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