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     if (Jalview.getInstance()!=null) {
  56       Jalview.getInstance().doMain(args);
  57     } else {
  58       Jalview.main(args);
  59     }
  60   }
  61
  62   /* --setprops is currently disabled so this test won't work
  63   @Test(groups = "Functional")
  64   public void setpropsTest()
  65   {
  66     final String MOSTLY_HARMLESS = "MOSTLY_HARMLESS";
  67     String cmdLine = "--setprop=" + MOSTLY_HARMLESS + "=Earth";
  68     String[] args = cmdLine.split("\\s+");
  69     Jalview.main(args);
  70     Assert.assertEquals(Cache.getDefault(MOSTLY_HARMLESS, "Magrathea"),
  71             "Earth");
  72   }
  73   */
  74
  75   @Test(groups = "Functional", dataProvider = "cmdLines")
  76   public void commandsOpenTest(String cmdLine, boolean cmdArgs,
  77           int numFrames, String[] sequences)
  78   {
  79     try
  80     {
  81       String[] args = (cmdLine + " --gui").split("\\s+");
  82       callJalviewMain(args);
  83       Commands cmds = Jalview.getInstance().getCommands();
  84       Assert.assertNotNull(cmds);
  85       Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs,
  86               "Commands were not provided in the args");
  87       Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
  88               "Overall command parse and operation is false");
  89
  90       Assert.assertEquals(Desktop.getAlignFrames().length, numFrames,
  91               "Wrong number of AlignFrames");
  92
  93       if (sequences != null)
  94       {
  95         Set<String> openedSequenceNames = new HashSet<>();
  96         AlignFrame[] afs = Desktop.getAlignFrames();
  97         for (AlignFrame af : afs)
  98         {
  99           openedSequenceNames.addAll(
 100                   af.getViewport().getAlignment().getSequenceNames());
 101         }
 102         for (String sequence : sequences)
 103         {
 104           Assert.assertTrue(openedSequenceNames.contains(sequence),
 105                   "Sequence '" + sequence
 106                           + "' was not found in opened alignment files: "
 107                           + cmdLine + ".\nOpened sequence names are:\n"
 108                           + String.join("\n", openedSequenceNames));
 109         }
 110       }
 111
 112       Assert.assertFalse(
 113               lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
 114     } catch (Exception x)
 115     {
 116       Assert.fail("Unexpected exception during commandsOpenTest", x);
 117     } finally
 118     {
 119       tearDown();
 120
 121     }
 122   }
 123
 124   @Test(groups = "Functional", dataProvider = "structureImageOutputFiles")
 125   public void structureImageOutputTest(String cmdLine, String[] filenames)
 126           throws IOException
 127   {
 128     cleanupFiles(filenames);
 129     String[] args = (cmdLine + " --gui").split("\\s+");
 130     try
 131     {
 132       callJalviewMain(args);
 133       Commands cmds = Jalview.getInstance().getCommands();
 134       Assert.assertNotNull(cmds);
 135       File lastFile = null;
 136       for (String filename : filenames)
 137       {
 138         File file = new File(filename);
 139         Assert.assertTrue(file.exists(), "File '" + filename
 140                 + "' was not created by '" + cmdLine + "'");
 141         Assert.assertTrue(file.isFile(), "File '" + filename
 142                 + "' is not a file from '" + cmdLine + "'");
 143         Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
 144                 + "' has no content from '" + cmdLine + "'");
 145         // make sure the successive output files get bigger!
 146         if (lastFile != null)
 147           Assert.assertTrue(Files.size(file.toPath()) > Files
 148                   .size(lastFile.toPath()));
 149       }
 150     } catch (Exception x)
 151     {
 152       Assert.fail("Unexpected exception during structureImageOutputTest",
 153               x);
 154     } finally
 155     {
 156       cleanupFiles(filenames);
 157       tearDown();
 158     }
 159   }
 160
 161   @Test(groups = "Functional", dataProvider = "argfileOutputFiles")
 162   public void argFilesGlobAndSubstitutionsTest(String cmdLine,
 163           String[] filenames) throws IOException
 164   {
 165     cleanupFiles(filenames);
 166     String[] args = (cmdLine + " --gui").split("\\s+");
 167     try {
 168     callJalviewMain(args);
 169     Commands cmds = Jalview.getInstance().getCommands();
 170     Assert.assertNotNull(cmds);
 171     File lastFile = null;
 172     for (String filename : filenames)
 173     {
 174       File file = new File(filename);
 175       Assert.assertTrue(file.exists(), "File '" + filename
 176               + "' was not created by '" + cmdLine + "'");
 177       Assert.assertTrue(file.isFile(), "File '" + filename
 178               + "' is not a file from '" + cmdLine + "'");
 179       Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
 180               + "' has no content from '" + cmdLine + "'");
 181       // make sure the successive output files get bigger!
 182       if (lastFile != null)
 183         Assert.assertTrue(
 184                 Files.size(file.toPath()) > Files.size(lastFile.toPath()));
 185     }
 186     } catch (Exception x)
 187     {
 188       Assert.fail("Unexpected exception during argFilesGlobAndSubstitutions",
 189               x);
 190     } finally
 191     {
 192       cleanupFiles(filenames);
 193       tearDown();
 194     }
 195   }
 196
 197   @DataProvider(name = "structureImageOutputFiles")
 198   public Object[][] structureImageOutputFiles()
 199   {
 200     return new Object[][] {
 201         //
 202         { "--gui --nonews --nosplash --open=./examples/test_fab41.result/sample.a2m "
 203                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 204                 + "--structureimage=" + testfiles + "/structureimage1.png "
 205                 + "--open=./examples/test_fab41.result/sample.a2m "
 206                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 207                 + "--structureimage=" + testfiles
 208                 + "/structureimage2.png --structureimagescale=1.5"
 209                 + "--open=./examples/test_fab41.result/sample.a2m "
 210                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 211                 + "--structureimage=" + testfiles
 212                 + "/structureimage3.png --structureimagescale=2.0",
 213             new String[]
 214             { testfiles + "/structureimage1.png",
 215                 testfiles + "/structureimage2.png",
 216                 testfiles + "/structureimage3.png" } },
 217         /*
 218         { "--headless --noquit --open=./examples/test_fab41.result/sample.a2m "
 219                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 220                 + "--structureimage=" + testfiles + "/structureimage1.png "
 221                 + "--open=./examples/test_fab41.result/sample.a2m "
 222                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 223                 + "--structureimage=" + testfiles
 224                 + "/structureimage2.png --structureimagescale=1.5"
 225                 + "--open=./examples/test_fab41.result/sample.a2m "
 226                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 227                 + "--structureimage=" + testfiles
 228                 + "/structureimage3.png --structureimagescale=2.0",
 229             new String[]
 230             { testfiles + "/structureimage1.png",
 231                 testfiles + "/structureimage2.png",
 232                 testfiles + "/structureimage3.png" } },
 233                 */
 234         //
 235     };
 236
 237   }
 238
 239   @DataProvider(name = "argfileOutputFiles")
 240   public Object[][] argfileOutputFiles()
 241   {
 242     return new Object[][] {
 243         //
 244         { "--gui --argfile=" + testfiles + "/**/*.txt", new String[]
 245         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
 246             testfiles + "/dir3/subdir/test0.png" } },
 247         { "--gui --argfile=" + testfiles + "/**/argfile.txt", new String[]
 248         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
 249         { "--gui --argfile=" + testfiles + "/dir*/argfile.txt", new String[]
 250         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
 251         { "--gui --initsubstitutions --append examples/uniref50.fa --image "
 252                 + testfiles + "/{basename}.png",
 253             new String[]
 254             { testfiles + "/uniref50.png" } },
 255         { "--gui --append examples/uniref50.fa --nosubstitutions --image "
 256                 + testfiles + "/{basename}.png",
 257             new String[]
 258             { testfiles + "/{basename}.png" } }
 259         //
 260     };
 261
 262   }
 263
 264   @DataProvider(name = "cmdLines")
 265   public Object[][] cmdLines()
 266   {
 267     String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN",
 268         "FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" };
 269     String[] t1 = new String[] { "TEST1" };
 270     String[] t2 = new String[] { "TEST2" };
 271     String[] t3 = new String[] { "TEST3" };
 272     return new Object[][] {
 273         /*
 274         */
 275         { "--append=examples/uniref50.fa", true, 1, someUniref50Seqs },
 276         { "--append examples/uniref50.fa", true, 1, someUniref50Seqs },
 277         { "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs },
 278         // NOTE we cannot use shell expansion in tests, so list all files!
 279         { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
 280             someUniref50Seqs },
 281         { "--append=[new]examples/uniref50*.fa", true, 2,
 282             someUniref50Seqs },
 283         { "--open=examples/uniref50*.fa", true, 2, someUniref50Seqs },
 284         { "examples/uniref50.fa", true, 1, someUniref50Seqs },
 285         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
 286             ArrayUtils.concatArrays(someUniref50Seqs, t1) },
 287         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
 288         { "--gui --argfile=" + testfiles + "/argfile0.txt", true, 1,
 289             ArrayUtils.concatArrays(t1, t3) },
 290         { "--gui --argfile=" + testfiles + "/argfile*.txt", true, 5,
 291             ArrayUtils.concatArrays(t1, t2, t3) },
 292         { "--gui --argfile=" + testfiles + "/argfile.autocounter", true, 3,
 293             ArrayUtils.concatArrays(t1, t2) } };
 294
 295   }
 296
 297   public static boolean lookForSequenceName(String sequenceName)
 298   {
 299     AlignFrame[] afs = Desktop.getAlignFrames();
 300     for (AlignFrame af : afs)
 301     {
 302       for (String name : af.getViewport().getAlignment().getSequenceNames())
 303       {
 304         if (sequenceName.equals(name))
 305         {
 306           return true;
 307         }
 308       }
 309     }
 310     return false;
 311   }
 312
 313   public static void cleanupFiles(String[] filenames)
 314   {
 315     for (String filename : filenames)
 316     {
 317       File file = new File(filename);
 318       if (file.exists())
 319       {
 320         file.delete();
 321       }
 322     }
 323   }
 324
 325   @Test(
 326     groups = "Functional",
 327     dataProvider = "allLinkedIdsData",
 328     singleThreaded = true)
 329   public void allLinkedIdsTest(String cmdLine, String[] filenames,
 330           String[] nonfilenames)
 331   {
 332     String[] args = (cmdLine + " --gui").split("\\s+");
 333     callJalviewMain(args);
 334     Commands cmds = Jalview.getInstance().getCommands();
 335     Assert.assertNotNull(cmds);
 336     for (String filename : filenames)
 337     {
 338       Assert.assertTrue(new File(filename).exists(),
 339               "File '" + filename + "' was not created");
 340     }
 341     cleanupFiles(filenames);
 342     if (nonfilenames != null)
 343     {
 344       for (String nonfilename : nonfilenames)
 345       {
 346         File nonfile = new File(nonfilename);
 347         Assert.assertFalse(nonfile.exists(),
 348                 "File " + nonfilename + " exists when it shouldn't!");
 349       }
 350     }
 351   }
 352
 353   @DataProvider(name = "allLinkedIdsData")
 354   public Object[][] allLinkedIdsData()
 355   {
 356     return new Object[][] {
 357         //
 358         /*
 359          */
 360         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
 361             new String[]
 362             { "test/jalview/bin/argparser/testfiles/test1.stk",
 363                 "test/jalview/bin/argparser/testfiles/test2.stk",
 364                 "test/jalview/bin/argparser/testfiles/test3.stk", },
 365             null },
 366         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
 367             new String[]
 368             { "test/jalview/bin/argparser/testfiles/test1.png",
 369                 "test/jalview/bin/argparser/testfiles/test2.png",
 370                 "test/jalview/bin/argparser/testfiles/test3.png", },
 371             null },
 372         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
 373             new String[]
 374             { "test/jalview/bin/argparser/testfiles/test1.stk",
 375                 "test/jalview/bin/argparser/testfiles/test2.stk",
 376                 "test/jalview/bin/argparser/testfiles/test3.stk", },
 377             new String[]
 378             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 379                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 380                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 381                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 382                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 383                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 384                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 385                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 386                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 387         { "--gui --open=test/jalview/bin/argparser/**/*.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                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 393                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 394                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 395                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 396                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 397                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 398                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 399                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 400                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
 401             null },
 402         { "--gui --open=test/jalview/bin/argparser/**/*.fa --output=*.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/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*.stk --close",
 418             new String[]
 419             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 420                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 421                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 422                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 423                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 424             new String[]
 425             { "test/jalview/bin/argparser/testfiles/test1.stk",
 426                 "test/jalview/bin/argparser/testfiles/test2.stk",
 427                 "test/jalview/bin/argparser/testfiles/test3.stk",
 428                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 429                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 430                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 431                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 432         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.stk --close",
 433             new String[]
 434             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 435                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 436                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 437             new String[]
 438             { "test/jalview/bin/argparser/testfiles/test1.stk",
 439                 "test/jalview/bin/argparser/testfiles/test2.stk",
 440                 "test/jalview/bin/argparser/testfiles/test3.stk",
 441                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 442                 "test/jalview/bin/argparser/testfiles/dir1/test2.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 --opened --output={dirname}/{basename}.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/dir1/test1.stk",
 457                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 458                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 459                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 460                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 461                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 462         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output open*.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.aln --close",
 463             new String[]
 464             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 465                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 466                 "test/jalview/bin/argparser/testfiles/dir2/test1.aln",
 467                 "test/jalview/bin/argparser/testfiles/dir2/test2.aln",
 468                 "test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
 469             new String[]
 470             { "test/jalview/bin/argparser/testfiles/test1.stk",
 471                 "test/jalview/bin/argparser/testfiles/test2.stk",
 472                 "test/jalview/bin/argparser/testfiles/test3.stk",
 473                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 474                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 475                 "test/jalview/bin/argparser/testfiles/dir2/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                 "test/jalview/bin/argparser/testfiles/test1.aln",
 481                 "test/jalview/bin/argparser/testfiles/test2.aln",
 482                 "test/jalview/bin/argparser/testfiles/test3.aln",
 483                 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 484                 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 485                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 486                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 487                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 488                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
 489         //
 490     };
 491   }
 492
 493 }