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         /*
 290                 */
 291         //
 292     };
 293
 294   }
 295
 296   @DataProvider(name = "argfileOutputFiles")
 297   public Object[][] argfileOutputFiles()
 298   {
 299     return new Object[][] {
 300         //
 301         { "--gui --argfile=" + testfiles + "/**/*.txt", new String[]
 302         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
 303             testfiles + "/dir3/subdir/test0.png" } },
 304         { "--gui --argfile=" + testfiles + "/**/argfile.txt", new String[]
 305         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
 306         { "--gui --argfile=" + testfiles + "/dir*/argfile.txt", new String[]
 307         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
 308         { "--gui --initsubstitutions --append examples/uniref50.fa --image "
 309                 + testfiles + "/{basename}.png",
 310             new String[]
 311             { testfiles + "/uniref50.png" } },
 312         { "--gui --append examples/uniref50.fa --nosubstitutions --image "
 313                 + testfiles + "/{basename}.png",
 314             new String[]
 315             { testfiles + "/{basename}.png" } }
 316         //
 317     };
 318
 319   }
 320
 321   @DataProvider(name = "cmdLines")
 322   public Object[][] cmdLines()
 323   {
 324     String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN",
 325         "FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" };
 326     String[] t1 = new String[] { "TEST1" };
 327     String[] t2 = new String[] { "TEST2" };
 328     String[] t3 = new String[] { "TEST3" };
 329     return new Object[][] {
 330         /*
 331         */
 332         { "--append=examples/uniref50.fa", true, 1, someUniref50Seqs },
 333         { "--append examples/uniref50.fa", true, 1, someUniref50Seqs },
 334         { "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs },
 335         // NOTE we cannot use shell expansion in tests, so list all files!
 336         { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
 337             someUniref50Seqs },
 338         { "--append=[new]examples/uniref50*.fa", true, 2,
 339             someUniref50Seqs },
 340         { "--open=examples/uniref50*.fa", true, 2, someUniref50Seqs },
 341         { "examples/uniref50.fa", true, 1, someUniref50Seqs },
 342         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
 343             ArrayUtils.concatArrays(someUniref50Seqs, t1) },
 344         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
 345         { "--gui --argfile=" + testfiles + "/argfile0.txt", true, 1,
 346             ArrayUtils.concatArrays(t1, t3) },
 347         { "--gui --argfile=" + testfiles + "/argfile*.txt", true, 5,
 348             ArrayUtils.concatArrays(t1, t2, t3) },
 349         { "--gui --argfile=" + testfiles + "/argfile.autocounter", true, 3,
 350             ArrayUtils.concatArrays(t1, t2) } };
 351
 352   }
 353
 354   public static boolean lookForSequenceName(String sequenceName)
 355   {
 356     AlignFrame[] afs = Desktop.getDesktopAlignFrames();
 357     for (AlignFrame af : afs)
 358     {
 359       for (String name : af.getViewport().getAlignment().getSequenceNames())
 360       {
 361         if (sequenceName.equals(name))
 362         {
 363           return true;
 364         }
 365       }
 366     }
 367     return false;
 368   }
 369
 370   public static void cleanupFiles(String[] filenames)
 371   {
 372     for (String filename : filenames)
 373     {
 374       File file = new File(filename);
 375       if (file.exists())
 376       {
 377         file.delete();
 378       }
 379     }
 380   }
 381
 382   private final String deleteDir = "test/deleteAfter";
 383
 384   @Test(
 385     groups = "Functional",
 386     dataProvider = "allLinkedIdsData",
 387     singleThreaded = true)
 388   public void allLinkedIdsTest(String cmdLine, String[] filenames,
 389           String[] nonfilenames)
 390   {
 391     String[] args = (cmdLine + " --gui").split("\\s+");
 392     callJalviewMain(args);
 393     Commands cmds = Jalview.getInstance().getCommands();
 394     Assert.assertNotNull(cmds);
 395     for (String filename : filenames)
 396     {
 397       Assert.assertTrue(new File(filename).exists(),
 398               "File '" + filename + "' was not created");
 399     }
 400     cleanupFiles(filenames);
 401     if (nonfilenames != null)
 402     {
 403       for (String nonfilename : nonfilenames)
 404       {
 405         File nonfile = new File(nonfilename);
 406         Assert.assertFalse(nonfile.exists(),
 407                 "File " + nonfilename + " exists when it shouldn't!");
 408       }
 409     }
 410
 411     File deleteDirF = new File(deleteDir);
 412     if (deleteDirF.exists())
 413     {
 414       deleteDirF.delete();
 415     }
 416   }
 417
 418   @DataProvider(name = "allLinkedIdsData")
 419   public Object[][] allLinkedIdsData()
 420   {
 421     return new Object[][] {
 422         //
 423         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
 424             new String[]
 425             { "test/jalview/bin/argparser/testfiles/test1.stk",
 426                 "test/jalview/bin/argparser/testfiles/test2.stk",
 427                 "test/jalview/bin/argparser/testfiles/test3.stk", },
 428             null },
 429         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
 430             new String[]
 431             { "test/jalview/bin/argparser/testfiles/test1.png",
 432                 "test/jalview/bin/argparser/testfiles/test2.png",
 433                 "test/jalview/bin/argparser/testfiles/test3.png", },
 434             null },
 435         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
 436             new String[]
 437             { "test/jalview/bin/argparser/testfiles/test1.stk",
 438                 "test/jalview/bin/argparser/testfiles/test2.stk",
 439                 "test/jalview/bin/argparser/testfiles/test3.stk", },
 440             new String[]
 441             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 442                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 443                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 444                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 445                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 446                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 447                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 448                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 449                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 450         { "--gui --open=test/jalview/bin/argparser/**/*.fa --all --output={dirname}/{basename}.stk --close",
 451             new String[]
 452             { "test/jalview/bin/argparser/testfiles/test1.stk",
 453                 "test/jalview/bin/argparser/testfiles/test2.stk",
 454                 "test/jalview/bin/argparser/testfiles/test3.stk",
 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             null },
 465         { "--gui --open=test/jalview/bin/argparser/**/*.fa --output=*/*.stk --close",
 466             new String[]
 467             { "test/jalview/bin/argparser/testfiles/test1.stk",
 468                 "test/jalview/bin/argparser/testfiles/test2.stk",
 469                 "test/jalview/bin/argparser/testfiles/test3.stk",
 470                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 471                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 472                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 473                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 474                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 475                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 476                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 477                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 478                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
 479             null },
 480         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --all --output=*/*.stk --close",
 481             new String[]
 482             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 483                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 484                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 485                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 486                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 487             new String[]
 488             { "test/jalview/bin/argparser/testfiles/test1.stk",
 489                 "test/jalview/bin/argparser/testfiles/test2.stk",
 490                 "test/jalview/bin/argparser/testfiles/test3.stk",
 491                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 492                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 493                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 494                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 495         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*/*.stk --close",
 496             new String[]
 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={dirname}/{basename}.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/dir1/test1.stk",
 518                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 519                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 520                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 521                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 522                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 523         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
 524             new String[]
 525             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 526                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 527                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 528             new String[]
 529             { "test/jalview/bin/argparser/testfiles/test1.stk",
 530                 "test/jalview/bin/argparser/testfiles/test2.stk",
 531                 "test/jalview/bin/argparser/testfiles/test3.stk",
 532                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 533                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 534                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 535                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 536                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 537                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 538         { "--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",
 539             new String[]
 540             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 541                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 542                 "test/jalview/bin/argparser/testfiles/dir2/test1.aln",
 543                 "test/jalview/bin/argparser/testfiles/dir2/test2.aln",
 544                 "test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
 545             new String[]
 546             { "test/jalview/bin/argparser/testfiles/test1.stk",
 547                 "test/jalview/bin/argparser/testfiles/test2.stk",
 548                 "test/jalview/bin/argparser/testfiles/test3.stk",
 549                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 550                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 551                 "test/jalview/bin/argparser/testfiles/dir2/test3.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                 "test/jalview/bin/argparser/testfiles/test1.aln",
 557                 "test/jalview/bin/argparser/testfiles/test2.aln",
 558                 "test/jalview/bin/argparser/testfiles/test3.aln",
 559                 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 560                 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 561                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 562                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 563                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 564                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
 565         // --mkdirs
 566         { "--headless --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output "
 567                 + deleteDir
 568                 + "/{dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output="
 569                 + deleteDir
 570                 + "/{dirname}/{basename}.aln --close --all --mkdirs",
 571             new String[]
 572             { deleteDir
 573                     + "/test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 574                 deleteDir
 575                         + "/test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 576                 deleteDir
 577                         + "/test/jalview/bin/argparser/testfiles/dir2/test1.aln",
 578                 deleteDir
 579                         + "/test/jalview/bin/argparser/testfiles/dir2/test2.aln",
 580                 deleteDir
 581                         + "/test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
 582             new String[]
 583             { "test/jalview/bin/argparser/testfiles/test1.stk",
 584                 "test/jalview/bin/argparser/testfiles/test2.stk",
 585                 "test/jalview/bin/argparser/testfiles/test3.stk",
 586                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 587                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 588                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 589                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 590                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 591                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 592                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
 593                 "test/jalview/bin/argparser/testfiles/test1.aln",
 594                 "test/jalview/bin/argparser/testfiles/test2.aln",
 595                 "test/jalview/bin/argparser/testfiles/test3.aln",
 596                 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 597                 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 598                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 599                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 600                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 601                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln",
 602                 deleteDir
 603                         + "test/jalview/bin/argparser/testfiles/test1.stk",
 604                 deleteDir
 605                         + "test/jalview/bin/argparser/testfiles/test2.stk",
 606                 deleteDir
 607                         + "test/jalview/bin/argparser/testfiles/test3.stk",
 608                 deleteDir
 609                         + "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 610                 deleteDir
 611                         + "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 612                 deleteDir
 613                         + "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 614                 deleteDir
 615                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 616                 deleteDir
 617                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 618                 deleteDir
 619                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 620                 deleteDir
 621                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
 622                 deleteDir
 623                         + "test/jalview/bin/argparser/testfiles/test1.aln",
 624                 deleteDir
 625                         + "test/jalview/bin/argparser/testfiles/test2.aln",
 626                 deleteDir
 627                         + "test/jalview/bin/argparser/testfiles/test3.aln",
 628                 deleteDir
 629                         + "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 630                 deleteDir
 631                         + "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 632                 deleteDir
 633                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 634                 deleteDir
 635                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 636                 deleteDir
 637                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 638                 deleteDir
 639                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
 640         //
 641     };
 642   }
 643
 644 }