test/jalview/bin/CommandsTest.java

   1 package jalview.bin;
   2
   3 import java.io.File;
   4 import java.io.IOException;
   5 import java.lang.reflect.InvocationTargetException;
   6 import java.nio.file.Files;
   7 import java.util.Date;
   8 import java.util.HashSet;
   9 import java.util.Set;
  10
  11 import javax.swing.SwingUtilities;
  12
  13 import org.testng.Assert;
  14 import org.testng.annotations.AfterClass;
  15 import org.testng.annotations.AfterMethod;
  16 import org.testng.annotations.BeforeClass;
  17 import org.testng.annotations.DataProvider;
  18 import org.testng.annotations.Test;
  19
  20 import jalview.gui.AlignFrame;
  21 import jalview.gui.Desktop;
  22 import jalview.gui.JvOptionPane;
  23 import jalview.util.ArrayUtils;
  24
  25 public class CommandsTest
  26 {
  27   private static final String testfiles = "test/jalview/bin/argparser/testfiles";
  28
  29   @BeforeClass(alwaysRun = true)
  30   public static void setUpBeforeClass() throws Exception
  31   {
  32     Cache.loadProperties("test/jalview/gui/quitProps.jvprops");
  33     Date oneHourFromNow = new Date(
  34             System.currentTimeMillis() + 3600 * 1000);
  35     Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
  36   }
  37
  38   @AfterClass(alwaysRun = true)
  39   public static void resetProps()
  40   {
  41     Cache.loadProperties("test/jalview/testProps.jvprops");
  42   }
  43
  44   @BeforeClass(alwaysRun = true)
  45   public void setUpJvOptionPane()
  46   {
  47     JvOptionPane.setInteractiveMode(false);
  48     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  49   }
  50
  51   @AfterMethod(alwaysRun = true)
  52   public void tearDown()
  53   {
  54     try
  55     {
  56       // occasionally we are blocked by Jmol redraws
  57       SwingUtilities.invokeAndWait(new Runnable()
  58       {
  59
  60         @Override
  61         public void run()
  62         {
  63           Desktop.closeDesktop();
  64         }
  65       });
  66     } catch (Exception foo)
  67     {
  68       System.err.println("Failed during teardown with exception");
  69       foo.printStackTrace();
  70     }
  71
  72   }
  73
  74   public static void callJalviewMain(String[] args)
  75   {
  76     if (Jalview.getInstance() != null)
  77     {
  78       Jalview.getInstance().doMain(args);
  79     }
  80     else
  81     {
  82       Jalview.main(args);
  83     }
  84   }
  85
  86   /* --setprops is currently disabled so this test won't work
  87   @Test(groups = "Functional")
  88   public void setpropsTest()
  89   {
  90     final String MOSTLY_HARMLESS = "MOSTLY_HARMLESS";
  91     String cmdLine = "--setprop=" + MOSTLY_HARMLESS + "=Earth";
  92     String[] args = cmdLine.split("\\s+");
  93     Jalview.main(args);
  94     Assert.assertEquals(Cache.getDefault(MOSTLY_HARMLESS, "Magrathea"),
  95             "Earth");
  96   }
  97   */
  98
  99   @Test(groups = { "Functional", "testTask3" }, dataProvider = "cmdLines")
 100   public void commandsOpenTest(String cmdLine, boolean cmdArgs,
 101           int numFrames, String[] sequences)
 102   {
 103     try
 104     {
 105       String[] args = (cmdLine + " --gui").split("\\s+");
 106       callJalviewMain(args);
 107       Commands cmds = Jalview.getInstance().getCommands();
 108       Assert.assertNotNull(cmds);
 109       Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs,
 110               "Commands were not provided in the args");
 111       Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
 112               "Overall command parse and operation is false");
 113
 114       Assert.assertEquals(Desktop.getDesktopAlignFrames().length, numFrames,
 115               "Wrong number of AlignFrames");
 116
 117       if (sequences != null)
 118       {
 119         Set<String> openedSequenceNames = new HashSet<>();
 120         AlignFrame[] afs = Desktop.getDesktopAlignFrames();
 121         for (AlignFrame af : afs)
 122         {
 123           openedSequenceNames.addAll(
 124                   af.getViewport().getAlignment().getSequenceNames());
 125         }
 126         for (String sequence : sequences)
 127         {
 128           Assert.assertTrue(openedSequenceNames.contains(sequence),
 129                   "Sequence '" + sequence
 130                           + "' was not found in opened alignment files: "
 131                           + cmdLine + ".\nOpened sequence names are:\n"
 132                           + String.join("\n", openedSequenceNames));
 133         }
 134       }
 135
 136       Assert.assertFalse(
 137               lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
 138     } catch (Exception x)
 139     {
 140       Assert.fail("Unexpected exception during commandsOpenTest", x);
 141     } finally
 142     {
 143       tearDown();
 144
 145     }
 146   }
 147
 148   @Test(
 149     groups =
 150     { "Functional", "testTask3" },
 151     dataProvider = "structureImageOutputFiles")
 152   public void structureImageOutputTest(String cmdLine, String[] filenames)
 153           throws IOException
 154   {
 155     cleanupFiles(filenames);
 156     String[] args = (cmdLine + " --gui").split("\\s+");
 157     try
 158     {
 159       callJalviewMain(args);
 160       Commands cmds = Jalview.getInstance().getCommands();
 161       Assert.assertNotNull(cmds);
 162       File lastFile = null;
 163       for (String filename : filenames)
 164       {
 165         File file = new File(filename);
 166         Assert.assertTrue(file.exists(), "File '" + filename
 167                 + "' was not created by '" + cmdLine + "'");
 168         Assert.assertTrue(file.isFile(), "File '" + filename
 169                 + "' is not a file from '" + cmdLine + "'");
 170         Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
 171                 + "' has no content from '" + cmdLine + "'");
 172         // make sure the successive output files get bigger!
 173         if (lastFile != null)
 174           Assert.assertTrue(Files.size(file.toPath()) > Files
 175                   .size(lastFile.toPath()));
 176       }
 177     } catch (Exception x)
 178     {
 179       Assert.fail("Unexpected exception during structureImageOutputTest",
 180               x);
 181     } finally
 182     {
 183       cleanupFiles(filenames);
 184       tearDown();
 185     }
 186   }
 187
 188   @Test(groups = "Functional", dataProvider = "argfileOutputFiles")
 189   public void argFilesGlobAndSubstitutionsTest(String cmdLine,
 190           String[] filenames) throws IOException
 191   {
 192     cleanupFiles(filenames);
 193     String[] args = (cmdLine + " --gui").split("\\s+");
 194     try
 195     {
 196       callJalviewMain(args);
 197       Commands cmds = Jalview.getInstance().getCommands();
 198       Assert.assertNotNull(cmds);
 199       File lastFile = null;
 200       for (String filename : filenames)
 201       {
 202         File file = new File(filename);
 203         Assert.assertTrue(file.exists(), "File '" + filename
 204                 + "' was not created by '" + cmdLine + "'");
 205         Assert.assertTrue(file.isFile(), "File '" + filename
 206                 + "' is not a file from '" + cmdLine + "'");
 207         Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
 208                 + "' has no content from '" + cmdLine + "'");
 209         // make sure the successive output files get bigger!
 210         if (lastFile != null)
 211           Assert.assertTrue(Files.size(file.toPath()) > Files
 212                   .size(lastFile.toPath()));
 213       }
 214     } catch (Exception x)
 215     {
 216       Assert.fail(
 217               "Unexpected exception during argFilesGlobAndSubstitutions",
 218               x);
 219     } finally
 220     {
 221       cleanupFiles(filenames);
 222       tearDown();
 223     }
 224   }
 225
 226   @DataProvider(name = "structureImageOutputFiles")
 227   public Object[][] structureImageOutputFiles()
 228   {
 229     return new Object[][] {
 230         //
 231         { "--gui --nonews --nosplash --open=./examples/test_fab41.result/sample.a2m "
 232                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 233                 + "--structureimage=" + testfiles + "/structureimage1.png "
 234                 + "--open=./examples/test_fab41.result/sample.a2m "
 235                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 236                 + "--structureimage=" + testfiles
 237                 + "/structureimage2.png --scale=1.5 "
 238                 + "--open=./examples/test_fab41.result/sample.a2m "
 239                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 240                 + "--structureimage=" + testfiles
 241                 + "/structureimage3.png --scale=2.0 ",
 242             new String[]
 243             { testfiles + "/structureimage1.png",
 244                 testfiles + "/structureimage2.png",
 245                 testfiles + "/structureimage3.png" } },
 246         { "--headless --noquit --open=./examples/test_fab41.result/sample.a2m "
 247                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 248                 + "--structureimage=" + testfiles + "/structureimage1.png "
 249                 + "--open=./examples/test_fab41.result/sample.a2m "
 250                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 251                 + "--structureimage=" + testfiles
 252                 + "/structureimage2.png --scale=1.5 "
 253                 + "--open=./examples/test_fab41.result/sample.a2m "
 254                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 255                 + "--structureimage=" + testfiles
 256                 + "/structureimage3.png --scale=2.0 ",
 257             new String[]
 258             { testfiles + "/structureimage1.png",
 259                 testfiles + "/structureimage2.png",
 260                 testfiles + "/structureimage3.png" } },
 261         /*
 262                 */
 263         //
 264     };
 265
 266   }
 267
 268   @DataProvider(name = "argfileOutputFiles")
 269   public Object[][] argfileOutputFiles()
 270   {
 271     return new Object[][] {
 272         //
 273         { "--gui --argfile=" + testfiles + "/**/*.txt", new String[]
 274         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
 275             testfiles + "/dir3/subdir/test0.png" } },
 276         { "--gui --argfile=" + testfiles + "/**/argfile.txt", new String[]
 277         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
 278         { "--gui --argfile=" + testfiles + "/dir*/argfile.txt", new String[]
 279         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
 280         { "--gui --initsubstitutions --append examples/uniref50.fa --image "
 281                 + testfiles + "/{basename}.png",
 282             new String[]
 283             { testfiles + "/uniref50.png" } },
 284         { "--gui --append examples/uniref50.fa --nosubstitutions --image "
 285                 + testfiles + "/{basename}.png",
 286             new String[]
 287             { testfiles + "/{basename}.png" } }
 288         //
 289     };
 290
 291   }
 292
 293   @DataProvider(name = "cmdLines")
 294   public Object[][] cmdLines()
 295   {
 296     String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN",
 297         "FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" };
 298     String[] t1 = new String[] { "TEST1" };
 299     String[] t2 = new String[] { "TEST2" };
 300     String[] t3 = new String[] { "TEST3" };
 301     return new Object[][] {
 302         /*
 303         */
 304         { "--append=examples/uniref50.fa", true, 1, someUniref50Seqs },
 305         { "--append examples/uniref50.fa", true, 1, someUniref50Seqs },
 306         { "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs },
 307         // NOTE we cannot use shell expansion in tests, so list all files!
 308         { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
 309             someUniref50Seqs },
 310         { "--append=[new]examples/uniref50*.fa", true, 2,
 311             someUniref50Seqs },
 312         { "--open=examples/uniref50*.fa", true, 2, someUniref50Seqs },
 313         { "examples/uniref50.fa", true, 1, someUniref50Seqs },
 314         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
 315             ArrayUtils.concatArrays(someUniref50Seqs, t1) },
 316         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
 317         { "--gui --argfile=" + testfiles + "/argfile0.txt", true, 1,
 318             ArrayUtils.concatArrays(t1, t3) },
 319         { "--gui --argfile=" + testfiles + "/argfile*.txt", true, 5,
 320             ArrayUtils.concatArrays(t1, t2, t3) },
 321         { "--gui --argfile=" + testfiles + "/argfile.autocounter", true, 3,
 322             ArrayUtils.concatArrays(t1, t2) } };
 323
 324   }
 325
 326   public static boolean lookForSequenceName(String sequenceName)
 327   {
 328     AlignFrame[] afs = Desktop.getDesktopAlignFrames();
 329     for (AlignFrame af : afs)
 330     {
 331       for (String name : af.getViewport().getAlignment().getSequenceNames())
 332       {
 333         if (sequenceName.equals(name))
 334         {
 335           return true;
 336         }
 337       }
 338     }
 339     return false;
 340   }
 341
 342   public static void cleanupFiles(String[] filenames)
 343   {
 344     for (String filename : filenames)
 345     {
 346       File file = new File(filename);
 347       if (file.exists())
 348       {
 349         file.delete();
 350       }
 351     }
 352   }
 353
 354   private final String deleteDir = "test/deleteAfter";
 355
 356   @Test(
 357     groups = "Functional",
 358     dataProvider = "allLinkedIdsData",
 359     singleThreaded = true)
 360   public void allLinkedIdsTest(String cmdLine, String[] filenames,
 361           String[] nonfilenames)
 362   {
 363     String[] args = (cmdLine + " --gui").split("\\s+");
 364     callJalviewMain(args);
 365     Commands cmds = Jalview.getInstance().getCommands();
 366     Assert.assertNotNull(cmds);
 367     for (String filename : filenames)
 368     {
 369       Assert.assertTrue(new File(filename).exists(),
 370               "File '" + filename + "' was not created");
 371     }
 372     cleanupFiles(filenames);
 373     if (nonfilenames != null)
 374     {
 375       for (String nonfilename : nonfilenames)
 376       {
 377         File nonfile = new File(nonfilename);
 378         Assert.assertFalse(nonfile.exists(),
 379                 "File " + nonfilename + " exists when it shouldn't!");
 380       }
 381     }
 382
 383     File deleteDirF = new File(deleteDir);
 384     if (deleteDirF.exists())
 385     {
 386       deleteDirF.delete();
 387     }
 388   }
 389
 390   @DataProvider(name = "allLinkedIdsData")
 391   public Object[][] allLinkedIdsData()
 392   {
 393     return new Object[][] {
 394         //
 395         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
 396             new String[]
 397             { "test/jalview/bin/argparser/testfiles/test1.stk",
 398                 "test/jalview/bin/argparser/testfiles/test2.stk",
 399                 "test/jalview/bin/argparser/testfiles/test3.stk", },
 400             null },
 401         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
 402             new String[]
 403             { "test/jalview/bin/argparser/testfiles/test1.png",
 404                 "test/jalview/bin/argparser/testfiles/test2.png",
 405                 "test/jalview/bin/argparser/testfiles/test3.png", },
 406             null },
 407         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
 408             new String[]
 409             { "test/jalview/bin/argparser/testfiles/test1.stk",
 410                 "test/jalview/bin/argparser/testfiles/test2.stk",
 411                 "test/jalview/bin/argparser/testfiles/test3.stk", },
 412             new String[]
 413             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 414                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 415                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 416                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 417                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 418                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 419                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 420                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 421                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 422         { "--gui --open=test/jalview/bin/argparser/**/*.fa --all --output={dirname}/{basename}.stk --close",
 423             new String[]
 424             { "test/jalview/bin/argparser/testfiles/test1.stk",
 425                 "test/jalview/bin/argparser/testfiles/test2.stk",
 426                 "test/jalview/bin/argparser/testfiles/test3.stk",
 427                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 428                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 429                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 430                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 431                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 432                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 433                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 434                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 435                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
 436             null },
 437         { "--gui --open=test/jalview/bin/argparser/**/*.fa --output=*/*.stk --close",
 438             new String[]
 439             { "test/jalview/bin/argparser/testfiles/test1.stk",
 440                 "test/jalview/bin/argparser/testfiles/test2.stk",
 441                 "test/jalview/bin/argparser/testfiles/test3.stk",
 442                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 443                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 444                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 445                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 446                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 447                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 448                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 449                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 450                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
 451             null },
 452         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --all --output=*/*.stk --close",
 453             new String[]
 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             new String[]
 460             { "test/jalview/bin/argparser/testfiles/test1.stk",
 461                 "test/jalview/bin/argparser/testfiles/test2.stk",
 462                 "test/jalview/bin/argparser/testfiles/test3.stk",
 463                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 464                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 465                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 466                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 467         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*/*.stk --close",
 468             new String[]
 469             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 470                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 471                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 472             new String[]
 473             { "test/jalview/bin/argparser/testfiles/test1.stk",
 474                 "test/jalview/bin/argparser/testfiles/test2.stk",
 475                 "test/jalview/bin/argparser/testfiles/test3.stk",
 476                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 477                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 478                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 479                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 480         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
 481             new String[]
 482             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 483                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 484                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 485             new String[]
 486             { "test/jalview/bin/argparser/testfiles/test1.stk",
 487                 "test/jalview/bin/argparser/testfiles/test2.stk",
 488                 "test/jalview/bin/argparser/testfiles/test3.stk",
 489                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 490                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 491                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 492                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 493                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 494                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 495         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
 496             new String[]
 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", },
 500             new String[]
 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/dir1/test1.stk",
 505                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 506                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 507                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 508                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 509                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 510         { "--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",
 511             new String[]
 512             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 513                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 514                 "test/jalview/bin/argparser/testfiles/dir2/test1.aln",
 515                 "test/jalview/bin/argparser/testfiles/dir2/test2.aln",
 516                 "test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
 517             new String[]
 518             { "test/jalview/bin/argparser/testfiles/test1.stk",
 519                 "test/jalview/bin/argparser/testfiles/test2.stk",
 520                 "test/jalview/bin/argparser/testfiles/test3.stk",
 521                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 522                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 523                 "test/jalview/bin/argparser/testfiles/dir2/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                 "test/jalview/bin/argparser/testfiles/test1.aln",
 529                 "test/jalview/bin/argparser/testfiles/test2.aln",
 530                 "test/jalview/bin/argparser/testfiles/test3.aln",
 531                 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 532                 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 533                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 534                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 535                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 536                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
 537         // --mkdirs
 538         { "--headless --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output "
 539                 + deleteDir
 540                 + "/{dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output="
 541                 + deleteDir
 542                 + "/{dirname}/{basename}.aln --close --all --mkdirs",
 543             new String[]
 544             { deleteDir
 545                     + "/test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 546                 deleteDir
 547                         + "/test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 548                 deleteDir
 549                         + "/test/jalview/bin/argparser/testfiles/dir2/test1.aln",
 550                 deleteDir
 551                         + "/test/jalview/bin/argparser/testfiles/dir2/test2.aln",
 552                 deleteDir
 553                         + "/test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
 554             new String[]
 555             { "test/jalview/bin/argparser/testfiles/test1.stk",
 556                 "test/jalview/bin/argparser/testfiles/test2.stk",
 557                 "test/jalview/bin/argparser/testfiles/test3.stk",
 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",
 561                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 562                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 563                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 564                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
 565                 "test/jalview/bin/argparser/testfiles/test1.aln",
 566                 "test/jalview/bin/argparser/testfiles/test2.aln",
 567                 "test/jalview/bin/argparser/testfiles/test3.aln",
 568                 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 569                 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 570                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 571                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 572                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 573                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln",
 574                 deleteDir
 575                         + "test/jalview/bin/argparser/testfiles/test1.stk",
 576                 deleteDir
 577                         + "test/jalview/bin/argparser/testfiles/test2.stk",
 578                 deleteDir
 579                         + "test/jalview/bin/argparser/testfiles/test3.stk",
 580                 deleteDir
 581                         + "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 582                 deleteDir
 583                         + "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 584                 deleteDir
 585                         + "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 586                 deleteDir
 587                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 588                 deleteDir
 589                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 590                 deleteDir
 591                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 592                 deleteDir
 593                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
 594                 deleteDir
 595                         + "test/jalview/bin/argparser/testfiles/test1.aln",
 596                 deleteDir
 597                         + "test/jalview/bin/argparser/testfiles/test2.aln",
 598                 deleteDir
 599                         + "test/jalview/bin/argparser/testfiles/test3.aln",
 600                 deleteDir
 601                         + "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 602                 deleteDir
 603                         + "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 604                 deleteDir
 605                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 606                 deleteDir
 607                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 608                 deleteDir
 609                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 610                 deleteDir
 611                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
 612         //
 613     };
 614   }
 615
 616 }