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", singleThreaded = true)
 120
 121   public void commandsOpenTest(String cmdLine, boolean cmdArgs,
 122           int numFrames, String[] sequences)
 123   {
 124     try
 125     {
 126       String[] args = (cmdLine + " --gui").split("\\s+");
 127       callJalviewMain(args);
 128       Commands cmds = Jalview.getInstance().getCommands();
 129       Assert.assertNotNull(cmds);
 130       Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs,
 131               "Commands were not provided in the args");
 132       Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
 133               "Overall command parse and operation is false");
 134
 135       Assert.assertEquals(Desktop.getDesktopAlignFrames().length, numFrames,
 136               "Wrong number of AlignFrames");
 137
 138       if (sequences != null)
 139       {
 140         Set<String> openedSequenceNames = new HashSet<>();
 141         AlignFrame[] afs = Desktop.getDesktopAlignFrames();
 142         for (AlignFrame af : afs)
 143         {
 144           openedSequenceNames.addAll(
 145                   af.getViewport().getAlignment().getSequenceNames());
 146         }
 147         for (String sequence : sequences)
 148         {
 149           Assert.assertTrue(openedSequenceNames.contains(sequence),
 150                   "Sequence '" + sequence
 151                           + "' was not found in opened alignment files: "
 152                           + cmdLine + ".\nOpened sequence names are:\n"
 153                           + String.join("\n", openedSequenceNames));
 154         }
 155       }
 156
 157       Assert.assertFalse(
 158               lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
 159     } catch (Exception x)
 160     {
 161       Assert.fail("Unexpected exception during commandsOpenTest", x);
 162     } finally
 163     {
 164       tearDown();
 165
 166     }
 167   }
 168
 169   @Test(
 170     groups =
 171     { "Functional", "testTask3" },
 172     dataProvider = "structureImageOutputFiles",    singleThreaded = true)
 173   public void structureImageOutputTest(String cmdLine, String[] filenames)
 174           throws IOException
 175   {
 176     cleanupFiles(filenames);
 177     String[] args = (cmdLine + " --gui").split("\\s+");
 178     try
 179     {
 180       callJalviewMain(args);
 181       Commands cmds = Jalview.getInstance().getCommands();
 182       Assert.assertNotNull(cmds);
 183       File lastFile = null;
 184       for (String filename : filenames)
 185       {
 186         File file = new File(filename);
 187         Assert.assertTrue(file.exists(), "File '" + filename
 188                 + "' was not created by '" + cmdLine + "'");
 189         Assert.assertTrue(file.isFile(), "File '" + filename
 190                 + "' is not a file from '" + cmdLine + "'");
 191         Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
 192                 + "' has no content from '" + cmdLine + "'");
 193         // make sure the successive output files get bigger!
 194         if (lastFile != null)
 195         {
 196           waitForLastWrite(file,25);
 197
 198           if (Files.size(file.toPath()) > Files
 199                   .size(lastFile.toPath()))
 200           Assert.assertTrue(Files.size(file.toPath()) > Files
 201                   .size(lastFile.toPath()));
 202         }
 203         // remember it for next file
 204         lastFile = file;
 205       }
 206     } catch (Exception x)
 207     {
 208       Assert.fail("Unexpected exception during structureImageOutputTest",
 209               x);
 210     } finally
 211     {
 212       cleanupFiles(filenames);
 213       tearDown();
 214     }
 215   }
 216
 217   private static long waitForLastWrite(File file, int i) throws IOException
 218   {
 219     long lastSize,stableSize =Files.size(file.toPath());
 220     // wait around until we are sure the file has been completely written.
 221     do {
 222       lastSize = stableSize;
 223       try {
 224         Thread.sleep(i);
 225       } catch (Exception x) {}
 226       stableSize=Files.size(file.toPath());
 227     } while (stableSize!=lastSize);
 228     return stableSize;
 229   }
 230
 231   @Test(groups = "Functional", dataProvider = "argfileOutputFiles", singleThreaded = true)
 232
 233   public void argFilesGlobAndSubstitutionsTest(String cmdLine,
 234           String[] filenames) throws IOException
 235   {
 236     cleanupFiles(filenames);
 237     String[] args = (cmdLine + " --gui").split("\\s+");
 238     try
 239     {
 240       callJalviewMain(args);
 241       Commands cmds = Jalview.getInstance().getCommands();
 242       Assert.assertNotNull(cmds);
 243       File lastFile = null;
 244       for (String filename : filenames)
 245       {
 246         File file = new File(filename);
 247         Assert.assertTrue(file.exists(), "File '" + filename
 248                 + "' was not created by '" + cmdLine + "'");
 249         Assert.assertTrue(file.isFile(), "File '" + filename
 250                 + "' is not a file from '" + cmdLine + "'");
 251         Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
 252                 + "' has no content from '" + cmdLine + "'");
 253         // make sure the successive output files get bigger!
 254         if (lastFile != null) {
 255           Assert.assertTrue(Files.size(file.toPath()) > Files
 256                   .size(lastFile.toPath()));
 257           System.out.println("this file: "+file+" +"+Files.size(file.toPath()) + " greater than " +Files.size(lastFile.toPath()));
 258         }
 259         // remember it for next file
 260         lastFile = file;
 261       }
 262     } catch (Exception x)
 263     {
 264       Assert.fail(
 265               "Unexpected exception during argFilesGlobAndSubstitutions",
 266               x);
 267     } finally
 268     {
 269       cleanupFiles(filenames);
 270       tearDown();
 271     }
 272   }
 273
 274   @DataProvider(name = "structureImageOutputFiles")
 275   public Object[][] structureImageOutputFiles()
 276   {
 277     return new Object[][] {
 278         //
 279         { "--gui --nonews --nosplash --open=./examples/test_fab41.result/sample.a2m "
 280                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 281                 + "--structureimage=" + testfiles + "/structureimage1.png "
 282                 + "--open=./examples/test_fab41.result/sample.a2m "
 283                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 284                 + "--structureimage=" + testfiles
 285                 + "/structureimage2.png --scale=1.5 "
 286                 + "--open=./examples/test_fab41.result/sample.a2m "
 287                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 288                 + "--structureimage=" + testfiles
 289                 + "/structureimage3.png --scale=2.0 ",
 290             new String[]
 291             { testfiles + "/structureimage1.png",
 292                 testfiles + "/structureimage2.png",
 293                 testfiles + "/structureimage3.png" } },
 294         { "--headless --noquit --open=./examples/test_fab41.result/sample.a2m "
 295                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 296                 + "--structureimage=" + testfiles + "/structureimage1.png "
 297                 + "--open=./examples/test_fab41.result/sample.a2m "
 298                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 299                 + "--structureimage=" + testfiles
 300                 + "/structureimage2.png --scale=1.5 "
 301                 + "--open=./examples/test_fab41.result/sample.a2m "
 302                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 303                 + "--structureimage=" + testfiles
 304                 + "/structureimage3.png --scale=2.0 ",
 305             new String[]
 306             { testfiles + "/structureimage1.png",
 307                 testfiles + "/structureimage2.png",
 308                 testfiles + "/structureimage3.png" } },
 309         { "--gui --nonews --nosplash --open examples/1gaq.txt --append ./examples/3W5V.pdb "+"--structure examples/1gaq.txt --seqid \"1GAQ|A\" "+"--structureimage "+testfiles+"/1gaq.png --structure examples/3W5V.pdb "+"--seqid \"3W5V|A\" --structureimage "+testfiles+"/3w5v.png --overwrite",
 310
 311                 new String[] {
 312                                 testfiles+"/1gaq.png",testfiles+"/3w5v.png"
 313                 }
 314         },
 315         { "--headless --noquit --open ./examples/1gaq.txt --append ./examples/3W5V.pdb "+"--structure examples/1gaq.txt --seqid \"1GAQ|A\" "+"--structureimage "+testfiles+"/1gaq.png --structure examples/3W5V.pdb "+"--seqid \"3W5V|A\" --structureimage "+testfiles+"/3w5v.png --overwrite",
 316
 317             new String[] {
 318                         testfiles+"/1gaq.png",testfiles+"/3w5v.png"
 319             }
 320     }
 321
 322         /*
 323                 */
 324         //
 325     };
 326
 327   }
 328
 329   @DataProvider(name = "argfileOutputFiles")
 330   public Object[][] argfileOutputFiles()
 331   {
 332     return new Object[][] {
 333         //
 334         { "--gui --argfile=" + testfiles + "/**/*.txt", new String[]
 335         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
 336             testfiles + "/dir3/subdir/test0.png" } },
 337         { "--gui --argfile=" + testfiles + "/**/argfile.txt", new String[]
 338         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
 339         { "--gui --argfile=" + testfiles + "/dir*/argfile.txt", new String[]
 340         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
 341         { "--gui --initsubstitutions --append examples/uniref50.fa --image "
 342                 + testfiles + "/{basename}.png",
 343             new String[]
 344             { testfiles + "/uniref50.png" } },
 345         { "--gui --append examples/uniref50.fa --nosubstitutions --image "
 346                 + testfiles + "/{basename}.png",
 347             new String[]
 348             { testfiles + "/{basename}.png" } }
 349         //
 350     };
 351
 352   }
 353
 354   @DataProvider(name = "cmdLines")
 355   public Object[][] cmdLines()
 356   {
 357     String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN",
 358         "FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" };
 359     String[] t1 = new String[] { "TEST1" };
 360     String[] t2 = new String[] { "TEST2" };
 361     String[] t3 = new String[] { "TEST3" };
 362     return new Object[][] {
 363         /*
 364         */
 365         { "--append=examples/uniref50.fa", true, 1, someUniref50Seqs },
 366         { "--append examples/uniref50.fa", true, 1, someUniref50Seqs },
 367         { "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs },
 368         // NOTE we cannot use shell expansion in tests, so list all files!
 369         { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
 370             someUniref50Seqs },
 371         { "--append=[new]examples/uniref50*.fa", true, 2,
 372             someUniref50Seqs },
 373         { "--open=examples/uniref50*.fa", true, 2, someUniref50Seqs },
 374         { "examples/uniref50.fa", true, 1, someUniref50Seqs },
 375         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
 376             ArrayUtils.concatArrays(someUniref50Seqs, t1) },
 377         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
 378         { "--gui --argfile=" + testfiles + "/argfile0.txt", true, 1,
 379             ArrayUtils.concatArrays(t1, t3) },
 380         { "--gui --argfile=" + testfiles + "/argfile*.txt", true, 5,
 381             ArrayUtils.concatArrays(t1, t2, t3) },
 382         { "--gui --argfile=" + testfiles + "/argfile.autocounter", true, 3,
 383             ArrayUtils.concatArrays(t1, t2) } };
 384
 385   }
 386
 387   public static boolean lookForSequenceName(String sequenceName)
 388   {
 389     AlignFrame[] afs = Desktop.getDesktopAlignFrames();
 390     for (AlignFrame af : afs)
 391     {
 392       for (String name : af.getViewport().getAlignment().getSequenceNames())
 393       {
 394         if (sequenceName.equals(name))
 395         {
 396           return true;
 397         }
 398       }
 399     }
 400     return false;
 401   }
 402
 403   public static void cleanupFiles(String[] filenames)
 404   {
 405     for (String filename : filenames)
 406     {
 407       File file = new File(filename);
 408       if (file.exists())
 409       {
 410         file.delete();
 411       }
 412     }
 413   }
 414
 415   private final String deleteDir = "test/deleteAfter";
 416
 417   @Test(
 418     groups = "Functional",
 419     dataProvider = "allLinkedIdsData",
 420     singleThreaded = true)
 421   public void allLinkedIdsTest(String cmdLine, String[] filenames,
 422           String[] nonfilenames)
 423   {
 424     String[] args = (cmdLine + " --gui").split("\\s+");
 425     callJalviewMain(args);
 426     Commands cmds = Jalview.getInstance().getCommands();
 427     Assert.assertNotNull(cmds);
 428     for (String filename : filenames)
 429     {
 430       Assert.assertTrue(new File(filename).exists(),
 431               "File '" + filename + "' was not created");
 432     }
 433     cleanupFiles(filenames);
 434     if (nonfilenames != null)
 435     {
 436       for (String nonfilename : nonfilenames)
 437       {
 438         File nonfile = new File(nonfilename);
 439         Assert.assertFalse(nonfile.exists(),
 440                 "File " + nonfilename + " exists when it shouldn't!");
 441       }
 442     }
 443
 444     File deleteDirF = new File(deleteDir);
 445     if (deleteDirF.exists())
 446     {
 447       deleteDirF.delete();
 448     }
 449   }
 450
 451   @DataProvider(name = "allLinkedIdsData")
 452   public Object[][] allLinkedIdsData()
 453   {
 454     return new Object[][] {
 455         //
 456         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
 457             new String[]
 458             { "test/jalview/bin/argparser/testfiles/test1.stk",
 459                 "test/jalview/bin/argparser/testfiles/test2.stk",
 460                 "test/jalview/bin/argparser/testfiles/test3.stk", },
 461             null },
 462         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
 463             new String[]
 464             { "test/jalview/bin/argparser/testfiles/test1.png",
 465                 "test/jalview/bin/argparser/testfiles/test2.png",
 466                 "test/jalview/bin/argparser/testfiles/test3.png", },
 467             null },
 468         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
 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             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                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 480                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 481                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 482                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 483         { "--gui --open=test/jalview/bin/argparser/**/*.fa --all --output={dirname}/{basename}.stk --close",
 484             new String[]
 485             { "test/jalview/bin/argparser/testfiles/test1.stk",
 486                 "test/jalview/bin/argparser/testfiles/test2.stk",
 487                 "test/jalview/bin/argparser/testfiles/test3.stk",
 488                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 489                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 490                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 491                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 492                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 493                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 494                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 495                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 496                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
 497             null },
 498         { "--gui --open=test/jalview/bin/argparser/**/*.fa --output=*/*.stk --close",
 499             new String[]
 500             { "test/jalview/bin/argparser/testfiles/test1.stk",
 501                 "test/jalview/bin/argparser/testfiles/test2.stk",
 502                 "test/jalview/bin/argparser/testfiles/test3.stk",
 503                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 504                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 505                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 506                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 507                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 508                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 509                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 510                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 511                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
 512             null },
 513         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --all --output=*/*.stk --close",
 514             new String[]
 515             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 516                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 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/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         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*/*.stk --close",
 529             new String[]
 530             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 531                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 532                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 533             new String[]
 534             { "test/jalview/bin/argparser/testfiles/test1.stk",
 535                 "test/jalview/bin/argparser/testfiles/test2.stk",
 536                 "test/jalview/bin/argparser/testfiles/test3.stk",
 537                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 538                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 539                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 540                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 541         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
 542             new String[]
 543             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 544                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 545                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 546             new String[]
 547             { "test/jalview/bin/argparser/testfiles/test1.stk",
 548                 "test/jalview/bin/argparser/testfiles/test2.stk",
 549                 "test/jalview/bin/argparser/testfiles/test3.stk",
 550                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 551                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 552                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 553                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 554                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 555                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 556         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
 557             new String[]
 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             new String[]
 562             { "test/jalview/bin/argparser/testfiles/test1.stk",
 563                 "test/jalview/bin/argparser/testfiles/test2.stk",
 564                 "test/jalview/bin/argparser/testfiles/test3.stk",
 565                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 566                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 567                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 568                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 569                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 570                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 571         { "--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",
 572             new String[]
 573             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 574                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 575                 "test/jalview/bin/argparser/testfiles/dir2/test1.aln",
 576                 "test/jalview/bin/argparser/testfiles/dir2/test2.aln",
 577                 "test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
 578             new String[]
 579             { "test/jalview/bin/argparser/testfiles/test1.stk",
 580                 "test/jalview/bin/argparser/testfiles/test2.stk",
 581                 "test/jalview/bin/argparser/testfiles/test3.stk",
 582                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 583                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 584                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 585                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 586                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 587                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 588                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
 589                 "test/jalview/bin/argparser/testfiles/test1.aln",
 590                 "test/jalview/bin/argparser/testfiles/test2.aln",
 591                 "test/jalview/bin/argparser/testfiles/test3.aln",
 592                 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 593                 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 594                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 595                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 596                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 597                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
 598         // --mkdirs
 599         { "--headless --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output "
 600                 + deleteDir
 601                 + "/{dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output="
 602                 + deleteDir
 603                 + "/{dirname}/{basename}.aln --close --all --mkdirs",
 604             new String[]
 605             { deleteDir
 606                     + "/test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 607                 deleteDir
 608                         + "/test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 609                 deleteDir
 610                         + "/test/jalview/bin/argparser/testfiles/dir2/test1.aln",
 611                 deleteDir
 612                         + "/test/jalview/bin/argparser/testfiles/dir2/test2.aln",
 613                 deleteDir
 614                         + "/test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
 615             new String[]
 616             { "test/jalview/bin/argparser/testfiles/test1.stk",
 617                 "test/jalview/bin/argparser/testfiles/test2.stk",
 618                 "test/jalview/bin/argparser/testfiles/test3.stk",
 619                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 620                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 621                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 622                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 623                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 624                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 625                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
 626                 "test/jalview/bin/argparser/testfiles/test1.aln",
 627                 "test/jalview/bin/argparser/testfiles/test2.aln",
 628                 "test/jalview/bin/argparser/testfiles/test3.aln",
 629                 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 630                 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 631                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 632                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 633                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 634                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln",
 635                 deleteDir
 636                         + "test/jalview/bin/argparser/testfiles/test1.stk",
 637                 deleteDir
 638                         + "test/jalview/bin/argparser/testfiles/test2.stk",
 639                 deleteDir
 640                         + "test/jalview/bin/argparser/testfiles/test3.stk",
 641                 deleteDir
 642                         + "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 643                 deleteDir
 644                         + "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 645                 deleteDir
 646                         + "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 647                 deleteDir
 648                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 649                 deleteDir
 650                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 651                 deleteDir
 652                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 653                 deleteDir
 654                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
 655                 deleteDir
 656                         + "test/jalview/bin/argparser/testfiles/test1.aln",
 657                 deleteDir
 658                         + "test/jalview/bin/argparser/testfiles/test2.aln",
 659                 deleteDir
 660                         + "test/jalview/bin/argparser/testfiles/test3.aln",
 661                 deleteDir
 662                         + "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 663                 deleteDir
 664                         + "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 665                 deleteDir
 666                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 667                 deleteDir
 668                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 669                 deleteDir
 670                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 671                 deleteDir
 672                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
 673         //
 674     };
 675   }
 676
 677 }