test/jalview/bin/CommandsTest.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   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.
  11  *
  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.
  16  *
  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.
  20  */
  21 package jalview.bin;
  22
  23 import java.io.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;
  29 import java.util.Set;
  30
  31 import javax.swing.SwingUtilities;
  32
  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;
  39
  40 import jalview.gui.AlignFrame;
  41 import jalview.gui.Desktop;
  42 import jalview.gui.JvOptionPane;
  43 import jalview.util.ArrayUtils;
  44
  45 public class CommandsTest
  46 {
  47   private static final String testfiles = "test/jalview/bin/argparser/testfiles";
  48
  49   @BeforeClass(alwaysRun = true)
  50   public static void setUpBeforeClass() throws Exception
  51   {
  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);
  56   }
  57
  58   @AfterClass(alwaysRun = true)
  59   public static void resetProps()
  60   {
  61     Cache.loadProperties("test/jalview/testProps.jvprops");
  62   }
  63
  64   @BeforeClass(alwaysRun = true)
  65   public void setUpJvOptionPane()
  66   {
  67     JvOptionPane.setInteractiveMode(false);
  68     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  69   }
  70
  71   @AfterMethod(alwaysRun = true)
  72   public void tearDown()
  73   {
  74     try
  75     {
  76       // occasionally we are blocked by Jmol redraws
  77       SwingUtilities.invokeAndWait(new Runnable()
  78       {
  79
  80         @Override
  81         public void run()
  82         {
  83           Desktop.closeDesktop();
  84         }
  85       });
  86     } catch (Exception foo)
  87     {
  88       System.err.println("Failed during teardown with exception");
  89       foo.printStackTrace();
  90     }
  91
  92   }
  93
  94   public static void callJalviewMain(String[] args)
  95   {
  96     if (Jalview.getInstance() != null)
  97     {
  98       Jalview.getInstance().doMain(args);
  99     }
 100     else
 101     {
 102       Jalview.main(args);
 103     }
 104   }
 105
 106   /* --setprops is currently disabled so this test won't work
 107   @Test(groups = "Functional")
 108   public void setpropsTest()
 109   {
 110     final String MOSTLY_HARMLESS = "MOSTLY_HARMLESS";
 111     String cmdLine = "--setprop=" + MOSTLY_HARMLESS + "=Earth";
 112     String[] args = cmdLine.split("\\s+");
 113     Jalview.main(args);
 114     Assert.assertEquals(Cache.getDefault(MOSTLY_HARMLESS, "Magrathea"),
 115             "Earth");
 116   }
 117   */
 118
 119   @Test(groups = { "Functional", "testTask3" }, dataProvider = "cmdLines")
 120   public void commandsOpenTest(String cmdLine, boolean cmdArgs,
 121           int numFrames, String[] sequences)
 122   {
 123     try
 124     {
 125       String[] args = (cmdLine + " --gui").split("\\s+");
 126       callJalviewMain(args);
 127       Commands cmds = Jalview.getInstance().getCommands();
 128       Assert.assertNotNull(cmds);
 129       Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs,
 130               "Commands were not provided in the args");
 131       Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
 132               "Overall command parse and operation is false");
 133
 134       Assert.assertEquals(Desktop.getDesktopAlignFrames().length, numFrames,
 135               "Wrong number of AlignFrames");
 136
 137       if (sequences != null)
 138       {
 139         Set<String> openedSequenceNames = new HashSet<>();
 140         AlignFrame[] afs = Desktop.getDesktopAlignFrames();
 141         for (AlignFrame af : afs)
 142         {
 143           openedSequenceNames.addAll(
 144                   af.getViewport().getAlignment().getSequenceNames());
 145         }
 146         for (String sequence : sequences)
 147         {
 148           Assert.assertTrue(openedSequenceNames.contains(sequence),
 149                   "Sequence '" + sequence
 150                           + "' was not found in opened alignment files: "
 151                           + cmdLine + ".\nOpened sequence names are:\n"
 152                           + String.join("\n", openedSequenceNames));
 153         }
 154       }
 155
 156       Assert.assertFalse(
 157               lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
 158     } catch (Exception x)
 159     {
 160       Assert.fail("Unexpected exception during commandsOpenTest", x);
 161     } finally
 162     {
 163       tearDown();
 164
 165     }
 166   }
 167
 168   @Test(
 169     groups =
 170     { "Functional", "testTask3" },
 171     dataProvider = "structureImageOutputFiles")
 172   public void structureImageOutputTest(String cmdLine, String[] filenames)
 173           throws IOException
 174   {
 175     cleanupFiles(filenames);
 176     String[] args = (cmdLine + " --gui").split("\\s+");
 177     try
 178     {
 179       callJalviewMain(args);
 180       Commands cmds = Jalview.getInstance().getCommands();
 181       Assert.assertNotNull(cmds);
 182       File lastFile = null;
 183       for (String filename : filenames)
 184       {
 185         File file = new File(filename);
 186         Assert.assertTrue(file.exists(), "File '" + filename
 187                 + "' was not created by '" + cmdLine + "'");
 188         Assert.assertTrue(file.isFile(), "File '" + filename
 189                 + "' is not a file from '" + cmdLine + "'");
 190         Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
 191                 + "' has no content from '" + cmdLine + "'");
 192         // make sure the successive output files get bigger!
 193         if (lastFile != null)
 194           Assert.assertTrue(Files.size(file.toPath()) > Files
 195                   .size(lastFile.toPath()));
 196       }
 197     } catch (Exception x)
 198     {
 199       Assert.fail("Unexpected exception during structureImageOutputTest",
 200               x);
 201     } finally
 202     {
 203       cleanupFiles(filenames);
 204       tearDown();
 205     }
 206   }
 207
 208   @Test(groups = "Functional", dataProvider = "argfileOutputFiles")
 209   public void argFilesGlobAndSubstitutionsTest(String cmdLine,
 210           String[] filenames) throws IOException
 211   {
 212     cleanupFiles(filenames);
 213     String[] args = (cmdLine + " --gui").split("\\s+");
 214     try
 215     {
 216       callJalviewMain(args);
 217       Commands cmds = Jalview.getInstance().getCommands();
 218       Assert.assertNotNull(cmds);
 219       File lastFile = null;
 220       for (String filename : filenames)
 221       {
 222         File file = new File(filename);
 223         Assert.assertTrue(file.exists(), "File '" + filename
 224                 + "' was not created by '" + cmdLine + "'");
 225         Assert.assertTrue(file.isFile(), "File '" + filename
 226                 + "' is not a file from '" + cmdLine + "'");
 227         Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
 228                 + "' has no content from '" + cmdLine + "'");
 229         // make sure the successive output files get bigger!
 230         if (lastFile != null)
 231           Assert.assertTrue(Files.size(file.toPath()) > Files
 232                   .size(lastFile.toPath()));
 233       }
 234     } catch (Exception x)
 235     {
 236       Assert.fail(
 237               "Unexpected exception during argFilesGlobAndSubstitutions",
 238               x);
 239     } finally
 240     {
 241       cleanupFiles(filenames);
 242       tearDown();
 243     }
 244   }
 245
 246   @DataProvider(name = "structureImageOutputFiles")
 247   public Object[][] structureImageOutputFiles()
 248   {
 249     return new Object[][] {
 250         //
 251         { "--gui --nonews --nosplash --open=./examples/test_fab41.result/sample.a2m "
 252                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 253                 + "--structureimage=" + testfiles + "/structureimage1.png "
 254                 + "--open=./examples/test_fab41.result/sample.a2m "
 255                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 256                 + "--structureimage=" + testfiles
 257                 + "/structureimage2.png --scale=1.5 "
 258                 + "--open=./examples/test_fab41.result/sample.a2m "
 259                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 260                 + "--structureimage=" + testfiles
 261                 + "/structureimage3.png --scale=2.0 ",
 262             new String[]
 263             { testfiles + "/structureimage1.png",
 264                 testfiles + "/structureimage2.png",
 265                 testfiles + "/structureimage3.png" } },
 266         { "--headless --noquit --open=./examples/test_fab41.result/sample.a2m "
 267                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 268                 + "--structureimage=" + testfiles + "/structureimage1.png "
 269                 + "--open=./examples/test_fab41.result/sample.a2m "
 270                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 271                 + "--structureimage=" + testfiles
 272                 + "/structureimage2.png --scale=1.5 "
 273                 + "--open=./examples/test_fab41.result/sample.a2m "
 274                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 275                 + "--structureimage=" + testfiles
 276                 + "/structureimage3.png --scale=2.0 ",
 277             new String[]
 278             { testfiles + "/structureimage1.png",
 279                 testfiles + "/structureimage2.png",
 280                 testfiles + "/structureimage3.png" } },
 281         /*
 282                 */
 283         //
 284     };
 285
 286   }
 287
 288   @DataProvider(name = "argfileOutputFiles")
 289   public Object[][] argfileOutputFiles()
 290   {
 291     return new Object[][] {
 292         //
 293         { "--gui --argfile=" + testfiles + "/**/*.txt", new String[]
 294         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
 295             testfiles + "/dir3/subdir/test0.png" } },
 296         { "--gui --argfile=" + testfiles + "/**/argfile.txt", new String[]
 297         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
 298         { "--gui --argfile=" + testfiles + "/dir*/argfile.txt", new String[]
 299         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
 300         { "--gui --initsubstitutions --append examples/uniref50.fa --image "
 301                 + testfiles + "/{basename}.png",
 302             new String[]
 303             { testfiles + "/uniref50.png" } },
 304         { "--gui --append examples/uniref50.fa --nosubstitutions --image "
 305                 + testfiles + "/{basename}.png",
 306             new String[]
 307             { testfiles + "/{basename}.png" } }
 308         //
 309     };
 310
 311   }
 312
 313   @DataProvider(name = "cmdLines")
 314   public Object[][] cmdLines()
 315   {
 316     String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN",
 317         "FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" };
 318     String[] t1 = new String[] { "TEST1" };
 319     String[] t2 = new String[] { "TEST2" };
 320     String[] t3 = new String[] { "TEST3" };
 321     return new Object[][] {
 322         /*
 323         */
 324         { "--append=examples/uniref50.fa", true, 1, someUniref50Seqs },
 325         { "--append examples/uniref50.fa", true, 1, someUniref50Seqs },
 326         { "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs },
 327         // NOTE we cannot use shell expansion in tests, so list all files!
 328         { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
 329             someUniref50Seqs },
 330         { "--append=[new]examples/uniref50*.fa", true, 2,
 331             someUniref50Seqs },
 332         { "--open=examples/uniref50*.fa", true, 2, someUniref50Seqs },
 333         { "examples/uniref50.fa", true, 1, someUniref50Seqs },
 334         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
 335             ArrayUtils.concatArrays(someUniref50Seqs, t1) },
 336         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
 337         { "--gui --argfile=" + testfiles + "/argfile0.txt", true, 1,
 338             ArrayUtils.concatArrays(t1, t3) },
 339         { "--gui --argfile=" + testfiles + "/argfile*.txt", true, 5,
 340             ArrayUtils.concatArrays(t1, t2, t3) },
 341         { "--gui --argfile=" + testfiles + "/argfile.autocounter", true, 3,
 342             ArrayUtils.concatArrays(t1, t2) } };
 343
 344   }
 345
 346   public static boolean lookForSequenceName(String sequenceName)
 347   {
 348     AlignFrame[] afs = Desktop.getDesktopAlignFrames();
 349     for (AlignFrame af : afs)
 350     {
 351       for (String name : af.getViewport().getAlignment().getSequenceNames())
 352       {
 353         if (sequenceName.equals(name))
 354         {
 355           return true;
 356         }
 357       }
 358     }
 359     return false;
 360   }
 361
 362   public static void cleanupFiles(String[] filenames)
 363   {
 364     for (String filename : filenames)
 365     {
 366       File file = new File(filename);
 367       if (file.exists())
 368       {
 369         file.delete();
 370       }
 371     }
 372   }
 373
 374   private final String deleteDir = "test/deleteAfter";
 375
 376   @Test(
 377     groups = "Functional",
 378     dataProvider = "allLinkedIdsData",
 379     singleThreaded = true)
 380   public void allLinkedIdsTest(String cmdLine, String[] filenames,
 381           String[] nonfilenames)
 382   {
 383     String[] args = (cmdLine + " --gui").split("\\s+");
 384     callJalviewMain(args);
 385     Commands cmds = Jalview.getInstance().getCommands();
 386     Assert.assertNotNull(cmds);
 387     for (String filename : filenames)
 388     {
 389       Assert.assertTrue(new File(filename).exists(),
 390               "File '" + filename + "' was not created");
 391     }
 392     cleanupFiles(filenames);
 393     if (nonfilenames != null)
 394     {
 395       for (String nonfilename : nonfilenames)
 396       {
 397         File nonfile = new File(nonfilename);
 398         Assert.assertFalse(nonfile.exists(),
 399                 "File " + nonfilename + " exists when it shouldn't!");
 400       }
 401     }
 402
 403     File deleteDirF = new File(deleteDir);
 404     if (deleteDirF.exists())
 405     {
 406       deleteDirF.delete();
 407     }
 408   }
 409
 410   @DataProvider(name = "allLinkedIdsData")
 411   public Object[][] allLinkedIdsData()
 412   {
 413     return new Object[][] {
 414         //
 415         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
 416             new String[]
 417             { "test/jalview/bin/argparser/testfiles/test1.stk",
 418                 "test/jalview/bin/argparser/testfiles/test2.stk",
 419                 "test/jalview/bin/argparser/testfiles/test3.stk", },
 420             null },
 421         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
 422             new String[]
 423             { "test/jalview/bin/argparser/testfiles/test1.png",
 424                 "test/jalview/bin/argparser/testfiles/test2.png",
 425                 "test/jalview/bin/argparser/testfiles/test3.png", },
 426             null },
 427         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
 428             new String[]
 429             { "test/jalview/bin/argparser/testfiles/test1.stk",
 430                 "test/jalview/bin/argparser/testfiles/test2.stk",
 431                 "test/jalview/bin/argparser/testfiles/test3.stk", },
 432             new String[]
 433             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 434                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 435                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 436                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 437                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 438                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 439                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 440                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 441                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 442         { "--gui --open=test/jalview/bin/argparser/**/*.fa --all --output={dirname}/{basename}.stk --close",
 443             new String[]
 444             { "test/jalview/bin/argparser/testfiles/test1.stk",
 445                 "test/jalview/bin/argparser/testfiles/test2.stk",
 446                 "test/jalview/bin/argparser/testfiles/test3.stk",
 447                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 448                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 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                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 453                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 454                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 455                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
 456             null },
 457         { "--gui --open=test/jalview/bin/argparser/**/*.fa --output=*/*.stk --close",
 458             new String[]
 459             { "test/jalview/bin/argparser/testfiles/test1.stk",
 460                 "test/jalview/bin/argparser/testfiles/test2.stk",
 461                 "test/jalview/bin/argparser/testfiles/test3.stk",
 462                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 463                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 464                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 465                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 466                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 467                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 468                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 469                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 470                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
 471             null },
 472         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --all --output=*/*.stk --close",
 473             new String[]
 474             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 475                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 476                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 477                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 478                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 479             new String[]
 480             { "test/jalview/bin/argparser/testfiles/test1.stk",
 481                 "test/jalview/bin/argparser/testfiles/test2.stk",
 482                 "test/jalview/bin/argparser/testfiles/test3.stk",
 483                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 484                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 485                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 486                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 487         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*/*.stk --close",
 488             new String[]
 489             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 490                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 491                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 492             new String[]
 493             { "test/jalview/bin/argparser/testfiles/test1.stk",
 494                 "test/jalview/bin/argparser/testfiles/test2.stk",
 495                 "test/jalview/bin/argparser/testfiles/test3.stk",
 496                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 497                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 498                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 499                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 500         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
 501             new String[]
 502             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 503                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 504                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 505             new String[]
 506             { "test/jalview/bin/argparser/testfiles/test1.stk",
 507                 "test/jalview/bin/argparser/testfiles/test2.stk",
 508                 "test/jalview/bin/argparser/testfiles/test3.stk",
 509                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 510                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 511                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 512                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 513                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 514                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 515         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
 516             new String[]
 517             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 518                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 519                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 520             new String[]
 521             { "test/jalview/bin/argparser/testfiles/test1.stk",
 522                 "test/jalview/bin/argparser/testfiles/test2.stk",
 523                 "test/jalview/bin/argparser/testfiles/test3.stk",
 524                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 525                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 526                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 527                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 528                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 529                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 530         { "--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",
 531             new String[]
 532             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 533                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 534                 "test/jalview/bin/argparser/testfiles/dir2/test1.aln",
 535                 "test/jalview/bin/argparser/testfiles/dir2/test2.aln",
 536                 "test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
 537             new String[]
 538             { "test/jalview/bin/argparser/testfiles/test1.stk",
 539                 "test/jalview/bin/argparser/testfiles/test2.stk",
 540                 "test/jalview/bin/argparser/testfiles/test3.stk",
 541                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 542                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 543                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 544                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 545                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 546                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 547                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
 548                 "test/jalview/bin/argparser/testfiles/test1.aln",
 549                 "test/jalview/bin/argparser/testfiles/test2.aln",
 550                 "test/jalview/bin/argparser/testfiles/test3.aln",
 551                 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 552                 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 553                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 554                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 555                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 556                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
 557         // --mkdirs
 558         { "--headless --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output "
 559                 + deleteDir
 560                 + "/{dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output="
 561                 + deleteDir
 562                 + "/{dirname}/{basename}.aln --close --all --mkdirs",
 563             new String[]
 564             { deleteDir
 565                     + "/test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 566                 deleteDir
 567                         + "/test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 568                 deleteDir
 569                         + "/test/jalview/bin/argparser/testfiles/dir2/test1.aln",
 570                 deleteDir
 571                         + "/test/jalview/bin/argparser/testfiles/dir2/test2.aln",
 572                 deleteDir
 573                         + "/test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
 574             new String[]
 575             { "test/jalview/bin/argparser/testfiles/test1.stk",
 576                 "test/jalview/bin/argparser/testfiles/test2.stk",
 577                 "test/jalview/bin/argparser/testfiles/test3.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",
 585                 "test/jalview/bin/argparser/testfiles/test1.aln",
 586                 "test/jalview/bin/argparser/testfiles/test2.aln",
 587                 "test/jalview/bin/argparser/testfiles/test3.aln",
 588                 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 589                 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 590                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 591                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 592                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 593                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln",
 594                 deleteDir
 595                         + "test/jalview/bin/argparser/testfiles/test1.stk",
 596                 deleteDir
 597                         + "test/jalview/bin/argparser/testfiles/test2.stk",
 598                 deleteDir
 599                         + "test/jalview/bin/argparser/testfiles/test3.stk",
 600                 deleteDir
 601                         + "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 602                 deleteDir
 603                         + "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 604                 deleteDir
 605                         + "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 606                 deleteDir
 607                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 608                 deleteDir
 609                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 610                 deleteDir
 611                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 612                 deleteDir
 613                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
 614                 deleteDir
 615                         + "test/jalview/bin/argparser/testfiles/test1.aln",
 616                 deleteDir
 617                         + "test/jalview/bin/argparser/testfiles/test2.aln",
 618                 deleteDir
 619                         + "test/jalview/bin/argparser/testfiles/test3.aln",
 620                 deleteDir
 621                         + "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 622                 deleteDir
 623                         + "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 624                 deleteDir
 625                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 626                 deleteDir
 627                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 628                 deleteDir
 629                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 630                 deleteDir
 631                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
 632         //
 633     };
 634   }
 635
 636 }