2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
24 import java.io.IOException;
25 import java.lang.reflect.InvocationTargetException;
26 import java.nio.file.Files;
27 import java.util.Date;
28 import java.util.HashSet;
31 import javax.swing.SwingUtilities;
33 import org.testng.Assert;
34 import org.testng.annotations.AfterClass;
35 import org.testng.annotations.AfterMethod;
36 import org.testng.annotations.BeforeClass;
37 import org.testng.annotations.DataProvider;
38 import org.testng.annotations.Test;
40 import jalview.gui.AlignFrame;
41 import jalview.gui.Desktop;
42 import jalview.gui.JvOptionPane;
43 import jalview.util.ArrayUtils;
45 public class CommandsTest
47 private static final String testfiles = "test/jalview/bin/argparser/testfiles";
49 @BeforeClass(alwaysRun = true)
50 public static void setUpBeforeClass() throws Exception
52 Cache.loadProperties("test/jalview/gui/quitProps.jvprops");
53 Date oneHourFromNow = new Date(
54 System.currentTimeMillis() + 3600 * 1000);
55 Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
58 @AfterClass(alwaysRun = true)
59 public static void resetProps()
61 Cache.loadProperties("test/jalview/testProps.jvprops");
64 @BeforeClass(alwaysRun = true)
65 public void setUpJvOptionPane()
67 JvOptionPane.setInteractiveMode(false);
68 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
71 @AfterMethod(alwaysRun = true)
72 public void tearDown()
76 // occasionally we are blocked by Jmol redraws
77 SwingUtilities.invokeAndWait(new Runnable()
83 Desktop.closeDesktop();
86 } catch (Exception foo)
88 System.err.println("Failed during teardown with exception");
89 foo.printStackTrace();
94 public static void callJalviewMain(String[] args)
96 if (Jalview.getInstance() != null)
98 Jalview.getInstance().doMain(args);
106 /* --setprops is currently disabled so this test won't work
107 @Test(groups = "Functional")
108 public void setpropsTest()
110 final String MOSTLY_HARMLESS = "MOSTLY_HARMLESS";
111 String cmdLine = "--setprop=" + MOSTLY_HARMLESS + "=Earth";
112 String[] args = cmdLine.split("\\s+");
114 Assert.assertEquals(Cache.getDefault(MOSTLY_HARMLESS, "Magrathea"),
119 @Test(groups = { "Functional", "testTask3" }, dataProvider = "cmdLines", singleThreaded = true)
121 public void commandsOpenTest(String cmdLine, boolean cmdArgs,
122 int numFrames, String[] sequences)
126 String[] args = (cmdLine + " --gui").split("\\s+");
127 callJalviewMain(args);
128 Commands cmds = Jalview.getInstance().getCommands();
129 Assert.assertNotNull(cmds);
130 Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs,
131 "Commands were not provided in the args");
132 Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
133 "Overall command parse and operation is false");
135 Assert.assertEquals(Desktop.getDesktopAlignFrames().length, numFrames,
136 "Wrong number of AlignFrames");
138 if (sequences != null)
140 Set<String> openedSequenceNames = new HashSet<>();
141 AlignFrame[] afs = Desktop.getDesktopAlignFrames();
142 for (AlignFrame af : afs)
144 openedSequenceNames.addAll(
145 af.getViewport().getAlignment().getSequenceNames());
147 for (String sequence : sequences)
149 Assert.assertTrue(openedSequenceNames.contains(sequence),
150 "Sequence '" + sequence
151 + "' was not found in opened alignment files: "
152 + cmdLine + ".\nOpened sequence names are:\n"
153 + String.join("\n", openedSequenceNames));
158 lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
159 } catch (Exception x)
161 Assert.fail("Unexpected exception during commandsOpenTest", x);
171 { "Functional", "testTask3" },
172 dataProvider = "structureImageOutputFiles", singleThreaded = true)
173 public void structureImageOutputTest(String cmdLine, String[] filenames)
176 cleanupFiles(filenames);
177 String[] args = (cmdLine + " --gui").split("\\s+");
180 callJalviewMain(args);
181 Commands cmds = Jalview.getInstance().getCommands();
182 Assert.assertNotNull(cmds);
183 File lastFile = null;
184 for (String filename : filenames)
186 File file = new File(filename);
187 Assert.assertTrue(file.exists(), "File '" + filename
188 + "' was not created by '" + cmdLine + "'");
189 Assert.assertTrue(file.isFile(), "File '" + filename
190 + "' is not a file from '" + cmdLine + "'");
191 Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
192 + "' has no content from '" + cmdLine + "'");
193 // make sure the successive output files get bigger!
194 if (lastFile != null) {
195 Assert.assertTrue(Files.size(file.toPath()) > Files.size(lastFile.toPath()));
196 System.out.println("this file: " + file + " +" + Files.size(file.toPath()) + " greater than "
197 + Files.size(lastFile.toPath()));
199 // remember it for next file
202 } catch (Exception x)
204 Assert.fail("Unexpected exception during structureImageOutputTest",
208 cleanupFiles(filenames);
213 @Test(groups = "Functional", dataProvider = "argfileOutputFiles", singleThreaded = true)
214 public void argFilesGlobAndSubstitutionsTest(String cmdLine,
215 String[] filenames) throws IOException
217 cleanupFiles(filenames);
218 String[] args = (cmdLine + " --gui").split("\\s+");
221 callJalviewMain(args);
222 Commands cmds = Jalview.getInstance().getCommands();
223 Assert.assertNotNull(cmds);
224 File lastFile = null;
225 for (String filename : filenames)
227 File file = new File(filename);
228 Assert.assertTrue(file.exists(), "File '" + filename
229 + "' was not created by '" + cmdLine + "'");
230 Assert.assertTrue(file.isFile(), "File '" + filename
231 + "' is not a file from '" + cmdLine + "'");
232 Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
233 + "' has no content from '" + cmdLine + "'");
234 // make sure the successive output files get bigger!
235 if (lastFile != null) {
236 Assert.assertTrue(Files.size(file.toPath()) > Files
237 .size(lastFile.toPath()));
238 System.out.println("this file: "+file+" +"+Files.size(file.toPath()) + " greater than " +Files.size(lastFile.toPath()));
240 // remember it for next file
243 } catch (Exception x)
246 "Unexpected exception during argFilesGlobAndSubstitutions",
250 cleanupFiles(filenames);
255 @DataProvider(name = "structureImageOutputFiles")
256 public Object[][] structureImageOutputFiles()
258 return new Object[][] {
260 { "--gui --nonews --nosplash --open=./examples/test_fab41.result/sample.a2m "
261 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
262 + "--structureimage=" + testfiles + "/structureimage1.png "
263 + "--open=./examples/test_fab41.result/sample.a2m "
264 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
265 + "--structureimage=" + testfiles
266 + "/structureimage2.png --scale=1.5 "
267 + "--open=./examples/test_fab41.result/sample.a2m "
268 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
269 + "--structureimage=" + testfiles
270 + "/structureimage3.png --scale=2.0 ",
272 { testfiles + "/structureimage1.png",
273 testfiles + "/structureimage2.png",
274 testfiles + "/structureimage3.png" } },
275 { "--headless --noquit --open=./examples/test_fab41.result/sample.a2m "
276 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
277 + "--structureimage=" + testfiles + "/structureimage1.png "
278 + "--open=./examples/test_fab41.result/sample.a2m "
279 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
280 + "--structureimage=" + testfiles
281 + "/structureimage2.png --scale=1.5 "
282 + "--open=./examples/test_fab41.result/sample.a2m "
283 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
284 + "--structureimage=" + testfiles
285 + "/structureimage3.png --scale=2.0 ",
287 { testfiles + "/structureimage1.png",
288 testfiles + "/structureimage2.png",
289 testfiles + "/structureimage3.png" } },
290 { "--gui --nonews --nosplash --open examples/1gaq.txt --append ./examples/3W5V.pdb "+"--structure examples/1gaq.txt --seqid \"1GAQ|A\" "+"--structureimage "+testfiles+"/1gaq.png --structure examples/3W5V.pdb "+"--seqid \"3W5V|A\" --structureimage "+testfiles+"/3w5v.png --overwrite",
293 testfiles+"/1gaq.png",testfiles+"/3w5v.png"
296 { "--headless --noquit --open ./examples/1gaq.txt --append ./examples/3W5V.pdb "+"--structure examples/1gaq.txt --seqid \"1GAQ|A\" "+"--structureimage "+testfiles+"/1gaq.png --structure examples/3W5V.pdb "+"--seqid \"3W5V|A\" --structureimage "+testfiles+"/3w5v.png --overwrite",
299 testfiles+"/1gaq.png",testfiles+"/3w5v.png"
310 @DataProvider(name = "argfileOutputFiles")
311 public Object[][] argfileOutputFiles()
313 return new Object[][] {
315 { "--gui --argfile=" + testfiles + "/**/*.txt", new String[]
316 { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
317 testfiles + "/dir3/subdir/test0.png" } },
318 { "--gui --argfile=" + testfiles + "/**/argfile.txt", new String[]
319 { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
320 { "--gui --argfile=" + testfiles + "/dir*/argfile.txt", new String[]
321 { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
322 { "--gui --initsubstitutions --append examples/uniref50.fa --image "
323 + testfiles + "/{basename}.png",
325 { testfiles + "/uniref50.png" } },
326 { "--gui --append examples/uniref50.fa --nosubstitutions --image "
327 + testfiles + "/{basename}.png",
329 { testfiles + "/{basename}.png" } }
335 @DataProvider(name = "cmdLines")
336 public Object[][] cmdLines()
338 String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN",
339 "FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" };
340 String[] t1 = new String[] { "TEST1" };
341 String[] t2 = new String[] { "TEST2" };
342 String[] t3 = new String[] { "TEST3" };
343 return new Object[][] {
346 { "--append=examples/uniref50.fa", true, 1, someUniref50Seqs },
347 { "--append examples/uniref50.fa", true, 1, someUniref50Seqs },
348 { "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs },
349 // NOTE we cannot use shell expansion in tests, so list all files!
350 { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
352 { "--append=[new]examples/uniref50*.fa", true, 2,
354 { "--open=examples/uniref50*.fa", true, 2, someUniref50Seqs },
355 { "examples/uniref50.fa", true, 1, someUniref50Seqs },
356 { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
357 ArrayUtils.concatArrays(someUniref50Seqs, t1) },
358 { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
359 { "--gui --argfile=" + testfiles + "/argfile0.txt", true, 1,
360 ArrayUtils.concatArrays(t1, t3) },
361 { "--gui --argfile=" + testfiles + "/argfile*.txt", true, 5,
362 ArrayUtils.concatArrays(t1, t2, t3) },
363 { "--gui --argfile=" + testfiles + "/argfile.autocounter", true, 3,
364 ArrayUtils.concatArrays(t1, t2) } };
368 public static boolean lookForSequenceName(String sequenceName)
370 AlignFrame[] afs = Desktop.getDesktopAlignFrames();
371 for (AlignFrame af : afs)
373 for (String name : af.getViewport().getAlignment().getSequenceNames())
375 if (sequenceName.equals(name))
384 public static void cleanupFiles(String[] filenames)
386 for (String filename : filenames)
388 File file = new File(filename);
396 private final String deleteDir = "test/deleteAfter";
399 groups = "Functional",
400 dataProvider = "allLinkedIdsData",
401 singleThreaded = true)
402 public void allLinkedIdsTest(String cmdLine, String[] filenames,
403 String[] nonfilenames)
405 String[] args = (cmdLine + " --gui").split("\\s+");
406 callJalviewMain(args);
407 Commands cmds = Jalview.getInstance().getCommands();
408 Assert.assertNotNull(cmds);
409 for (String filename : filenames)
411 Assert.assertTrue(new File(filename).exists(),
412 "File '" + filename + "' was not created");
414 cleanupFiles(filenames);
415 if (nonfilenames != null)
417 for (String nonfilename : nonfilenames)
419 File nonfile = new File(nonfilename);
420 Assert.assertFalse(nonfile.exists(),
421 "File " + nonfilename + " exists when it shouldn't!");
425 File deleteDirF = new File(deleteDir);
426 if (deleteDirF.exists())
432 @DataProvider(name = "allLinkedIdsData")
433 public Object[][] allLinkedIdsData()
435 return new Object[][] {
437 { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
439 { "test/jalview/bin/argparser/testfiles/test1.stk",
440 "test/jalview/bin/argparser/testfiles/test2.stk",
441 "test/jalview/bin/argparser/testfiles/test3.stk", },
443 { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
445 { "test/jalview/bin/argparser/testfiles/test1.png",
446 "test/jalview/bin/argparser/testfiles/test2.png",
447 "test/jalview/bin/argparser/testfiles/test3.png", },
449 { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
451 { "test/jalview/bin/argparser/testfiles/test1.stk",
452 "test/jalview/bin/argparser/testfiles/test2.stk",
453 "test/jalview/bin/argparser/testfiles/test3.stk", },
455 { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
456 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
457 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
458 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
459 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
460 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
461 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
462 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
463 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
464 { "--gui --open=test/jalview/bin/argparser/**/*.fa --all --output={dirname}/{basename}.stk --close",
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/dir2/test1.stk",
472 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
473 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
474 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
475 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
476 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
477 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
479 { "--gui --open=test/jalview/bin/argparser/**/*.fa --output=*/*.stk --close",
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/dir2/test1.stk",
487 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
488 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
489 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
490 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
491 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
492 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
494 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --all --output=*/*.stk --close",
496 { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
497 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
498 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
499 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
500 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
502 { "test/jalview/bin/argparser/testfiles/test1.stk",
503 "test/jalview/bin/argparser/testfiles/test2.stk",
504 "test/jalview/bin/argparser/testfiles/test3.stk",
505 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
506 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
507 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
508 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
509 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*/*.stk --close",
511 { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
512 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
513 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
515 { "test/jalview/bin/argparser/testfiles/test1.stk",
516 "test/jalview/bin/argparser/testfiles/test2.stk",
517 "test/jalview/bin/argparser/testfiles/test3.stk",
518 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
519 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
520 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
521 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
522 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
524 { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
525 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
526 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
528 { "test/jalview/bin/argparser/testfiles/test1.stk",
529 "test/jalview/bin/argparser/testfiles/test2.stk",
530 "test/jalview/bin/argparser/testfiles/test3.stk",
531 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
532 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
533 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
534 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
535 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
536 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
537 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
539 { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
540 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
541 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
543 { "test/jalview/bin/argparser/testfiles/test1.stk",
544 "test/jalview/bin/argparser/testfiles/test2.stk",
545 "test/jalview/bin/argparser/testfiles/test3.stk",
546 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
547 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
548 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
549 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
550 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
551 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
552 { "--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",
554 { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
555 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
556 "test/jalview/bin/argparser/testfiles/dir2/test1.aln",
557 "test/jalview/bin/argparser/testfiles/dir2/test2.aln",
558 "test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
560 { "test/jalview/bin/argparser/testfiles/test1.stk",
561 "test/jalview/bin/argparser/testfiles/test2.stk",
562 "test/jalview/bin/argparser/testfiles/test3.stk",
563 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
564 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
565 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
566 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
567 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
568 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
569 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
570 "test/jalview/bin/argparser/testfiles/test1.aln",
571 "test/jalview/bin/argparser/testfiles/test2.aln",
572 "test/jalview/bin/argparser/testfiles/test3.aln",
573 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
574 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
575 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
576 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
577 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
578 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
580 { "--headless --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output "
582 + "/{dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output="
584 + "/{dirname}/{basename}.aln --close --all --mkdirs",
587 + "/test/jalview/bin/argparser/testfiles/dir1/test1.stk",
589 + "/test/jalview/bin/argparser/testfiles/dir1/test2.stk",
591 + "/test/jalview/bin/argparser/testfiles/dir2/test1.aln",
593 + "/test/jalview/bin/argparser/testfiles/dir2/test2.aln",
595 + "/test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
597 { "test/jalview/bin/argparser/testfiles/test1.stk",
598 "test/jalview/bin/argparser/testfiles/test2.stk",
599 "test/jalview/bin/argparser/testfiles/test3.stk",
600 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
601 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
602 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
603 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
604 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
605 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
606 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
607 "test/jalview/bin/argparser/testfiles/test1.aln",
608 "test/jalview/bin/argparser/testfiles/test2.aln",
609 "test/jalview/bin/argparser/testfiles/test3.aln",
610 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
611 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
612 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
613 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
614 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
615 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln",
617 + "test/jalview/bin/argparser/testfiles/test1.stk",
619 + "test/jalview/bin/argparser/testfiles/test2.stk",
621 + "test/jalview/bin/argparser/testfiles/test3.stk",
623 + "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
625 + "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
627 + "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
629 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
631 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
633 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
635 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
637 + "test/jalview/bin/argparser/testfiles/test1.aln",
639 + "test/jalview/bin/argparser/testfiles/test2.aln",
641 + "test/jalview/bin/argparser/testfiles/test3.aln",
643 + "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
645 + "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
647 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
649 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
651 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
653 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },