test/jalview/bin/CommandsTest.java

   1 package jalview.bin;
   2
   3 import java.io.File;
   4 import java.io.IOException;
   5 import java.nio.file.Files;
   6 import java.util.Date;
   7 import java.util.HashSet;
   8 import java.util.Set;
   9
  10 import org.testng.Assert;
  11 import org.testng.annotations.AfterClass;
  12 import org.testng.annotations.AfterMethod;
  13 import org.testng.annotations.BeforeClass;
  14 import org.testng.annotations.DataProvider;
  15 import org.testng.annotations.Test;
  16
  17 import jalview.gui.AlignFrame;
  18 import jalview.gui.Desktop;
  19 import jalview.gui.JvOptionPane;
  20 import jalview.util.ArrayUtils;
  21
  22 public class CommandsTest
  23 {
  24   private static final String testfiles = "test/jalview/bin/argparser/testfiles";
  25
  26   @BeforeClass(alwaysRun = true)
  27   public static void setUpBeforeClass() throws Exception
  28   {
  29     Cache.loadProperties("test/jalview/gui/quitProps.jvprops");
  30     Date oneHourFromNow = new Date(
  31             System.currentTimeMillis() + 3600 * 1000);
  32     Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
  33   }
  34
  35   @AfterClass(alwaysRun = true)
  36   public static void resetProps()
  37   {
  38     Cache.loadProperties("test/jalview/testProps.jvprops");
  39   }
  40
  41   @BeforeClass(alwaysRun = true)
  42   public void setUpJvOptionPane()
  43   {
  44     JvOptionPane.setInteractiveMode(false);
  45     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  46   }
  47
  48   @AfterMethod(alwaysRun = true)
  49   public void tearDown()
  50   {
  51     Desktop.closeDesktop();
  52   }
  53
  54   public static void callJalviewMain(String[] args)
  55   {
  56     if (Jalview.getInstance() != null)
  57     {
  58       Jalview.getInstance().doMain(args);
  59     }
  60     else
  61     {
  62       Jalview.main(args);
  63     }
  64   }
  65
  66   /* --setprops is currently disabled so this test won't work
  67   @Test(groups = "Functional")
  68   public void setpropsTest()
  69   {
  70     final String MOSTLY_HARMLESS = "MOSTLY_HARMLESS";
  71     String cmdLine = "--setprop=" + MOSTLY_HARMLESS + "=Earth";
  72     String[] args = cmdLine.split("\\s+");
  73     Jalview.main(args);
  74     Assert.assertEquals(Cache.getDefault(MOSTLY_HARMLESS, "Magrathea"),
  75             "Earth");
  76   }
  77   */
  78
  79   @Test(groups = "Functional", dataProvider = "cmdLines")
  80   public void commandsOpenTest(String cmdLine, boolean cmdArgs,
  81           int numFrames, String[] sequences)
  82   {
  83     try
  84     {
  85       String[] args = (cmdLine + " --gui").split("\\s+");
  86       callJalviewMain(args);
  87       Commands cmds = Jalview.getInstance().getCommands();
  88       Assert.assertNotNull(cmds);
  89       Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs,
  90               "Commands were not provided in the args");
  91       Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
  92               "Overall command parse and operation is false");
  93
  94       Assert.assertEquals(Desktop.getAlignFrames().length, numFrames,
  95               "Wrong number of AlignFrames");
  96
  97       if (sequences != null)
  98       {
  99         Set<String> openedSequenceNames = new HashSet<>();
 100         AlignFrame[] afs = Desktop.getAlignFrames();
 101         for (AlignFrame af : afs)
 102         {
 103           openedSequenceNames.addAll(
 104                   af.getViewport().getAlignment().getSequenceNames());
 105         }
 106         for (String sequence : sequences)
 107         {
 108           Assert.assertTrue(openedSequenceNames.contains(sequence),
 109                   "Sequence '" + sequence
 110                           + "' was not found in opened alignment files: "
 111                           + cmdLine + ".\nOpened sequence names are:\n"
 112                           + String.join("\n", openedSequenceNames));
 113         }
 114       }
 115
 116       Assert.assertFalse(
 117               lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
 118     } catch (Exception x)
 119     {
 120       Assert.fail("Unexpected exception during commandsOpenTest", x);
 121     } finally
 122     {
 123       tearDown();
 124
 125     }
 126   }
 127
 128   @Test(
 129     groups =
 130     { "Functional", "testTask1" },
 131     dataProvider = "structureImageOutputFiles")
 132   public void structureImageOutputTest(String cmdLine, String[] filenames)
 133           throws IOException
 134   {
 135     cleanupFiles(filenames);
 136     String[] args = (cmdLine + " --gui").split("\\s+");
 137     try
 138     {
 139       callJalviewMain(args);
 140       Commands cmds = Jalview.getInstance().getCommands();
 141       Assert.assertNotNull(cmds);
 142       File lastFile = null;
 143       for (String filename : filenames)
 144       {
 145         File file = new File(filename);
 146         Assert.assertTrue(file.exists(), "File '" + filename
 147                 + "' was not created by '" + cmdLine + "'");
 148         Assert.assertTrue(file.isFile(), "File '" + filename
 149                 + "' is not a file from '" + cmdLine + "'");
 150         Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
 151                 + "' has no content from '" + cmdLine + "'");
 152         // make sure the successive output files get bigger!
 153         if (lastFile != null)
 154           Assert.assertTrue(Files.size(file.toPath()) > Files
 155                   .size(lastFile.toPath()));
 156       }
 157     } catch (Exception x)
 158     {
 159       Assert.fail("Unexpected exception during structureImageOutputTest",
 160               x);
 161     } finally
 162     {
 163       cleanupFiles(filenames);
 164       tearDown();
 165     }
 166   }
 167
 168   @Test(groups = "Functional", dataProvider = "argfileOutputFiles")
 169   public void argFilesGlobAndSubstitutionsTest(String cmdLine,
 170           String[] filenames) throws IOException
 171   {
 172     cleanupFiles(filenames);
 173     String[] args = (cmdLine + " --gui").split("\\s+");
 174     try
 175     {
 176       callJalviewMain(args);
 177       Commands cmds = Jalview.getInstance().getCommands();
 178       Assert.assertNotNull(cmds);
 179       File lastFile = null;
 180       for (String filename : filenames)
 181       {
 182         File file = new File(filename);
 183         Assert.assertTrue(file.exists(), "File '" + filename
 184                 + "' was not created by '" + cmdLine + "'");
 185         Assert.assertTrue(file.isFile(), "File '" + filename
 186                 + "' is not a file from '" + cmdLine + "'");
 187         Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
 188                 + "' has no content from '" + cmdLine + "'");
 189         // make sure the successive output files get bigger!
 190         if (lastFile != null)
 191           Assert.assertTrue(Files.size(file.toPath()) > Files
 192                   .size(lastFile.toPath()));
 193       }
 194     } catch (Exception x)
 195     {
 196       Assert.fail(
 197               "Unexpected exception during argFilesGlobAndSubstitutions",
 198               x);
 199     } finally
 200     {
 201       cleanupFiles(filenames);
 202       tearDown();
 203     }
 204   }
 205
 206   @DataProvider(name = "structureImageOutputFiles")
 207   public Object[][] structureImageOutputFiles()
 208   {
 209     return new Object[][] {
 210         //
 211         { "--gui --nonews --nosplash --open=./examples/test_fab41.result/sample.a2m "
 212                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 213                 + "--structureimage=" + testfiles + "/structureimage1.png "
 214                 + "--open=./examples/test_fab41.result/sample.a2m "
 215                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 216                 + "--structureimage=" + testfiles
 217                 + "/structureimage2.png --scale=1.5 "
 218                 + "--open=./examples/test_fab41.result/sample.a2m "
 219                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 220                 + "--structureimage=" + testfiles
 221                 + "/structureimage3.png --scale=2.0 ",
 222             new String[]
 223             { testfiles + "/structureimage1.png",
 224                 testfiles + "/structureimage2.png",
 225                 testfiles + "/structureimage3.png" } },
 226         { "--headless --noquit --open=./examples/test_fab41.result/sample.a2m "
 227                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 228                 + "--structureimage=" + testfiles + "/structureimage1.png "
 229                 + "--open=./examples/test_fab41.result/sample.a2m "
 230                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 231                 + "--structureimage=" + testfiles
 232                 + "/structureimage2.png --scale=1.5 "
 233                 + "--open=./examples/test_fab41.result/sample.a2m "
 234                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 235                 + "--structureimage=" + testfiles
 236                 + "/structureimage3.png --scale=2.0 ",
 237             new String[]
 238             { testfiles + "/structureimage1.png",
 239                 testfiles + "/structureimage2.png",
 240                 testfiles + "/structureimage3.png" } },
 241         /*
 242                 */
 243         //
 244     };
 245
 246   }
 247
 248   @DataProvider(name = "argfileOutputFiles")
 249   public Object[][] argfileOutputFiles()
 250   {
 251     return new Object[][] {
 252         //
 253         { "--gui --argfile=" + testfiles + "/**/*.txt", new String[]
 254         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
 255             testfiles + "/dir3/subdir/test0.png" } },
 256         { "--gui --argfile=" + testfiles + "/**/argfile.txt", new String[]
 257         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
 258         { "--gui --argfile=" + testfiles + "/dir*/argfile.txt", new String[]
 259         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
 260         { "--gui --initsubstitutions --append examples/uniref50.fa --image "
 261                 + testfiles + "/{basename}.png",
 262             new String[]
 263             { testfiles + "/uniref50.png" } },
 264         { "--gui --append examples/uniref50.fa --nosubstitutions --image "
 265                 + testfiles + "/{basename}.png",
 266             new String[]
 267             { testfiles + "/{basename}.png" } }
 268         //
 269     };
 270
 271   }
 272
 273   @DataProvider(name = "cmdLines")
 274   public Object[][] cmdLines()
 275   {
 276     String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN",
 277         "FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" };
 278     String[] t1 = new String[] { "TEST1" };
 279     String[] t2 = new String[] { "TEST2" };
 280     String[] t3 = new String[] { "TEST3" };
 281     return new Object[][] {
 282         /*
 283         */
 284         { "--append=examples/uniref50.fa", true, 1, someUniref50Seqs },
 285         { "--append examples/uniref50.fa", true, 1, someUniref50Seqs },
 286         { "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs },
 287         // NOTE we cannot use shell expansion in tests, so list all files!
 288         { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
 289             someUniref50Seqs },
 290         { "--append=[new]examples/uniref50*.fa", true, 2,
 291             someUniref50Seqs },
 292         { "--open=examples/uniref50*.fa", true, 2, someUniref50Seqs },
 293         { "examples/uniref50.fa", true, 1, someUniref50Seqs },
 294         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
 295             ArrayUtils.concatArrays(someUniref50Seqs, t1) },
 296         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
 297         { "--gui --argfile=" + testfiles + "/argfile0.txt", true, 1,
 298             ArrayUtils.concatArrays(t1, t3) },
 299         { "--gui --argfile=" + testfiles + "/argfile*.txt", true, 5,
 300             ArrayUtils.concatArrays(t1, t2, t3) },
 301         { "--gui --argfile=" + testfiles + "/argfile.autocounter", true, 3,
 302             ArrayUtils.concatArrays(t1, t2) } };
 303
 304   }
 305
 306   public static boolean lookForSequenceName(String sequenceName)
 307   {
 308     AlignFrame[] afs = Desktop.getAlignFrames();
 309     for (AlignFrame af : afs)
 310     {
 311       for (String name : af.getViewport().getAlignment().getSequenceNames())
 312       {
 313         if (sequenceName.equals(name))
 314         {
 315           return true;
 316         }
 317       }
 318     }
 319     return false;
 320   }
 321
 322   public static void cleanupFiles(String[] filenames)
 323   {
 324     for (String filename : filenames)
 325     {
 326       File file = new File(filename);
 327       if (file.exists())
 328       {
 329         file.delete();
 330       }
 331     }
 332   }
 333
 334   private final String deleteDir = "test/deleteAfter";
 335
 336   @Test(
 337     groups = "Functional",
 338     dataProvider = "allLinkedIdsData",
 339     singleThreaded = true)
 340   public void allLinkedIdsTest(String cmdLine, String[] filenames,
 341           String[] nonfilenames)
 342   {
 343     String[] args = (cmdLine + " --gui").split("\\s+");
 344     callJalviewMain(args);
 345     Commands cmds = Jalview.getInstance().getCommands();
 346     Assert.assertNotNull(cmds);
 347     for (String filename : filenames)
 348     {
 349       Assert.assertTrue(new File(filename).exists(),
 350               "File '" + filename + "' was not created");
 351     }
 352     cleanupFiles(filenames);
 353     if (nonfilenames != null)
 354     {
 355       for (String nonfilename : nonfilenames)
 356       {
 357         File nonfile = new File(nonfilename);
 358         Assert.assertFalse(nonfile.exists(),
 359                 "File " + nonfilename + " exists when it shouldn't!");
 360       }
 361     }
 362
 363     File deleteDirF = new File(deleteDir);
 364     if (deleteDirF.exists())
 365     {
 366       deleteDirF.delete();
 367     }
 368   }
 369
 370   @DataProvider(name = "allLinkedIdsData")
 371   public Object[][] allLinkedIdsData()
 372   {
 373     return new Object[][] {
 374         //
 375         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
 376             new String[]
 377             { "test/jalview/bin/argparser/testfiles/test1.stk",
 378                 "test/jalview/bin/argparser/testfiles/test2.stk",
 379                 "test/jalview/bin/argparser/testfiles/test3.stk", },
 380             null },
 381         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
 382             new String[]
 383             { "test/jalview/bin/argparser/testfiles/test1.png",
 384                 "test/jalview/bin/argparser/testfiles/test2.png",
 385                 "test/jalview/bin/argparser/testfiles/test3.png", },
 386             null },
 387         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
 388             new String[]
 389             { "test/jalview/bin/argparser/testfiles/test1.stk",
 390                 "test/jalview/bin/argparser/testfiles/test2.stk",
 391                 "test/jalview/bin/argparser/testfiles/test3.stk", },
 392             new String[]
 393             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 394                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 395                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 396                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 397                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 398                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 399                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 400                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 401                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 402         { "--gui --open=test/jalview/bin/argparser/**/*.fa --all --output={dirname}/{basename}.stk --close",
 403             new String[]
 404             { "test/jalview/bin/argparser/testfiles/test1.stk",
 405                 "test/jalview/bin/argparser/testfiles/test2.stk",
 406                 "test/jalview/bin/argparser/testfiles/test3.stk",
 407                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 408                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 409                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 410                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 411                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 412                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 413                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 414                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 415                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
 416             null },
 417         { "--gui --open=test/jalview/bin/argparser/**/*.fa --output=*/*.stk --close",
 418             new String[]
 419             { "test/jalview/bin/argparser/testfiles/test1.stk",
 420                 "test/jalview/bin/argparser/testfiles/test2.stk",
 421                 "test/jalview/bin/argparser/testfiles/test3.stk",
 422                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 423                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 424                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 425                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 426                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 427                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 428                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 429                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 430                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
 431             null },
 432         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --all --output=*/*.stk --close",
 433             new String[]
 434             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 435                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 436                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 437                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 438                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 439             new String[]
 440             { "test/jalview/bin/argparser/testfiles/test1.stk",
 441                 "test/jalview/bin/argparser/testfiles/test2.stk",
 442                 "test/jalview/bin/argparser/testfiles/test3.stk",
 443                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 444                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 445                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 446                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 447         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*/*.stk --close",
 448             new String[]
 449             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 450                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 451                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 452             new String[]
 453             { "test/jalview/bin/argparser/testfiles/test1.stk",
 454                 "test/jalview/bin/argparser/testfiles/test2.stk",
 455                 "test/jalview/bin/argparser/testfiles/test3.stk",
 456                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 457                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 458                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 459                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 460         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
 461             new String[]
 462             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 463                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 464                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 465             new String[]
 466             { "test/jalview/bin/argparser/testfiles/test1.stk",
 467                 "test/jalview/bin/argparser/testfiles/test2.stk",
 468                 "test/jalview/bin/argparser/testfiles/test3.stk",
 469                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 470                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 471                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 472                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 473                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 474                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 475         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
 476             new String[]
 477             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 478                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 479                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 480             new String[]
 481             { "test/jalview/bin/argparser/testfiles/test1.stk",
 482                 "test/jalview/bin/argparser/testfiles/test2.stk",
 483                 "test/jalview/bin/argparser/testfiles/test3.stk",
 484                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 485                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 486                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 487                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 488                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 489                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 490         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output {dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.aln --close",
 491             new String[]
 492             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 493                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 494                 "test/jalview/bin/argparser/testfiles/dir2/test1.aln",
 495                 "test/jalview/bin/argparser/testfiles/dir2/test2.aln",
 496                 "test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
 497             new String[]
 498             { "test/jalview/bin/argparser/testfiles/test1.stk",
 499                 "test/jalview/bin/argparser/testfiles/test2.stk",
 500                 "test/jalview/bin/argparser/testfiles/test3.stk",
 501                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 502                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 503                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 504                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 505                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 506                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 507                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
 508                 "test/jalview/bin/argparser/testfiles/test1.aln",
 509                 "test/jalview/bin/argparser/testfiles/test2.aln",
 510                 "test/jalview/bin/argparser/testfiles/test3.aln",
 511                 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 512                 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 513                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 514                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 515                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 516                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
 517         // --mkdirs
 518         { "--headless --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output "
 519                 + deleteDir
 520                 + "/{dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output="
 521                 + deleteDir
 522                 + "/{dirname}/{basename}.aln --close --all --mkdirs",
 523             new String[]
 524             { deleteDir
 525                     + "/test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 526                 deleteDir
 527                         + "/test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 528                 deleteDir
 529                         + "/test/jalview/bin/argparser/testfiles/dir2/test1.aln",
 530                 deleteDir
 531                         + "/test/jalview/bin/argparser/testfiles/dir2/test2.aln",
 532                 deleteDir
 533                         + "/test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
 534             new String[]
 535             { "test/jalview/bin/argparser/testfiles/test1.stk",
 536                 "test/jalview/bin/argparser/testfiles/test2.stk",
 537                 "test/jalview/bin/argparser/testfiles/test3.stk",
 538                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 539                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 540                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 541                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 542                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 543                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 544                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
 545                 "test/jalview/bin/argparser/testfiles/test1.aln",
 546                 "test/jalview/bin/argparser/testfiles/test2.aln",
 547                 "test/jalview/bin/argparser/testfiles/test3.aln",
 548                 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 549                 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 550                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 551                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 552                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 553                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln",
 554                 deleteDir
 555                         + "test/jalview/bin/argparser/testfiles/test1.stk",
 556                 deleteDir
 557                         + "test/jalview/bin/argparser/testfiles/test2.stk",
 558                 deleteDir
 559                         + "test/jalview/bin/argparser/testfiles/test3.stk",
 560                 deleteDir
 561                         + "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 562                 deleteDir
 563                         + "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 564                 deleteDir
 565                         + "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 566                 deleteDir
 567                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 568                 deleteDir
 569                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 570                 deleteDir
 571                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 572                 deleteDir
 573                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
 574                 deleteDir
 575                         + "test/jalview/bin/argparser/testfiles/test1.aln",
 576                 deleteDir
 577                         + "test/jalview/bin/argparser/testfiles/test2.aln",
 578                 deleteDir
 579                         + "test/jalview/bin/argparser/testfiles/test3.aln",
 580                 deleteDir
 581                         + "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 582                 deleteDir
 583                         + "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 584                 deleteDir
 585                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 586                 deleteDir
 587                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 588                 deleteDir
 589                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 590                 deleteDir
 591                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
 592         //
 593     };
 594   }
 595
 596 }