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       verifyIncreasingSize(cmdLine, filenames);
 184     } catch (Exception x)
 185     {
 186       Assert.fail("Unexpected exception during structureImageOutputTest",
 187               x);
 188     } finally
 189     {
 190       cleanupFiles(filenames);
 191       tearDown();
 192     }
 193   }
 194
 195   /**
 196    * given two command lines, compare the output files produced - they should exist and be equal in size
 197    */
 198   @Test(
 199     groups =
 200     { "Functional", "testTask3" },
 201     dataProvider = "compareHeadlessAndGUIOps",
 202     singleThreaded = true)
 203   public void headlessOrGuiImageOutputTest(String[] cmdLines,
 204           String[] filenames) throws IOException
 205   {
 206     cleanupFiles(filenames);
 207     try
 208     {
 209       for (String cmdLine : cmdLines)
 210       {
 211         CommandLineOperations.Worker runner = CommandLineOperations.getJalviewDesktopRunner(false, cmdLine, 1000);
 212         long timeOut = 10000;
 213         while (runner.isAlive() && timeOut>0)
 214         {
 215           Thread.sleep(25);
 216           timeOut-=25;
 217         }
 218       }
 219       verifyOrderedFileSet(cmdLines[0] + " vs " + cmdLines[1], filenames,
 220               false);
 221     } catch (Exception x)
 222     {
 223       Assert.fail("Unexpected exception during structureImageOutputTest",
 224               x);
 225     } finally
 226     {
 227       cleanupFiles(filenames);
 228       tearDown();
 229     }
 230   }
 231   @DataProvider(name = "compareHeadlessAndGUIOps")
 232   public Object[][] compareHeadlessAndGUIOps()
 233   {
 234     return new Object[][] {
 235         new Object[]
 236         { new String[] { "--open examples/uniref50.fa "
 237                 + "--structure [seqid=FER1_SPIOL,tempfac=plddt,showssannotations,structureviewer=jmol]"
 238                 + "examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
 239                 + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json --image="
 240                 + testfiles + "test-al-pae-ss-gui.png --overwrite --gui --quit",
 241             "--open examples/uniref50.fa "
 242                     + "--structure [seqid=FER1_SPIOL,tempfac=plddt,showssannotations,structureviewer=jmol]"
 243                     + "examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
 244                     + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json --image="
 245                     + testfiles
 246                     + "test-al-pae-ss-nogui.png --overwrite --nogui"
 247
 248         }, new String[] {
 249             testfiles + "test-al-pae-ss-gui.png",
 250             testfiles
 251             + "test-al-pae-ss-nogui.png",
 252         } } };
 253   }
 254
 255   private static void verifyIncreasingSize(String cmdLine, String[] filenames) throws Exception
 256   {
 257     verifyOrderedFileSet(cmdLine, filenames, true);
 258   }
 259
 260   private static void verifyOrderedFileSet(String cmdLine, String[] filenames, boolean increasingSize) throws Exception
 261   {
 262     File lastFile = null;
 263     for (String filename : filenames)
 264     {
 265       File file = new File(filename);
 266       Assert.assertTrue(file.exists(), "File '" + filename
 267               + "' was not created by '" + cmdLine + "'");
 268       Assert.assertTrue(file.isFile(), "File '" + filename
 269               + "' is not a file from '" + cmdLine + "'");
 270       Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
 271               + "' has no content from '" + cmdLine + "'");
 272       // make sure the successive output files get bigger!
 273       if (lastFile != null)
 274       {
 275         waitForLastWrite(file,25);
 276
 277         if (increasingSize)
 278         { Assert.assertTrue(Files.size(file.toPath()) > Files
 279                 .size(lastFile.toPath()),"Expected " + file.toPath()+ " to be larger than "+lastFile.toPath());
 280         } else {
 281           Assert.assertEquals(Files.size(file.toPath()), Files
 282                 .size(lastFile.toPath()), "New file "+file.toPath()+" (actual size) not same as last file's size "+lastFile.toString());
 283         }
 284       }
 285       // remember it for next file
 286       lastFile = file;
 287     }
 288
 289   }
 290   private static long waitForLastWrite(File file, int i) throws IOException
 291   {
 292     long lastSize,stableSize =Files.size(file.toPath());
 293     // wait around until we are sure the file has been completely written.
 294     do {
 295       lastSize = stableSize;
 296       try {
 297         Thread.sleep(i);
 298       } catch (Exception x) {}
 299       stableSize=Files.size(file.toPath());
 300     } while (stableSize!=lastSize);
 301     return stableSize;
 302   }
 303
 304   @Test(groups = "Functional", dataProvider = "argfileOutputFiles", singleThreaded = true)
 305
 306   public void argFilesGlobAndSubstitutionsTest(String cmdLine,
 307           String[] filenames) throws IOException
 308   {
 309     cleanupFiles(filenames);
 310     String[] args = (cmdLine + " --gui").split("\\s+");
 311     try
 312     {
 313       callJalviewMain(args);
 314       Commands cmds = Jalview.getInstance().getCommands();
 315       Assert.assertNotNull(cmds);
 316       File lastFile = null;
 317       for (String filename : filenames)
 318       {
 319         File file = new File(filename);
 320         Assert.assertTrue(file.exists(), "File '" + filename
 321                 + "' was not created by '" + cmdLine + "'");
 322         Assert.assertTrue(file.isFile(), "File '" + filename
 323                 + "' is not a file from '" + cmdLine + "'");
 324         Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
 325                 + "' has no content from '" + cmdLine + "'");
 326         // make sure the successive output files get bigger!
 327         if (lastFile != null) {
 328           Assert.assertTrue(Files.size(file.toPath()) > Files
 329                   .size(lastFile.toPath()));
 330           System.out.println("this file: "+file+" +"+Files.size(file.toPath()) + " greater than " +Files.size(lastFile.toPath()));
 331         }
 332         // remember it for next file
 333         lastFile = file;
 334       }
 335     } catch (Exception x)
 336     {
 337       Assert.fail(
 338               "Unexpected exception during argFilesGlobAndSubstitutions",
 339               x);
 340     } finally
 341     {
 342       cleanupFiles(filenames);
 343       tearDown();
 344     }
 345   }
 346
 347   @DataProvider(name = "structureImageOutputFiles")
 348   public Object[][] structureImageOutputFiles()
 349   {
 350     return new Object[][] {
 351         //
 352         { "--gui --nonews --nosplash --open=./examples/test_fab41.result/sample.a2m "
 353                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 354                 + "--structureimage=" + testfiles + "/structureimage1.png "
 355                 + "--open=./examples/test_fab41.result/sample.a2m "
 356                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 357                 + "--structureimage=" + testfiles
 358                 + "/structureimage2.png --scale=1.5 "
 359                 + "--open=./examples/test_fab41.result/sample.a2m "
 360                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 361                 + "--structureimage=" + testfiles
 362                 + "/structureimage3.png --scale=2.0 ",
 363             new String[]
 364             { testfiles + "/structureimage1.png",
 365                 testfiles + "/structureimage2.png",
 366                 testfiles + "/structureimage3.png" } },
 367         { "--headless --noquit --open=./examples/test_fab41.result/sample.a2m "
 368                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 369                 + "--structureimage=" + testfiles + "/structureimage1.png "
 370                 + "--open=./examples/test_fab41.result/sample.a2m "
 371                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 372                 + "--structureimage=" + testfiles
 373                 + "/structureimage2.png --scale=1.5 "
 374                 + "--open=./examples/test_fab41.result/sample.a2m "
 375                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 376                 + "--structureimage=" + testfiles
 377                 + "/structureimage3.png --scale=2.0 ",
 378             new String[]
 379             { testfiles + "/structureimage1.png",
 380                 testfiles + "/structureimage2.png",
 381                 testfiles + "/structureimage3.png" } },
 382         { "--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",
 383
 384                 new String[] {
 385                                 testfiles+"/1gaq.png",testfiles+"/3w5v.png"
 386                 }
 387         },
 388         { "--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",
 389
 390             new String[] {
 391                         testfiles+"/1gaq.png",testfiles+"/3w5v.png"
 392             }
 393     }
 394
 395         /*
 396                 */
 397         //
 398     };
 399
 400   }
 401
 402   @DataProvider(name = "argfileOutputFiles")
 403   public Object[][] argfileOutputFiles()
 404   {
 405     return new Object[][] {
 406         //
 407         { "--gui --argfile=" + testfiles + "/**/*.txt", new String[]
 408         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
 409             testfiles + "/dir3/subdir/test0.png" } },
 410         { "--gui --argfile=" + testfiles + "/**/argfile.txt", new String[]
 411         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
 412         { "--gui --argfile=" + testfiles + "/dir*/argfile.txt", new String[]
 413         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
 414         { "--gui --initsubstitutions --append examples/uniref50.fa --image "
 415                 + testfiles + "/{basename}.png",
 416             new String[]
 417             { testfiles + "/uniref50.png" } },
 418         { "--gui --append examples/uniref50.fa --nosubstitutions --image "
 419                 + testfiles + "/{basename}.png",
 420             new String[]
 421             { testfiles + "/{basename}.png" } }
 422         //
 423     };
 424
 425   }
 426
 427   @DataProvider(name = "cmdLines")
 428   public Object[][] cmdLines()
 429   {
 430     String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN",
 431         "FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" };
 432     String[] t1 = new String[] { "TEST1" };
 433     String[] t2 = new String[] { "TEST2" };
 434     String[] t3 = new String[] { "TEST3" };
 435     return new Object[][] {
 436         /*
 437         */
 438         { "--append=examples/uniref50.fa", true, 1, someUniref50Seqs },
 439         { "--append examples/uniref50.fa", true, 1, someUniref50Seqs },
 440         { "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs },
 441         // NOTE we cannot use shell expansion in tests, so list all files!
 442         { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
 443             someUniref50Seqs },
 444         { "--append=[new]examples/uniref50*.fa", true, 2,
 445             someUniref50Seqs },
 446         { "--open=examples/uniref50*.fa", true, 2, someUniref50Seqs },
 447         { "examples/uniref50.fa", true, 1, someUniref50Seqs },
 448         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
 449             ArrayUtils.concatArrays(someUniref50Seqs, t1) },
 450         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
 451         { "--gui --argfile=" + testfiles + "/argfile0.txt", true, 1,
 452             ArrayUtils.concatArrays(t1, t3) },
 453         { "--gui --argfile=" + testfiles + "/argfile*.txt", true, 5,
 454             ArrayUtils.concatArrays(t1, t2, t3) },
 455         { "--gui --argfile=" + testfiles + "/argfile.autocounter", true, 3,
 456             ArrayUtils.concatArrays(t1, t2) } };
 457
 458   }
 459
 460   public static boolean lookForSequenceName(String sequenceName)
 461   {
 462     AlignFrame[] afs = Desktop.getDesktopAlignFrames();
 463     for (AlignFrame af : afs)
 464     {
 465       for (String name : af.getViewport().getAlignment().getSequenceNames())
 466       {
 467         if (sequenceName.equals(name))
 468         {
 469           return true;
 470         }
 471       }
 472     }
 473     return false;
 474   }
 475
 476   public static void cleanupFiles(String[] filenames)
 477   {
 478     for (String filename : filenames)
 479     {
 480       File file = new File(filename);
 481       if (file.exists())
 482       {
 483         file.delete();
 484       }
 485     }
 486   }
 487
 488   private final String deleteDir = "test/deleteAfter";
 489
 490   @Test(
 491     groups = "Functional",
 492     dataProvider = "allLinkedIdsData",
 493     singleThreaded = true)
 494   public void allLinkedIdsTest(String cmdLine, String[] filenames,
 495           String[] nonfilenames)
 496   {
 497     String[] args = (cmdLine + " --gui").split("\\s+");
 498     callJalviewMain(args);
 499     Commands cmds = Jalview.getInstance().getCommands();
 500     Assert.assertNotNull(cmds);
 501     for (String filename : filenames)
 502     {
 503       Assert.assertTrue(new File(filename).exists(),
 504               "File '" + filename + "' was not created");
 505     }
 506     cleanupFiles(filenames);
 507     if (nonfilenames != null)
 508     {
 509       for (String nonfilename : nonfilenames)
 510       {
 511         File nonfile = new File(nonfilename);
 512         Assert.assertFalse(nonfile.exists(),
 513                 "File " + nonfilename + " exists when it shouldn't!");
 514       }
 515     }
 516
 517     File deleteDirF = new File(deleteDir);
 518     if (deleteDirF.exists())
 519     {
 520       deleteDirF.delete();
 521     }
 522   }
 523
 524   @DataProvider(name = "allLinkedIdsData")
 525   public Object[][] allLinkedIdsData()
 526   {
 527     return new Object[][] {
 528         //
 529         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
 530             new String[]
 531             { "test/jalview/bin/argparser/testfiles/test1.stk",
 532                 "test/jalview/bin/argparser/testfiles/test2.stk",
 533                 "test/jalview/bin/argparser/testfiles/test3.stk", },
 534             null },
 535         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
 536             new String[]
 537             { "test/jalview/bin/argparser/testfiles/test1.png",
 538                 "test/jalview/bin/argparser/testfiles/test2.png",
 539                 "test/jalview/bin/argparser/testfiles/test3.png", },
 540             null },
 541         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
 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             new String[]
 547             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 548                 "test/jalview/bin/argparser/testfiles/dir1/test2.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         { "--gui --open=test/jalview/bin/argparser/**/*.fa --all --output={dirname}/{basename}.stk --close",
 557             new String[]
 558             { "test/jalview/bin/argparser/testfiles/test1.stk",
 559                 "test/jalview/bin/argparser/testfiles/test2.stk",
 560                 "test/jalview/bin/argparser/testfiles/test3.stk",
 561                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 562                 "test/jalview/bin/argparser/testfiles/dir1/test2.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             null },
 571         { "--gui --open=test/jalview/bin/argparser/**/*.fa --output=*/*.stk --close",
 572             new String[]
 573             { "test/jalview/bin/argparser/testfiles/test1.stk",
 574                 "test/jalview/bin/argparser/testfiles/test2.stk",
 575                 "test/jalview/bin/argparser/testfiles/test3.stk",
 576                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 577                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 578                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 579                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 580                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 581                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 582                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 583                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 584                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
 585             null },
 586         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --all --output=*/*.stk --close",
 587             new String[]
 588             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 589                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 590                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 591                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 592                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 593             new String[]
 594             { "test/jalview/bin/argparser/testfiles/test1.stk",
 595                 "test/jalview/bin/argparser/testfiles/test2.stk",
 596                 "test/jalview/bin/argparser/testfiles/test3.stk",
 597                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 598                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 599                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 600                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 601         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*/*.stk --close",
 602             new String[]
 603             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 604                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 605                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 606             new String[]
 607             { "test/jalview/bin/argparser/testfiles/test1.stk",
 608                 "test/jalview/bin/argparser/testfiles/test2.stk",
 609                 "test/jalview/bin/argparser/testfiles/test3.stk",
 610                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 611                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 612                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 613                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 614         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
 615             new String[]
 616             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 617                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 618                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 619             new String[]
 620             { "test/jalview/bin/argparser/testfiles/test1.stk",
 621                 "test/jalview/bin/argparser/testfiles/test2.stk",
 622                 "test/jalview/bin/argparser/testfiles/test3.stk",
 623                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 624                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 625                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 626                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 627                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 628                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 629         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
 630             new String[]
 631             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 632                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 633                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 634             new String[]
 635             { "test/jalview/bin/argparser/testfiles/test1.stk",
 636                 "test/jalview/bin/argparser/testfiles/test2.stk",
 637                 "test/jalview/bin/argparser/testfiles/test3.stk",
 638                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 639                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 640                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 641                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 642                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 643                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 644         { "--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",
 645             new String[]
 646             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 647                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 648                 "test/jalview/bin/argparser/testfiles/dir2/test1.aln",
 649                 "test/jalview/bin/argparser/testfiles/dir2/test2.aln",
 650                 "test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
 651             new String[]
 652             { "test/jalview/bin/argparser/testfiles/test1.stk",
 653                 "test/jalview/bin/argparser/testfiles/test2.stk",
 654                 "test/jalview/bin/argparser/testfiles/test3.stk",
 655                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 656                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 657                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 658                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 659                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 660                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 661                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
 662                 "test/jalview/bin/argparser/testfiles/test1.aln",
 663                 "test/jalview/bin/argparser/testfiles/test2.aln",
 664                 "test/jalview/bin/argparser/testfiles/test3.aln",
 665                 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 666                 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 667                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 668                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 669                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 670                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
 671         // --mkdirs
 672         { "--headless --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output "
 673                 + deleteDir
 674                 + "/{dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output="
 675                 + deleteDir
 676                 + "/{dirname}/{basename}.aln --close --all --mkdirs",
 677             new String[]
 678             { deleteDir
 679                     + "/test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 680                 deleteDir
 681                         + "/test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 682                 deleteDir
 683                         + "/test/jalview/bin/argparser/testfiles/dir2/test1.aln",
 684                 deleteDir
 685                         + "/test/jalview/bin/argparser/testfiles/dir2/test2.aln",
 686                 deleteDir
 687                         + "/test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
 688             new String[]
 689             { "test/jalview/bin/argparser/testfiles/test1.stk",
 690                 "test/jalview/bin/argparser/testfiles/test2.stk",
 691                 "test/jalview/bin/argparser/testfiles/test3.stk",
 692                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 693                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 694                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 695                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 696                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 697                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 698                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
 699                 "test/jalview/bin/argparser/testfiles/test1.aln",
 700                 "test/jalview/bin/argparser/testfiles/test2.aln",
 701                 "test/jalview/bin/argparser/testfiles/test3.aln",
 702                 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 703                 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 704                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 705                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 706                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 707                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln",
 708                 deleteDir
 709                         + "test/jalview/bin/argparser/testfiles/test1.stk",
 710                 deleteDir
 711                         + "test/jalview/bin/argparser/testfiles/test2.stk",
 712                 deleteDir
 713                         + "test/jalview/bin/argparser/testfiles/test3.stk",
 714                 deleteDir
 715                         + "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 716                 deleteDir
 717                         + "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 718                 deleteDir
 719                         + "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 720                 deleteDir
 721                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 722                 deleteDir
 723                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 724                 deleteDir
 725                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 726                 deleteDir
 727                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
 728                 deleteDir
 729                         + "test/jalview/bin/argparser/testfiles/test1.aln",
 730                 deleteDir
 731                         + "test/jalview/bin/argparser/testfiles/test2.aln",
 732                 deleteDir
 733                         + "test/jalview/bin/argparser/testfiles/test3.aln",
 734                 deleteDir
 735                         + "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 736                 deleteDir
 737                         + "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 738                 deleteDir
 739                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 740                 deleteDir
 741                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 742                 deleteDir
 743                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 744                 deleteDir
 745                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
 746         //
 747     };
 748   }
 749
 750 }