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 verifyIncreasingSize(cmdLine, filenames);
184 } catch (Exception x)
186 Assert.fail("Unexpected exception during structureImageOutputTest",
190 cleanupFiles(filenames);
196 * given two command lines, compare the output files produced - they should exist and be equal in size
200 { "Functional", "testTask3" },
201 dataProvider = "compareHeadlessAndGUIOps",
202 singleThreaded = true)
203 public void headlessOrGuiImageOutputTest(String[] cmdLines,
204 String[] filenames) throws IOException
206 cleanupFiles(filenames);
209 for (String cmdLine : cmdLines)
211 CommandLineOperations.Worker runner = CommandLineOperations.getJalviewDesktopRunner(false, cmdLine, 1000);
212 long timeOut = 10000;
213 while (runner.isAlive() && timeOut>0)
219 verifyOrderedFileSet(cmdLines[0] + " vs " + cmdLines[1], filenames,
221 } catch (Exception x)
223 Assert.fail("Unexpected exception during structureImageOutputTest",
227 cleanupFiles(filenames);
231 @DataProvider(name = "compareHeadlessAndGUIOps")
232 public Object[][] compareHeadlessAndGUIOps()
234 return new Object[][] {
236 { new String[] { "--open examples/uniref50.fa "
237 + "--structure [seqid=FER1_SPIOL,tempfac=plddt,showssannotations,structureviewer=jmol]"
238 + "examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
239 + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json --image="
240 + testfiles + "test-al-pae-ss-gui.png --overwrite --gui --quit",
241 "--open examples/uniref50.fa "
242 + "--structure [seqid=FER1_SPIOL,tempfac=plddt,showssannotations,structureviewer=jmol]"
243 + "examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
244 + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json --image="
246 + "test-al-pae-ss-nogui.png --overwrite --nogui"
249 testfiles + "test-al-pae-ss-gui.png",
251 + "test-al-pae-ss-nogui.png",
255 private static void verifyIncreasingSize(String cmdLine, String[] filenames) throws Exception
257 verifyOrderedFileSet(cmdLine, filenames, true);
260 private static void verifyOrderedFileSet(String cmdLine, String[] filenames, boolean increasingSize) throws Exception
262 File lastFile = null;
263 for (String filename : filenames)
265 File file = new File(filename);
266 Assert.assertTrue(file.exists(), "File '" + filename
267 + "' was not created by '" + cmdLine + "'");
268 Assert.assertTrue(file.isFile(), "File '" + filename
269 + "' is not a file from '" + cmdLine + "'");
270 Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
271 + "' has no content from '" + cmdLine + "'");
272 // make sure the successive output files get bigger!
273 if (lastFile != null)
275 waitForLastWrite(file,25);
278 { Assert.assertTrue(Files.size(file.toPath()) > Files
279 .size(lastFile.toPath()),"Expected " + file.toPath()+ " to be larger than "+lastFile.toPath());
281 Assert.assertEquals(Files.size(file.toPath()), Files
282 .size(lastFile.toPath()), "New file "+file.toPath()+" (actual size) not same as last file's size "+lastFile.toString());
285 // remember it for next file
290 private static long waitForLastWrite(File file, int i) throws IOException
292 long lastSize,stableSize =Files.size(file.toPath());
293 // wait around until we are sure the file has been completely written.
295 lastSize = stableSize;
298 } catch (Exception x) {}
299 stableSize=Files.size(file.toPath());
300 } while (stableSize!=lastSize);
304 @Test(groups = "Functional", dataProvider = "argfileOutputFiles", singleThreaded = true)
306 public void argFilesGlobAndSubstitutionsTest(String cmdLine,
307 String[] filenames) throws IOException
309 cleanupFiles(filenames);
310 String[] args = (cmdLine + " --gui").split("\\s+");
313 callJalviewMain(args);
314 Commands cmds = Jalview.getInstance().getCommands();
315 Assert.assertNotNull(cmds);
316 File lastFile = null;
317 for (String filename : filenames)
319 File file = new File(filename);
320 Assert.assertTrue(file.exists(), "File '" + filename
321 + "' was not created by '" + cmdLine + "'");
322 Assert.assertTrue(file.isFile(), "File '" + filename
323 + "' is not a file from '" + cmdLine + "'");
324 Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
325 + "' has no content from '" + cmdLine + "'");
326 // make sure the successive output files get bigger!
327 if (lastFile != null) {
328 Assert.assertTrue(Files.size(file.toPath()) > Files
329 .size(lastFile.toPath()));
330 System.out.println("this file: "+file+" +"+Files.size(file.toPath()) + " greater than " +Files.size(lastFile.toPath()));
332 // remember it for next file
335 } catch (Exception x)
338 "Unexpected exception during argFilesGlobAndSubstitutions",
342 cleanupFiles(filenames);
347 @DataProvider(name = "structureImageOutputFiles")
348 public Object[][] structureImageOutputFiles()
350 return new Object[][] {
352 { "--gui --nonews --nosplash --open=./examples/test_fab41.result/sample.a2m "
353 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
354 + "--structureimage=" + testfiles + "/structureimage1.png "
355 + "--open=./examples/test_fab41.result/sample.a2m "
356 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
357 + "--structureimage=" + testfiles
358 + "/structureimage2.png --scale=1.5 "
359 + "--open=./examples/test_fab41.result/sample.a2m "
360 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
361 + "--structureimage=" + testfiles
362 + "/structureimage3.png --scale=2.0 ",
364 { testfiles + "/structureimage1.png",
365 testfiles + "/structureimage2.png",
366 testfiles + "/structureimage3.png" } },
367 { "--headless --noquit --open=./examples/test_fab41.result/sample.a2m "
368 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
369 + "--structureimage=" + testfiles + "/structureimage1.png "
370 + "--open=./examples/test_fab41.result/sample.a2m "
371 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
372 + "--structureimage=" + testfiles
373 + "/structureimage2.png --scale=1.5 "
374 + "--open=./examples/test_fab41.result/sample.a2m "
375 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
376 + "--structureimage=" + testfiles
377 + "/structureimage3.png --scale=2.0 ",
379 { testfiles + "/structureimage1.png",
380 testfiles + "/structureimage2.png",
381 testfiles + "/structureimage3.png" } },
382 { "--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",
385 testfiles+"/1gaq.png",testfiles+"/3w5v.png"
388 { "--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",
391 testfiles+"/1gaq.png",testfiles+"/3w5v.png"
402 @DataProvider(name = "argfileOutputFiles")
403 public Object[][] argfileOutputFiles()
405 return new Object[][] {
407 { "--gui --argfile=" + testfiles + "/**/*.txt", new String[]
408 { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
409 testfiles + "/dir3/subdir/test0.png" } },
410 { "--gui --argfile=" + testfiles + "/**/argfile.txt", new String[]
411 { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
412 { "--gui --argfile=" + testfiles + "/dir*/argfile.txt", new String[]
413 { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
414 { "--gui --initsubstitutions --append examples/uniref50.fa --image "
415 + testfiles + "/{basename}.png",
417 { testfiles + "/uniref50.png" } },
418 { "--gui --append examples/uniref50.fa --nosubstitutions --image "
419 + testfiles + "/{basename}.png",
421 { testfiles + "/{basename}.png" } }
427 @DataProvider(name = "cmdLines")
428 public Object[][] cmdLines()
430 String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN",
431 "FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" };
432 String[] t1 = new String[] { "TEST1" };
433 String[] t2 = new String[] { "TEST2" };
434 String[] t3 = new String[] { "TEST3" };
435 return new Object[][] {
438 { "--append=examples/uniref50.fa", true, 1, someUniref50Seqs },
439 { "--append examples/uniref50.fa", true, 1, someUniref50Seqs },
440 { "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs },
441 // NOTE we cannot use shell expansion in tests, so list all files!
442 { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
444 { "--append=[new]examples/uniref50*.fa", true, 2,
446 { "--open=examples/uniref50*.fa", true, 2, someUniref50Seqs },
447 { "examples/uniref50.fa", true, 1, someUniref50Seqs },
448 { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
449 ArrayUtils.concatArrays(someUniref50Seqs, t1) },
450 { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
451 { "--gui --argfile=" + testfiles + "/argfile0.txt", true, 1,
452 ArrayUtils.concatArrays(t1, t3) },
453 { "--gui --argfile=" + testfiles + "/argfile*.txt", true, 5,
454 ArrayUtils.concatArrays(t1, t2, t3) },
455 { "--gui --argfile=" + testfiles + "/argfile.autocounter", true, 3,
456 ArrayUtils.concatArrays(t1, t2) } };
460 public static boolean lookForSequenceName(String sequenceName)
462 AlignFrame[] afs = Desktop.getDesktopAlignFrames();
463 for (AlignFrame af : afs)
465 for (String name : af.getViewport().getAlignment().getSequenceNames())
467 if (sequenceName.equals(name))
476 public static void cleanupFiles(String[] filenames)
478 for (String filename : filenames)
480 File file = new File(filename);
488 private final String deleteDir = "test/deleteAfter";
491 groups = "Functional",
492 dataProvider = "allLinkedIdsData",
493 singleThreaded = true)
494 public void allLinkedIdsTest(String cmdLine, String[] filenames,
495 String[] nonfilenames)
497 String[] args = (cmdLine + " --gui").split("\\s+");
498 callJalviewMain(args);
499 Commands cmds = Jalview.getInstance().getCommands();
500 Assert.assertNotNull(cmds);
501 for (String filename : filenames)
503 Assert.assertTrue(new File(filename).exists(),
504 "File '" + filename + "' was not created");
506 cleanupFiles(filenames);
507 if (nonfilenames != null)
509 for (String nonfilename : nonfilenames)
511 File nonfile = new File(nonfilename);
512 Assert.assertFalse(nonfile.exists(),
513 "File " + nonfilename + " exists when it shouldn't!");
517 File deleteDirF = new File(deleteDir);
518 if (deleteDirF.exists())
524 @DataProvider(name = "allLinkedIdsData")
525 public Object[][] allLinkedIdsData()
527 return new Object[][] {
529 { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
531 { "test/jalview/bin/argparser/testfiles/test1.stk",
532 "test/jalview/bin/argparser/testfiles/test2.stk",
533 "test/jalview/bin/argparser/testfiles/test3.stk", },
535 { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
537 { "test/jalview/bin/argparser/testfiles/test1.png",
538 "test/jalview/bin/argparser/testfiles/test2.png",
539 "test/jalview/bin/argparser/testfiles/test3.png", },
541 { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
543 { "test/jalview/bin/argparser/testfiles/test1.stk",
544 "test/jalview/bin/argparser/testfiles/test2.stk",
545 "test/jalview/bin/argparser/testfiles/test3.stk", },
547 { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
548 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
549 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
550 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
551 "test/jalview/bin/argparser/testfiles/dir2/test3.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/**/*.fa --all --output={dirname}/{basename}.stk --close",
558 { "test/jalview/bin/argparser/testfiles/test1.stk",
559 "test/jalview/bin/argparser/testfiles/test2.stk",
560 "test/jalview/bin/argparser/testfiles/test3.stk",
561 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
562 "test/jalview/bin/argparser/testfiles/dir1/test2.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", },
571 { "--gui --open=test/jalview/bin/argparser/**/*.fa --output=*/*.stk --close",
573 { "test/jalview/bin/argparser/testfiles/test1.stk",
574 "test/jalview/bin/argparser/testfiles/test2.stk",
575 "test/jalview/bin/argparser/testfiles/test3.stk",
576 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
577 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
578 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
579 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
580 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
581 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
582 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
583 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
584 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
586 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --all --output=*/*.stk --close",
588 { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
589 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
590 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
591 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
592 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
594 { "test/jalview/bin/argparser/testfiles/test1.stk",
595 "test/jalview/bin/argparser/testfiles/test2.stk",
596 "test/jalview/bin/argparser/testfiles/test3.stk",
597 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
598 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
599 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
600 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
601 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*/*.stk --close",
603 { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
604 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
605 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
607 { "test/jalview/bin/argparser/testfiles/test1.stk",
608 "test/jalview/bin/argparser/testfiles/test2.stk",
609 "test/jalview/bin/argparser/testfiles/test3.stk",
610 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
611 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
612 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
613 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
614 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
616 { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
617 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
618 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
620 { "test/jalview/bin/argparser/testfiles/test1.stk",
621 "test/jalview/bin/argparser/testfiles/test2.stk",
622 "test/jalview/bin/argparser/testfiles/test3.stk",
623 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
624 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
625 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
626 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
627 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
628 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
629 { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
631 { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
632 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
633 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
635 { "test/jalview/bin/argparser/testfiles/test1.stk",
636 "test/jalview/bin/argparser/testfiles/test2.stk",
637 "test/jalview/bin/argparser/testfiles/test3.stk",
638 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
639 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
640 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
641 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
642 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
643 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
644 { "--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",
646 { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
647 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
648 "test/jalview/bin/argparser/testfiles/dir2/test1.aln",
649 "test/jalview/bin/argparser/testfiles/dir2/test2.aln",
650 "test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
652 { "test/jalview/bin/argparser/testfiles/test1.stk",
653 "test/jalview/bin/argparser/testfiles/test2.stk",
654 "test/jalview/bin/argparser/testfiles/test3.stk",
655 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
656 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
657 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
658 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
659 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
660 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
661 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
662 "test/jalview/bin/argparser/testfiles/test1.aln",
663 "test/jalview/bin/argparser/testfiles/test2.aln",
664 "test/jalview/bin/argparser/testfiles/test3.aln",
665 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
666 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
667 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
668 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
669 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
670 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
672 { "--headless --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output "
674 + "/{dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output="
676 + "/{dirname}/{basename}.aln --close --all --mkdirs",
679 + "/test/jalview/bin/argparser/testfiles/dir1/test1.stk",
681 + "/test/jalview/bin/argparser/testfiles/dir1/test2.stk",
683 + "/test/jalview/bin/argparser/testfiles/dir2/test1.aln",
685 + "/test/jalview/bin/argparser/testfiles/dir2/test2.aln",
687 + "/test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
689 { "test/jalview/bin/argparser/testfiles/test1.stk",
690 "test/jalview/bin/argparser/testfiles/test2.stk",
691 "test/jalview/bin/argparser/testfiles/test3.stk",
692 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
693 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
694 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
695 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
696 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
697 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
698 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
699 "test/jalview/bin/argparser/testfiles/test1.aln",
700 "test/jalview/bin/argparser/testfiles/test2.aln",
701 "test/jalview/bin/argparser/testfiles/test3.aln",
702 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
703 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
704 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
705 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
706 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
707 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln",
709 + "test/jalview/bin/argparser/testfiles/test1.stk",
711 + "test/jalview/bin/argparser/testfiles/test2.stk",
713 + "test/jalview/bin/argparser/testfiles/test3.stk",
715 + "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
717 + "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
719 + "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
721 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
723 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
725 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
727 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
729 + "test/jalview/bin/argparser/testfiles/test1.aln",
731 + "test/jalview/bin/argparser/testfiles/test2.aln",
733 + "test/jalview/bin/argparser/testfiles/test3.aln",
735 + "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
737 + "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
739 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
741 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
743 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
745 + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },