser/testfiles/test2.stk",
391 "test/jalview/bin/argparser/testfiles/test3.stk", },
393 { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
394 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
395 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
396 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
397 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
398 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
399 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
400 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
401 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
402 { "--gui --open=test/jalview/bin/argparser/**/*.fa --all --output={dirname}/{basename}.stk --close",
404 { "test/jalview/bin/argparser/testfiles/test1.stk",
405 "test/jalview/bin/argparser/testfiles/test2.stk",
406 "test/jalview/bin/argparser/testfiles/test3.stk",
407 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
408 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
409 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
410 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
411 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
412 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
413 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
414 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
415 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
417 { "--gui --open=test/jalview/bin/argparser/**/*.fa --output=*/*.stk --close",
419 { "test/jalview/bin/argparser/testfiles/test1.stk",
420 "test/jalview/bin/argparser/testfiles/test2.stk",
421 "test/jalview/bin/argparser/testfiles/test3.stk",
422 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
423 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
424 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
425 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
426 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
427 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
428 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
429 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
430 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
432 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --all --output=*/*.stk --close",
434 { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
435 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
436 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
437 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
438 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
440 { "test/jalview/bin/argparser/testfiles/test1.stk",
441 "test/jalview/bin/argparser/testfiles/test2.stk",
442 "test/jalview/bin/argparser/testfiles/test3.stk",
443 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
444 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
445 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
446 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
447 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*/*.stk --close",
449 { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
450 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
451 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
453 { "test/jalview/bin/argparser/testfiles/test1.stk",
454 "test/jalview/bin/argparser/testfiles/test2.stk",
455 "test/jalview/bin/argparser/testfiles/test3.stk",
456 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
457 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
458 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
459 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
460 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
462 { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
463 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
464 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
466 { "test/jalview/bin/argparser/testfiles/test1.stk",
467 "test/jalview/bin/argparser/testfiles/test2.stk",
468 "test/jalview/bin/argparser/testfiles/test3.stk",
469 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
470 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
471 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
472 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
473 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
474 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
475 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
477 { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
478 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
479 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
481 { "test/jalview/bin/argparser/testfiles/test1.stk",
482 "test/jalview/bin/argparser/testfiles/test2.stk",
483 "test/jalview/bin/argparser/testfiles/test3.stk",
484 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
485 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
486 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
487 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
488 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
489 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
490 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output {dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.aln --close",
492 { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
493 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
494 "test/jalview/bin/argparser/testfiles/dir2/test1.aln",
495 "test/jalview/bin/argparser/testfiles/dir2/test2.aln",
496 "test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
498 { "test/jalview/bin/argparser/testfiles/test1.stk",
499 "test/jalview/bin/argparser/testfiles/test2.stk",
500 "test/jalview/bin/argparser/testfiles/test3.stk",
501 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
502 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
503 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
504 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
505 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
506 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
507 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
508 "test/jalview/bin/argparser/testfiles/test1.aln",
509 "test/jalview/bin/argparser/testfiles/test2.aln",
510 "test/jalview/bin/argparser/testfiles/test3.aln",
511 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
512 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
513 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
514 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
515 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
516 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
518 { "--headless --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output "
520 + "/{dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output="
522 + "/{dirname}/{basename}.aln --close --all --mkdirs",
525 + "/test/jalview/bin/argparser/testfiles/dir1/test1.stk",
527 + "/test/jalview/bin/argparser/testfiles/dir1/test2.stk",
529 + "/test/jalview/bin/argparser/testfiles/dir2/test1.aln",
531 + "/test/jalview/bin/argparser/testfiles/dir2/test2.aln",
533 + "/test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
535 { "test/jalview/bin/argparser/testfiles/test1.stk",
536 "test/jalview/bin/argparser/testfiles/test2.stk",
537 "test/jalview/bin/argparser/testfiles/test3.stk",
538 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
539 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
540 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
541 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
542 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
543 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
544 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
545 "test/jalview/bin/argparser/testfiles/test1.aln",
546 "test/jalview/bin/argparser/testfiles/test2.aln",
547 "test/jalview/bin/argparser/testfiles/test3.aln",
548 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
549 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
550 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
551 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
552 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
553 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln",
555 + "test/jalview/bin/argparser/testfiles/test1.stk",
557 + "test/jalview/bin/argparser/testfiles/test2.stk",
559 + "test/jalview/bin/argparser/testfiles/test3.stk",
561 + "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
563 + "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
565 + "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
567 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
569 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
571 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
573 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
575 + "test/jalview/bin/argparser/testfiles/test1.aln",
577 + "test/jalview/bin/argparser/testfiles/test2.aln",
579 + "test/jalview/bin/argparser/testfiles/test3.aln",
581 + "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
583 + "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
585 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
587 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
589 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
591 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },