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                         Assert.assertTrue(Files.size(file.toPath()) > Files.size(lastFile.toPath()));
 196                         System.out.println("this file: " + file + " +" + Files.size(file.toPath()) + " greater than "
 197                                         + Files.size(lastFile.toPath()));
 198                 }
 199                 // remember it for next file
 200                 lastFile = file;
 201       }
 202     } catch (Exception x)
 203     {
 204       Assert.fail("Unexpected exception during structureImageOutputTest",
 205               x);
 206     } finally
 207     {
 208       cleanupFiles(filenames);
 209       tearDown();
 210     }
 211   }
 212
 213   @Test(groups = "Functional", dataProvider = "argfileOutputFiles", singleThreaded = true)
 214   public void argFilesGlobAndSubstitutionsTest(String cmdLine,
 215           String[] filenames) throws IOException
 216   {
 217     cleanupFiles(filenames);
 218     String[] args = (cmdLine + " --gui").split("\\s+");
 219     try
 220     {
 221       callJalviewMain(args);
 222       Commands cmds = Jalview.getInstance().getCommands();
 223       Assert.assertNotNull(cmds);
 224       File lastFile = null;
 225       for (String filename : filenames)
 226       {
 227         File file = new File(filename);
 228         Assert.assertTrue(file.exists(), "File '" + filename
 229                 + "' was not created by '" + cmdLine + "'");
 230         Assert.assertTrue(file.isFile(), "File '" + filename
 231                 + "' is not a file from '" + cmdLine + "'");
 232         Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
 233                 + "' has no content from '" + cmdLine + "'");
 234         // make sure the successive output files get bigger!
 235         if (lastFile != null) {
 236           Assert.assertTrue(Files.size(file.toPath()) > Files
 237                   .size(lastFile.toPath()));
 238           System.out.println("this file: "+file+" +"+Files.size(file.toPath()) + " greater than " +Files.size(lastFile.toPath()));
 239         }
 240         // remember it for next file
 241         lastFile = file;
 242       }
 243     } catch (Exception x)
 244     {
 245       Assert.fail(
 246               "Unexpected exception during argFilesGlobAndSubstitutions",
 247               x);
 248     } finally
 249     {
 250       cleanupFiles(filenames);
 251       tearDown();
 252     }
 253   }
 254
 255   @DataProvider(name = "structureImageOutputFiles")
 256   public Object[][] structureImageOutputFiles()
 257   {
 258     return new Object[][] {
 259         //
 260         { "--gui --nonews --nosplash --open=./examples/test_fab41.result/sample.a2m "
 261                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 262                 + "--structureimage=" + testfiles + "/structureimage1.png "
 263                 + "--open=./examples/test_fab41.result/sample.a2m "
 264                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 265                 + "--structureimage=" + testfiles
 266                 + "/structureimage2.png --scale=1.5 "
 267                 + "--open=./examples/test_fab41.result/sample.a2m "
 268                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 269                 + "--structureimage=" + testfiles
 270                 + "/structureimage3.png --scale=2.0 ",
 271             new String[]
 272             { testfiles + "/structureimage1.png",
 273                 testfiles + "/structureimage2.png",
 274                 testfiles + "/structureimage3.png" } },
 275         { "--headless --noquit --open=./examples/test_fab41.result/sample.a2m "
 276                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 277                 + "--structureimage=" + testfiles + "/structureimage1.png "
 278                 + "--open=./examples/test_fab41.result/sample.a2m "
 279                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 280                 + "--structureimage=" + testfiles
 281                 + "/structureimage2.png --scale=1.5 "
 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                 + "/structureimage3.png --scale=2.0 ",
 286             new String[]
 287             { testfiles + "/structureimage1.png",
 288                 testfiles + "/structureimage2.png",
 289                 testfiles + "/structureimage3.png" } },
 290         { "--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",
 291
 292                 new String[] {
 293                                 testfiles+"/1gaq.png",testfiles+"/3w5v.png"
 294                 }
 295         },
 296         { "--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",
 297
 298             new String[] {
 299                         testfiles+"/1gaq.png",testfiles+"/3w5v.png"
 300             }
 301     }
 302
 303         /*
 304                 */
 305         //
 306     };
 307
 308   }
 309
 310   @DataProvider(name = "argfileOutputFiles")
 311   public Object[][] argfileOutputFiles()
 312   {
 313     return new Object[][] {
 314         //
 315         { "--gui --argfile=" + testfiles + "/**/*.txt", new String[]
 316         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
 317             testfiles + "/dir3/subdir/test0.png" } },
 318         { "--gui --argfile=" + testfiles + "/**/argfile.txt", new String[]
 319         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
 320         { "--gui --argfile=" + testfiles + "/dir*/argfile.txt", new String[]
 321         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
 322         { "--gui --initsubstitutions --append examples/uniref50.fa --image "
 323                 + testfiles + "/{basename}.png",
 324             new String[]
 325             { testfiles + "/uniref50.png" } },
 326         { "--gui --append examples/uniref50.fa --nosubstitutions --image "
 327                 + testfiles + "/{basename}.png",
 328             new String[]
 329             { testfiles + "/{basename}.png" } }
 330         //
 331     };
 332
 333   }
 334
 335   @DataProvider(name = "cmdLines")
 336   public Object[][] cmdLines()
 337   {
 338     String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN",
 339         "FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" };
 340     String[] t1 = new String[] { "TEST1" };
 341     String[] t2 = new String[] { "TEST2" };
 342     String[] t3 = new String[] { "TEST3" };
 343     return new Object[][] {
 344         /*
 345         */
 346         { "--append=examples/uniref50.fa", true, 1, someUniref50Seqs },
 347         { "--append examples/uniref50.fa", true, 1, someUniref50Seqs },
 348         { "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs },
 349         // NOTE we cannot use shell expansion in tests, so list all files!
 350         { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
 351             someUniref50Seqs },
 352         { "--append=[new]examples/uniref50*.fa", true, 2,
 353             someUniref50Seqs },
 354         { "--open=examples/uniref50*.fa", true, 2, someUniref50Seqs },
 355         { "examples/uniref50.fa", true, 1, someUniref50Seqs },
 356         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
 357             ArrayUtils.concatArrays(someUniref50Seqs, t1) },
 358         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
 359         { "--gui --argfile=" + testfiles + "/argfile0.txt", true, 1,
 360             ArrayUtils.concatArrays(t1, t3) },
 361         { "--gui --argfile=" + testfiles + "/argfile*.txt", true, 5,
 362             ArrayUtils.concatArrays(t1, t2, t3) },
 363         { "--gui --argfile=" + testfiles + "/argfile.autocounter", true, 3,
 364             ArrayUtils.concatArrays(t1, t2) } };
 365
 366   }
 367
 368   public static boolean lookForSequenceName(String sequenceName)
 369   {
 370     AlignFrame[] afs = Desktop.getDesktopAlignFrames();
 371     for (AlignFrame af : afs)
 372     {
 373       for (String name : af.getViewport().getAlignment().getSequenceNames())
 374       {
 375         if (sequenceName.equals(name))
 376         {
 377           return true;
 378         }
 379       }
 380     }
 381     return false;
 382   }
 383
 384   public static void cleanupFiles(String[] filenames)
 385   {
 386     for (String filename : filenames)
 387     {
 388       File file = new File(filename);
 389       if (file.exists())
 390       {
 391         file.delete();
 392       }
 393     }
 394   }
 395
 396   private final String deleteDir = "test/deleteAfter";
 397
 398   @Test(
 399     groups = "Functional",
 400     dataProvider = "allLinkedIdsData",
 401     singleThreaded = true)
 402   public void allLinkedIdsTest(String cmdLine, String[] filenames,
 403           String[] nonfilenames)
 404   {
 405     String[] args = (cmdLine + " --gui").split("\\s+");
 406     callJalviewMain(args);
 407     Commands cmds = Jalview.getInstance().getCommands();
 408     Assert.assertNotNull(cmds);
 409     for (String filename : filenames)
 410     {
 411       Assert.assertTrue(new File(filename).exists(),
 412               "File '" + filename + "' was not created");
 413     }
 414     cleanupFiles(filenames);
 415     if (nonfilenames != null)
 416     {
 417       for (String nonfilename : nonfilenames)
 418       {
 419         File nonfile = new File(nonfilename);
 420         Assert.assertFalse(nonfile.exists(),
 421                 "File " + nonfilename + " exists when it shouldn't!");
 422       }
 423     }
 424
 425     File deleteDirF = new File(deleteDir);
 426     if (deleteDirF.exists())
 427     {
 428       deleteDirF.delete();
 429     }
 430   }
 431
 432   @DataProvider(name = "allLinkedIdsData")
 433   public Object[][] allLinkedIdsData()
 434   {
 435     return new Object[][] {
 436         //
 437         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.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             null },
 443         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
 444             new String[]
 445             { "test/jalview/bin/argparser/testfiles/test1.png",
 446                 "test/jalview/bin/argparser/testfiles/test2.png",
 447                 "test/jalview/bin/argparser/testfiles/test3.png", },
 448             null },
 449         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
 450             new String[]
 451             { "test/jalview/bin/argparser/testfiles/test1.stk",
 452                 "test/jalview/bin/argparser/testfiles/test2.stk",
 453                 "test/jalview/bin/argparser/testfiles/test3.stk", },
 454             new String[]
 455             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 456                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 457                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 458                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 459                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 460                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 461                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 462                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 463                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 464         { "--gui --open=test/jalview/bin/argparser/**/*.fa --all --output={dirname}/{basename}.stk --close",
 465             new String[]
 466             { "test/jalview/bin/argparser/testfiles/test1.stk",
 467                 "test/jalview/bin/argparser/testfiles/test2.stk",
 468                 "test/jalview/bin/argparser/testfiles/test3.stk",
 469                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 470                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 471                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 472                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 473                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 474                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 475                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 476                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 477                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
 478             null },
 479         { "--gui --open=test/jalview/bin/argparser/**/*.fa --output=*/*.stk --close",
 480             new String[]
 481             { "test/jalview/bin/argparser/testfiles/test1.stk",
 482                 "test/jalview/bin/argparser/testfiles/test2.stk",
 483                 "test/jalview/bin/argparser/testfiles/test3.stk",
 484                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 485                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 486                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 487                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 488                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 489                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 490                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 491                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 492                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
 493             null },
 494         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --all --output=*/*.stk --close",
 495             new String[]
 496             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 497                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 498                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 499                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 500                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 501             new String[]
 502             { "test/jalview/bin/argparser/testfiles/test1.stk",
 503                 "test/jalview/bin/argparser/testfiles/test2.stk",
 504                 "test/jalview/bin/argparser/testfiles/test3.stk",
 505                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 506                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 507                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 508                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 509         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*/*.stk --close",
 510             new String[]
 511             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 512                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 513                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 514             new String[]
 515             { "test/jalview/bin/argparser/testfiles/test1.stk",
 516                 "test/jalview/bin/argparser/testfiles/test2.stk",
 517                 "test/jalview/bin/argparser/testfiles/test3.stk",
 518                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 519                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 520                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 521                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 522         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
 523             new String[]
 524             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 525                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 526                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 527             new String[]
 528             { "test/jalview/bin/argparser/testfiles/test1.stk",
 529                 "test/jalview/bin/argparser/testfiles/test2.stk",
 530                 "test/jalview/bin/argparser/testfiles/test3.stk",
 531                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 532                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 533                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 534                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 535                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 536                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 537         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
 538             new String[]
 539             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 540                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 541                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 542             new String[]
 543             { "test/jalview/bin/argparser/testfiles/test1.stk",
 544                 "test/jalview/bin/argparser/testfiles/test2.stk",
 545                 "test/jalview/bin/argparser/testfiles/test3.stk",
 546                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 547                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 548                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 549                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 550                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 551                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 552         { "--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",
 553             new String[]
 554             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 555                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 556                 "test/jalview/bin/argparser/testfiles/dir2/test1.aln",
 557                 "test/jalview/bin/argparser/testfiles/dir2/test2.aln",
 558                 "test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
 559             new String[]
 560             { "test/jalview/bin/argparser/testfiles/test1.stk",
 561                 "test/jalview/bin/argparser/testfiles/test2.stk",
 562                 "test/jalview/bin/argparser/testfiles/test3.stk",
 563                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 564                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 565                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 566                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 567                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 568                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 569                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
 570                 "test/jalview/bin/argparser/testfiles/test1.aln",
 571                 "test/jalview/bin/argparser/testfiles/test2.aln",
 572                 "test/jalview/bin/argparser/testfiles/test3.aln",
 573                 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 574                 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 575                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 576                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 577                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 578                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
 579         // --mkdirs
 580         { "--headless --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output "
 581                 + deleteDir
 582                 + "/{dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output="
 583                 + deleteDir
 584                 + "/{dirname}/{basename}.aln --close --all --mkdirs",
 585             new String[]
 586             { deleteDir
 587                     + "/test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 588                 deleteDir
 589                         + "/test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 590                 deleteDir
 591                         + "/test/jalview/bin/argparser/testfiles/dir2/test1.aln",
 592                 deleteDir
 593                         + "/test/jalview/bin/argparser/testfiles/dir2/test2.aln",
 594                 deleteDir
 595                         + "/test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
 596             new String[]
 597             { "test/jalview/bin/argparser/testfiles/test1.stk",
 598                 "test/jalview/bin/argparser/testfiles/test2.stk",
 599                 "test/jalview/bin/argparser/testfiles/test3.stk",
 600                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 601                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 602                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 603                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 604                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 605                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 606                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
 607                 "test/jalview/bin/argparser/testfiles/test1.aln",
 608                 "test/jalview/bin/argparser/testfiles/test2.aln",
 609                 "test/jalview/bin/argparser/testfiles/test3.aln",
 610                 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 611                 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 612                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 613                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 614                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 615                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln",
 616                 deleteDir
 617                         + "test/jalview/bin/argparser/testfiles/test1.stk",
 618                 deleteDir
 619                         + "test/jalview/bin/argparser/testfiles/test2.stk",
 620                 deleteDir
 621                         + "test/jalview/bin/argparser/testfiles/test3.stk",
 622                 deleteDir
 623                         + "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 624                 deleteDir
 625                         + "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 626                 deleteDir
 627                         + "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 628                 deleteDir
 629                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 630                 deleteDir
 631                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 632                 deleteDir
 633                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 634                 deleteDir
 635                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
 636                 deleteDir
 637                         + "test/jalview/bin/argparser/testfiles/test1.aln",
 638                 deleteDir
 639                         + "test/jalview/bin/argparser/testfiles/test2.aln",
 640                 deleteDir
 641                         + "test/jalview/bin/argparser/testfiles/test3.aln",
 642                 deleteDir
 643                         + "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 644                 deleteDir
 645                         + "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 646                 deleteDir
 647                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 648                 deleteDir
 649                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 650                 deleteDir
 651                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 652                 deleteDir
 653                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
 654         //
 655     };
 656   }
 657
 658 }