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")
120 public void commandsOpenTest(String cmdLine, boolean cmdArgs,
121 int numFrames, String[] sequences)
125 String[] args = (cmdLine + " --gui").split("\\s+");
126 callJalviewMain(args);
127 Commands cmds = Jalview.getInstance().getCommands();
128 Assert.assertNotNull(cmds);
129 Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs,
130 "Commands were not provided in the args");
131 Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
132 "Overall command parse and operation is false");
134 Assert.assertEquals(Desktop.getDesktopAlignFrames().length, numFrames,
135 "Wrong number of AlignFrames");
137 if (sequences != null)
139 Set<String> openedSequenceNames = new HashSet<>();
140 AlignFrame[] afs = Desktop.getDesktopAlignFrames();
141 for (AlignFrame af : afs)
143 openedSequenceNames.addAll(
144 af.getViewport().getAlignment().getSequenceNames());
146 for (String sequence : sequences)
148 Assert.assertTrue(openedSequenceNames.contains(sequence),
149 "Sequence '" + sequence
150 + "' was not found in opened alignment files: "
151 + cmdLine + ".\nOpened sequence names are:\n"
152 + String.join("\n", openedSequenceNames));
157 lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
158 } catch (Exception x)
160 Assert.fail("Unexpected exception during commandsOpenTest", x);
170 { "Functional", "testTask3" },
171 dataProvider = "structureImageOutputFiles")
172 public void structureImageOutputTest(String cmdLine, String[] filenames)
175 cleanupFiles(filenames);
176 String[] args = (cmdLine + " --gui").split("\\s+");
179 callJalviewMain(args);
180 Commands cmds = Jalview.getInstance().getCommands();
181 Assert.assertNotNull(cmds);
182 File lastFile = null;
183 for (String filename : filenames)
185 File file = new File(filename);
186 Assert.assertTrue(file.exists(), "File '" + filename
187 + "' was not created by '" + cmdLine + "'");
188 Assert.assertTrue(file.isFile(), "File '" + filename
189 + "' is not a file from '" + cmdLine + "'");
190 Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
191 + "' has no content from '" + cmdLine + "'");
192 // make sure the successive output files get bigger!
193 if (lastFile != null) {
194 Assert.assertTrue(Files.size(file.toPath()) > Files.size(lastFile.toPath()));
195 System.out.println("this file: " + file + " +" + Files.size(file.toPath()) + " greater than "
196 + Files.size(lastFile.toPath()));
198 // remember it for next file
201 } catch (Exception x)
203 Assert.fail("Unexpected exception during structureImageOutputTest",
207 cleanupFiles(filenames);
212 @Test(groups = "Functional", dataProvider = "argfileOutputFiles")
213 public void argFilesGlobAndSubstitutionsTest(String cmdLine,
214 String[] filenames) throws IOException
216 cleanupFiles(filenames);
217 String[] args = (cmdLine + " --gui").split("\\s+");
220 callJalviewMain(args);
221 Commands cmds = Jalview.getInstance().getCommands();
222 Assert.assertNotNull(cmds);
223 File lastFile = null;
224 for (String filename : filenames)
226 File file = new File(filename);
227 Assert.assertTrue(file.exists(), "File '" + filename
228 + "' was not created by '" + cmdLine + "'");
229 Assert.assertTrue(file.isFile(), "File '" + filename
230 + "' is not a file from '" + cmdLine + "'");
231 Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
232 + "' has no content from '" + cmdLine + "'");
233 // make sure the successive output files get bigger!
234 if (lastFile != null) {
235 Assert.assertTrue(Files.size(file.toPath()) > Files
236 .size(lastFile.toPath()));
237 System.out.println("this file: "+file+" +"+Files.size(file.toPath()) + " greater than " +Files.size(lastFile.toPath()));
239 // remember it for next file
242 } catch (Exception x)
245 "Unexpected exception during argFilesGlobAndSubstitutions",
249 cleanupFiles(filenames);
254 @DataProvider(name = "structureImageOutputFiles")
255 public Object[][] structureImageOutputFiles()
257 return new Object[][] {
259 { "--gui --nonews --nosplash --open=./examples/test_fab41.result/sample.a2m "
260 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
261 + "--structureimage=" + testfiles + "/structureimage1.png "
262 + "--open=./examples/test_fab41.result/sample.a2m "
263 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
264 + "--structureimage=" + testfiles
265 + "/structureimage2.png --scale=1.5 "
266 + "--open=./examples/test_fab41.result/sample.a2m "
267 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
268 + "--structureimage=" + testfiles
269 + "/structureimage3.png --scale=2.0 ",
271 { testfiles + "/structureimage1.png",
272 testfiles + "/structureimage2.png",
273 testfiles + "/structureimage3.png" } },
274 { "--headless --noquit --open=./examples/test_fab41.result/sample.a2m "
275 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
276 + "--structureimage=" + testfiles + "/structureimage1.png "
277 + "--open=./examples/test_fab41.result/sample.a2m "
278 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
279 + "--structureimage=" + testfiles
280 + "/structureimage2.png --scale=1.5 "
281 + "--open=./examples/test_fab41.result/sample.a2m "
282 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
283 + "--structureimage=" + testfiles
284 + "/structureimage3.png --scale=2.0 ",
286 { testfiles + "/structureimage1.png",
287 testfiles + "/structureimage2.png",
288 testfiles + "/structureimage3.png" } },
289 { "--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",
292 testfiles+"/1gaq.png",testfiles+"/3w5v.png"
295 { "--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",
298 testfiles+"/1gaq.png",testfiles+"/3w5v.png"
309 @DataProvider(name = "argfileOutputFiles")
310 public Object[][] argfileOutputFiles()
312 return new Object[][] {
314 { "--gui --argfile=" + testfiles + "/**/*.txt", new String[]
315 { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
316 testfiles + "/dir3/subdir/test0.png" } },
317 { "--gui --argfile=" + testfiles + "/**/argfile.txt", new String[]
318 { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
319 { "--gui --argfile=" + testfiles + "/dir*/argfile.txt", new String[]
320 { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
321 { "--gui --initsubstitutions --append examples/uniref50.fa --image "
322 + testfiles + "/{basename}.png",
324 { testfiles + "/uniref50.png" } },
325 { "--gui --append examples/uniref50.fa --nosubstitutions --image "
326 + testfiles + "/{basename}.png",
328 { testfiles + "/{basename}.png" } }
334 @DataProvider(name = "cmdLines")
335 public Object[][] cmdLines()
337 String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN",
338 "FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" };
339 String[] t1 = new String[] { "TEST1" };
340 String[] t2 = new String[] { "TEST2" };
341 String[] t3 = new String[] { "TEST3" };
342 return new Object[][] {
345 { "--append=examples/uniref50.fa", true, 1, someUniref50Seqs },
346 { "--append examples/uniref50.fa", true, 1, someUniref50Seqs },
347 { "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs },
348 // NOTE we cannot use shell expansion in tests, so list all files!
349 { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
351 { "--append=[new]examples/uniref50*.fa", true, 2,
353 { "--open=examples/uniref50*.fa", true, 2, someUniref50Seqs },
354 { "examples/uniref50.fa", true, 1, someUniref50Seqs },
355 { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
356 ArrayUtils.concatArrays(someUniref50Seqs, t1) },
357 { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
358 { "--gui --argfile=" + testfiles + "/argfile0.txt", true, 1,
359 ArrayUtils.concatArrays(t1, t3) },
360 { "--gui --argfile=" + testfiles + "/argfile*.txt", true, 5,
361 ArrayUtils.concatArrays(t1, t2, t3) },
362 { "--gui --argfile=" + testfiles + "/argfile.autocounter", true, 3,
363 ArrayUtils.concatArrays(t1, t2) } };
367 public static boolean lookForSequenceName(String sequenceName)
369 AlignFrame[] afs = Desktop.getDesktopAlignFrames();
370 for (AlignFrame af : afs)
372 for (String name : af.getViewport().getAlignment().getSequenceNames())
374 if (sequenceName.equals(name))
383 public static void cleanupFiles(String[] filenames)
385 for (String filename : filenames)
387 File file = new File(filename);
395 private final String deleteDir = "test/deleteAfter";
398 groups = "Functional",
399 dataProvider = "allLinkedIdsData",
400 singleThreaded = true)
401 public void allLinkedIdsTest(String cmdLine, String[] filenames,
402 String[] nonfilenames)
404 String[] args = (cmdLine + " --gui").split("\\s+");
405 callJalviewMain(args);
406 Commands cmds = Jalview.getInstance().getCommands();
407 Assert.assertNotNull(cmds);
408 for (String filename : filenames)
410 Assert.assertTrue(new File(filename).exists(),
411 "File '" + filename + "' was not created");
413 cleanupFiles(filenames);
414 if (nonfilenames != null)
416 for (String nonfilename : nonfilenames)
418 File nonfile = new File(nonfilename);
419 Assert.assertFalse(nonfile.exists(),
420 "File " + nonfilename + " exists when it shouldn't!");
424 File deleteDirF = new File(deleteDir);
425 if (deleteDirF.exists())
431 @DataProvider(name = "allLinkedIdsData")
432 public Object[][] allLinkedIdsData()
434 return new Object[][] {
436 { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
438 { "test/jalview/bin/argparser/testfiles/test1.stk",
439 "test/jalview/bin/argparser/testfiles/test2.stk",
440 "test/jalview/bin/argparser/testfiles/test3.stk", },
442 { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
444 { "test/jalview/bin/argparser/testfiles/test1.png",
445 "test/jalview/bin/argparser/testfiles/test2.png",
446 "test/jalview/bin/argparser/testfiles/test3.png", },
448 { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
450 { "test/jalview/bin/argparser/testfiles/test1.stk",
451 "test/jalview/bin/argparser/testfiles/test2.stk",
452 "test/jalview/bin/argparser/testfiles/test3.stk", },
454 { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
455 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
456 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
457 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
458 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
459 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
460 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
461 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
462 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
463 { "--gui --open=test/jalview/bin/argparser/**/*.fa --all --output={dirname}/{basename}.stk --close",
465 { "test/jalview/bin/argparser/testfiles/test1.stk",
466 "test/jalview/bin/argparser/testfiles/test2.stk",
467 "test/jalview/bin/argparser/testfiles/test3.stk",
468 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
469 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
470 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
471 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
472 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
473 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
474 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
475 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
476 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
478 { "--gui --open=test/jalview/bin/argparser/**/*.fa --output=*/*.stk --close",
480 { "test/jalview/bin/argparser/testfiles/test1.stk",
481 "test/jalview/bin/argparser/testfiles/test2.stk",
482 "test/jalview/bin/argparser/testfiles/test3.stk",
483 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
484 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
485 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
486 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
487 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
488 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
489 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
490 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
491 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
493 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --all --output=*/*.stk --close",
495 { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
496 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
497 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
498 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
499 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
501 { "test/jalview/bin/argparser/testfiles/test1.stk",
502 "test/jalview/bin/argparser/testfiles/test2.stk",
503 "test/jalview/bin/argparser/testfiles/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 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*/*.stk --close",
510 { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
511 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
512 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
514 { "test/jalview/bin/argparser/testfiles/test1.stk",
515 "test/jalview/bin/argparser/testfiles/test2.stk",
516 "test/jalview/bin/argparser/testfiles/test3.stk",
517 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
518 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
519 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
520 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
521 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
523 { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
524 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
525 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
527 { "test/jalview/bin/argparser/testfiles/test1.stk",
528 "test/jalview/bin/argparser/testfiles/test2.stk",
529 "test/jalview/bin/argparser/testfiles/test3.stk",
530 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
531 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
532 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
533 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
534 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
535 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
536 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
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", },
542 { "test/jalview/bin/argparser/testfiles/test1.stk",
543 "test/jalview/bin/argparser/testfiles/test2.stk",
544 "test/jalview/bin/argparser/testfiles/test3.stk",
545 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
546 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
547 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
548 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
549 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
550 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
551 { "--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",
553 { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
554 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
555 "test/jalview/bin/argparser/testfiles/dir2/test1.aln",
556 "test/jalview/bin/argparser/testfiles/dir2/test2.aln",
557 "test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
559 { "test/jalview/bin/argparser/testfiles/test1.stk",
560 "test/jalview/bin/argparser/testfiles/test2.stk",
561 "test/jalview/bin/argparser/testfiles/test3.stk",
562 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
563 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
564 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
565 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
566 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
567 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
568 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
569 "test/jalview/bin/argparser/testfiles/test1.aln",
570 "test/jalview/bin/argparser/testfiles/test2.aln",
571 "test/jalview/bin/argparser/testfiles/test3.aln",
572 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
573 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
574 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
575 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
576 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
577 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
579 { "--headless --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output "
581 + "/{dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output="
583 + "/{dirname}/{basename}.aln --close --all --mkdirs",
586 + "/test/jalview/bin/argparser/testfiles/dir1/test1.stk",
588 + "/test/jalview/bin/argparser/testfiles/dir1/test2.stk",
590 + "/test/jalview/bin/argparser/testfiles/dir2/test1.aln",
592 + "/test/jalview/bin/argparser/testfiles/dir2/test2.aln",
594 + "/test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
596 { "test/jalview/bin/argparser/testfiles/test1.stk",
597 "test/jalview/bin/argparser/testfiles/test2.stk",
598 "test/jalview/bin/argparser/testfiles/test3.stk",
599 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
600 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
601 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
602 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
603 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
604 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
605 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
606 "test/jalview/bin/argparser/testfiles/test1.aln",
607 "test/jalview/bin/argparser/testfiles/test2.aln",
608 "test/jalview/bin/argparser/testfiles/test3.aln",
609 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
610 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
611 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
612 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
613 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
614 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln",
616 + "test/jalview/bin/argparser/testfiles/test1.stk",
618 + "test/jalview/bin/argparser/testfiles/test2.stk",
620 + "test/jalview/bin/argparser/testfiles/test3.stk",
622 + "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
624 + "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
626 + "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
628 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
630 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
632 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
634 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
636 + "test/jalview/bin/argparser/testfiles/test1.aln",
638 + "test/jalview/bin/argparser/testfiles/test2.aln",
640 + "test/jalview/bin/argparser/testfiles/test3.aln",
642 + "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
644 + "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
646 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
648 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
650 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
652 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },