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)
196 waitForLastWrite(file,25);
198 if (Files.size(file.toPath()) > Files
199 .size(lastFile.toPath()))
200 Assert.assertTrue(Files.size(file.toPath()) > Files
201 .size(lastFile.toPath()));
203 // remember it for next file
206 } catch (Exception x)
208 Assert.fail("Unexpected exception during structureImageOutputTest",
212 cleanupFiles(filenames);
217 private static long waitForLastWrite(File file, int i) throws IOException
219 long lastSize,stableSize =Files.size(file.toPath());
220 // wait around until we are sure the file has been completely written.
222 lastSize = stableSize;
225 } catch (Exception x) {}
226 stableSize=Files.size(file.toPath());
227 } while (stableSize!=lastSize);
231 @Test(groups = "Functional", dataProvider = "argfileOutputFiles", singleThreaded = true)
233 public void argFilesGlobAndSubstitutionsTest(String cmdLine,
234 String[] filenames) throws IOException
236 cleanupFiles(filenames);
237 String[] args = (cmdLine + " --gui").split("\\s+");
240 callJalviewMain(args);
241 Commands cmds = Jalview.getInstance().getCommands();
242 Assert.assertNotNull(cmds);
243 File lastFile = null;
244 for (String filename : filenames)
246 File file = new File(filename);
247 Assert.assertTrue(file.exists(), "File '" + filename
248 + "' was not created by '" + cmdLine + "'");
249 Assert.assertTrue(file.isFile(), "File '" + filename
250 + "' is not a file from '" + cmdLine + "'");
251 Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
252 + "' has no content from '" + cmdLine + "'");
253 // make sure the successive output files get bigger!
254 if (lastFile != null) {
255 Assert.assertTrue(Files.size(file.toPath()) > Files
256 .size(lastFile.toPath()));
257 System.out.println("this file: "+file+" +"+Files.size(file.toPath()) + " greater than " +Files.size(lastFile.toPath()));
259 // remember it for next file
262 } catch (Exception x)
265 "Unexpected exception during argFilesGlobAndSubstitutions",
269 cleanupFiles(filenames);
274 @DataProvider(name = "structureImageOutputFiles")
275 public Object[][] structureImageOutputFiles()
277 return new Object[][] {
279 { "--gui --nonews --nosplash --open=./examples/test_fab41.result/sample.a2m "
280 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
281 + "--structureimage=" + testfiles + "/structureimage1.png "
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 + "/structureimage2.png --scale=1.5 "
286 + "--open=./examples/test_fab41.result/sample.a2m "
287 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
288 + "--structureimage=" + testfiles
289 + "/structureimage3.png --scale=2.0 ",
291 { testfiles + "/structureimage1.png",
292 testfiles + "/structureimage2.png",
293 testfiles + "/structureimage3.png" } },
294 { "--headless --noquit --open=./examples/test_fab41.result/sample.a2m "
295 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
296 + "--structureimage=" + testfiles + "/structureimage1.png "
297 + "--open=./examples/test_fab41.result/sample.a2m "
298 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
299 + "--structureimage=" + testfiles
300 + "/structureimage2.png --scale=1.5 "
301 + "--open=./examples/test_fab41.result/sample.a2m "
302 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
303 + "--structureimage=" + testfiles
304 + "/structureimage3.png --scale=2.0 ",
306 { testfiles + "/structureimage1.png",
307 testfiles + "/structureimage2.png",
308 testfiles + "/structureimage3.png" } },
309 { "--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",
312 testfiles+"/1gaq.png",testfiles+"/3w5v.png"
315 { "--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",
318 testfiles+"/1gaq.png",testfiles+"/3w5v.png"
329 @DataProvider(name = "argfileOutputFiles")
330 public Object[][] argfileOutputFiles()
332 return new Object[][] {
334 { "--gui --argfile=" + testfiles + "/**/*.txt", new String[]
335 { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
336 testfiles + "/dir3/subdir/test0.png" } },
337 { "--gui --argfile=" + testfiles + "/**/argfile.txt", new String[]
338 { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
339 { "--gui --argfile=" + testfiles + "/dir*/argfile.txt", new String[]
340 { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
341 { "--gui --initsubstitutions --append examples/uniref50.fa --image "
342 + testfiles + "/{basename}.png",
344 { testfiles + "/uniref50.png" } },
345 { "--gui --append examples/uniref50.fa --nosubstitutions --image "
346 + testfiles + "/{basename}.png",
348 { testfiles + "/{basename}.png" } }
354 @DataProvider(name = "cmdLines")
355 public Object[][] cmdLines()
357 String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN",
358 "FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" };
359 String[] t1 = new String[] { "TEST1" };
360 String[] t2 = new String[] { "TEST2" };
361 String[] t3 = new String[] { "TEST3" };
362 return new Object[][] {
365 { "--append=examples/uniref50.fa", true, 1, someUniref50Seqs },
366 { "--append examples/uniref50.fa", true, 1, someUniref50Seqs },
367 { "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs },
368 // NOTE we cannot use shell expansion in tests, so list all files!
369 { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
371 { "--append=[new]examples/uniref50*.fa", true, 2,
373 { "--open=examples/uniref50*.fa", true, 2, someUniref50Seqs },
374 { "examples/uniref50.fa", true, 1, someUniref50Seqs },
375 { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
376 ArrayUtils.concatArrays(someUniref50Seqs, t1) },
377 { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
378 { "--gui --argfile=" + testfiles + "/argfile0.txt", true, 1,
379 ArrayUtils.concatArrays(t1, t3) },
380 { "--gui --argfile=" + testfiles + "/argfile*.txt", true, 5,
381 ArrayUtils.concatArrays(t1, t2, t3) },
382 { "--gui --argfile=" + testfiles + "/argfile.autocounter", true, 3,
383 ArrayUtils.concatArrays(t1, t2) } };
387 public static boolean lookForSequenceName(String sequenceName)
389 AlignFrame[] afs = Desktop.getDesktopAlignFrames();
390 for (AlignFrame af : afs)
392 for (String name : af.getViewport().getAlignment().getSequenceNames())
394 if (sequenceName.equals(name))
403 public static void cleanupFiles(String[] filenames)
405 for (String filename : filenames)
407 File file = new File(filename);
415 private final String deleteDir = "test/deleteAfter";
418 groups = "Functional",
419 dataProvider = "allLinkedIdsData",
420 singleThreaded = true)
421 public void allLinkedIdsTest(String cmdLine, String[] filenames,
422 String[] nonfilenames)
424 String[] args = (cmdLine + " --gui").split("\\s+");
425 callJalviewMain(args);
426 Commands cmds = Jalview.getInstance().getCommands();
427 Assert.assertNotNull(cmds);
428 for (String filename : filenames)
430 Assert.assertTrue(new File(filename).exists(),
431 "File '" + filename + "' was not created");
433 cleanupFiles(filenames);
434 if (nonfilenames != null)
436 for (String nonfilename : nonfilenames)
438 File nonfile = new File(nonfilename);
439 Assert.assertFalse(nonfile.exists(),
440 "File " + nonfilename + " exists when it shouldn't!");
444 File deleteDirF = new File(deleteDir);
445 if (deleteDirF.exists())
451 @DataProvider(name = "allLinkedIdsData")
452 public Object[][] allLinkedIdsData()
454 return new Object[][] {
456 { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
458 { "test/jalview/bin/argparser/testfiles/test1.stk",
459 "test/jalview/bin/argparser/testfiles/test2.stk",
460 "test/jalview/bin/argparser/testfiles/test3.stk", },
462 { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
464 { "test/jalview/bin/argparser/testfiles/test1.png",
465 "test/jalview/bin/argparser/testfiles/test2.png",
466 "test/jalview/bin/argparser/testfiles/test3.png", },
468 { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
470 { "test/jalview/bin/argparser/testfiles/test1.stk",
471 "test/jalview/bin/argparser/testfiles/test2.stk",
472 "test/jalview/bin/argparser/testfiles/test3.stk", },
474 { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
475 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
476 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
477 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
478 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
479 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
480 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
481 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
482 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
483 { "--gui --open=test/jalview/bin/argparser/**/*.fa --all --output={dirname}/{basename}.stk --close",
485 { "test/jalview/bin/argparser/testfiles/test1.stk",
486 "test/jalview/bin/argparser/testfiles/test2.stk",
487 "test/jalview/bin/argparser/testfiles/test3.stk",
488 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
489 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
490 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
491 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
492 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
493 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
494 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
495 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
496 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
498 { "--gui --open=test/jalview/bin/argparser/**/*.fa --output=*/*.stk --close",
500 { "test/jalview/bin/argparser/testfiles/test1.stk",
501 "test/jalview/bin/argparser/testfiles/test2.stk",
502 "test/jalview/bin/argparser/testfiles/test3.stk",
503 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
504 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
505 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
506 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
507 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
508 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
509 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
510 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
511 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
513 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --all --output=*/*.stk --close",
515 { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
516 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
517 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
518 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
519 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
521 { "test/jalview/bin/argparser/testfiles/test1.stk",
522 "test/jalview/bin/argparser/testfiles/test2.stk",
523 "test/jalview/bin/argparser/testfiles/test3.stk",
524 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
525 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
526 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
527 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
528 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*/*.stk --close",
530 { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
531 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
532 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
534 { "test/jalview/bin/argparser/testfiles/test1.stk",
535 "test/jalview/bin/argparser/testfiles/test2.stk",
536 "test/jalview/bin/argparser/testfiles/test3.stk",
537 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
538 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
539 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
540 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
541 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
543 { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
544 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
545 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
547 { "test/jalview/bin/argparser/testfiles/test1.stk",
548 "test/jalview/bin/argparser/testfiles/test2.stk",
549 "test/jalview/bin/argparser/testfiles/test3.stk",
550 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
551 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
552 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
553 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
554 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
555 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
556 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
558 { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
559 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
560 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
562 { "test/jalview/bin/argparser/testfiles/test1.stk",
563 "test/jalview/bin/argparser/testfiles/test2.stk",
564 "test/jalview/bin/argparser/testfiles/test3.stk",
565 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
566 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
567 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
568 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
569 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
570 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
571 { "--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",
573 { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
574 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
575 "test/jalview/bin/argparser/testfiles/dir2/test1.aln",
576 "test/jalview/bin/argparser/testfiles/dir2/test2.aln",
577 "test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
579 { "test/jalview/bin/argparser/testfiles/test1.stk",
580 "test/jalview/bin/argparser/testfiles/test2.stk",
581 "test/jalview/bin/argparser/testfiles/test3.stk",
582 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
583 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
584 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
585 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
586 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
587 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
588 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
589 "test/jalview/bin/argparser/testfiles/test1.aln",
590 "test/jalview/bin/argparser/testfiles/test2.aln",
591 "test/jalview/bin/argparser/testfiles/test3.aln",
592 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
593 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
594 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
595 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
596 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
597 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
599 { "--headless --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output "
601 + "/{dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output="
603 + "/{dirname}/{basename}.aln --close --all --mkdirs",
606 + "/test/jalview/bin/argparser/testfiles/dir1/test1.stk",
608 + "/test/jalview/bin/argparser/testfiles/dir1/test2.stk",
610 + "/test/jalview/bin/argparser/testfiles/dir2/test1.aln",
612 + "/test/jalview/bin/argparser/testfiles/dir2/test2.aln",
614 + "/test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
616 { "test/jalview/bin/argparser/testfiles/test1.stk",
617 "test/jalview/bin/argparser/testfiles/test2.stk",
618 "test/jalview/bin/argparser/testfiles/test3.stk",
619 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
620 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
621 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
622 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
623 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
624 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
625 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
626 "test/jalview/bin/argparser/testfiles/test1.aln",
627 "test/jalview/bin/argparser/testfiles/test2.aln",
628 "test/jalview/bin/argparser/testfiles/test3.aln",
629 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
630 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
631 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
632 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
633 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
634 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln",
636 + "test/jalview/bin/argparser/testfiles/test1.stk",
638 + "test/jalview/bin/argparser/testfiles/test2.stk",
640 + "test/jalview/bin/argparser/testfiles/test3.stk",
642 + "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
644 + "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
646 + "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
648 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
650 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
652 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
654 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
656 + "test/jalview/bin/argparser/testfiles/test1.aln",
658 + "test/jalview/bin/argparser/testfiles/test2.aln",
660 + "test/jalview/bin/argparser/testfiles/test3.aln",
662 + "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
664 + "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
666 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
668 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
670 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
672 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },