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.awt.image.BufferedImage;
  24 import java.io.File;
  25 import java.io.IOException;
  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.imageio.ImageIO;
  32 import javax.swing.SwingUtilities;
  33
  34 import org.testng.Assert;
  35 import org.testng.annotations.AfterClass;
  36 import org.testng.annotations.AfterMethod;
  37 import org.testng.annotations.BeforeClass;
  38 import org.testng.annotations.DataProvider;
  39 import org.testng.annotations.Test;
  40
  41 import jalview.gui.AlignFrame;
  42 import jalview.gui.Desktop;
  43 import jalview.gui.JvOptionPane;
  44 import jalview.util.ArrayUtils;
  45
  46 public class CommandsTest
  47 {
  48   private static final String testfiles = "test/jalview/bin/argparser/testfiles";
  49
  50   @BeforeClass(alwaysRun = true)
  51   public static void setUpBeforeClass() throws Exception
  52   {
  53     Cache.loadProperties("test/jalview/gui/quitProps.jvprops");
  54     Date oneHourFromNow = new Date(
  55             System.currentTimeMillis() + 3600 * 1000);
  56     Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
  57   }
  58
  59   @AfterClass(alwaysRun = true)
  60   public static void resetProps()
  61   {
  62     Cache.loadProperties("test/jalview/testProps.jvprops");
  63   }
  64
  65   @BeforeClass(alwaysRun = true)
  66   public void setUpJvOptionPane()
  67   {
  68     JvOptionPane.setInteractiveMode(false);
  69     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  70   }
  71
  72   @AfterMethod(alwaysRun = true)
  73   public void tearDown()
  74   {
  75     try
  76     {
  77       // occasionally we are blocked by Jmol redraws
  78       SwingUtilities.invokeAndWait(new Runnable()
  79       {
  80
  81         @Override
  82         public void run()
  83         {
  84           Desktop.closeDesktop();
  85         }
  86       });
  87     } catch (Exception foo)
  88     {
  89       System.err.println("Failed during teardown with exception");
  90       foo.printStackTrace();
  91     }
  92
  93   }
  94
  95   public static void callJalviewMain(String[] args)
  96   {
  97     callJalviewMain(args, false);
  98   }
  99
 100   public static void callJalviewMain(String[] args, boolean newJalview)
 101   {
 102     if (!newJalview || Jalview.getInstance() != null)
 103     {
 104       Jalview.getInstance().doMain(args);
 105     }
 106     else
 107     {
 108       Jalview.main(args);
 109     }
 110   }
 111
 112   /* --setprops is currently disabled so this test won't work
 113   @Test(groups = "Functional")
 114   public void setpropsTest()
 115   {
 116     final String MOSTLY_HARMLESS = "MOSTLY_HARMLESS";
 117     String cmdLine = "--setprop=" + MOSTLY_HARMLESS + "=Earth";
 118     String[] args = cmdLine.split("\\s+");
 119     Jalview.main(args);
 120     Assert.assertEquals(Cache.getDefault(MOSTLY_HARMLESS, "Magrathea"),
 121             "Earth");
 122   }
 123   */
 124
 125   @Test(
 126     groups =
 127     { "Functional", "testTask3" },
 128     dataProvider = "cmdLines",
 129     singleThreaded = true)
 130
 131   public void commandsOpenTest(String cmdLine, boolean cmdArgs,
 132           int numFrames, String[] sequences)
 133   {
 134     try
 135     {
 136       String[] args = (cmdLine + " --gui").split("\\s+");
 137       callJalviewMain(args);
 138       Commands cmds = Jalview.getInstance().getCommands();
 139       Assert.assertNotNull(cmds);
 140       Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs,
 141               "Commands were not provided in the args");
 142       Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
 143               "Overall command parse and operation is false");
 144
 145       Assert.assertEquals(Desktop.getDesktopAlignFrames().length, numFrames,
 146               "Wrong number of AlignFrames");
 147
 148       if (sequences != null)
 149       {
 150         Set<String> openedSequenceNames = new HashSet<>();
 151         AlignFrame[] afs = Desktop.getDesktopAlignFrames();
 152         for (AlignFrame af : afs)
 153         {
 154           openedSequenceNames.addAll(
 155                   af.getViewport().getAlignment().getSequenceNames());
 156         }
 157         for (String sequence : sequences)
 158         {
 159           Assert.assertTrue(openedSequenceNames.contains(sequence),
 160                   "Sequence '" + sequence
 161                           + "' was not found in opened alignment files: "
 162                           + cmdLine + ".\nOpened sequence names are:\n"
 163                           + String.join("\n", openedSequenceNames));
 164         }
 165       }
 166
 167       Assert.assertFalse(
 168               lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
 169     } catch (Exception x)
 170     {
 171       Assert.fail("Unexpected exception during commandsOpenTest", x);
 172     } finally
 173     {
 174       tearDown();
 175
 176     }
 177   }
 178
 179   @Test(
 180     groups =
 181     { "Functional", "testTask3" },
 182     dataProvider = "structureImageOutputFiles",
 183     singleThreaded = true)
 184   public void structureImageOutputTest(String cmdLine, String[] filenames)
 185           throws IOException
 186   {
 187     cleanupFiles(filenames);
 188     String[] args = (cmdLine + " --gui").split("\\s+");
 189     try
 190     {
 191       callJalviewMain(args);
 192       Commands cmds = Jalview.getInstance().getCommands();
 193       Assert.assertNotNull(cmds);
 194       verifyIncreasingSize(cmdLine, filenames);
 195     } catch (Exception x)
 196     {
 197       Assert.fail("Unexpected exception during structureImageOutputTest",
 198               x);
 199     } finally
 200     {
 201       cleanupFiles(filenames);
 202       tearDown();
 203     }
 204   }
 205
 206   /**
 207    * given two command lines, compare the output files produced - they should
 208    * exist and be equal in size
 209    */
 210   @Test(
 211     groups =
 212     { "Functional", "testTask3" },
 213     dataProvider = "compareHeadlessAndGUIOps",
 214     singleThreaded = true)
 215   public void headlessOrGuiImageOutputTest(String[] cmdLines,
 216           String[] filenames) throws IOException
 217   {
 218     cleanupFiles(filenames);
 219     try
 220     {
 221       for (String cmdLine : cmdLines)
 222       {
 223         CommandLineOperations.Worker runner = CommandLineOperations
 224                 .getJalviewDesktopRunner(false, cmdLine, 1000);
 225         long timeOut = 10000;
 226         while (runner.isAlive() && timeOut > 0)
 227         {
 228           Thread.sleep(25);
 229           timeOut -= 25;
 230         }
 231       }
 232       verifyOrderedFileSet(cmdLines[0] + " vs " + cmdLines[1], filenames,
 233               false);
 234     } catch (Exception x)
 235     {
 236       Assert.fail("Unexpected exception during structureImageOutputTest",
 237               x);
 238     } finally
 239     {
 240       cleanupFiles(filenames);
 241       tearDown();
 242     }
 243   }
 244
 245   @DataProvider(name = "compareHeadlessAndGUIOps")
 246   public Object[][] compareHeadlessAndGUIOps()
 247   {
 248     return new Object[][] {
 249         new Object[]
 250         { new String[] { "--open examples/uniref50.fa "
 251                 + "--structure [seqid=FER1_SPIOL,tempfac=plddt,showssannotations,structureviewer=jmol]"
 252                 + "examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
 253                 + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json --image="
 254                 + testfiles
 255                 + "test-al-pae-ss-gui.png --overwrite --gui --quit",
 256             "--open examples/uniref50.fa "
 257                     + "--structure [seqid=FER1_SPIOL,tempfac=plddt,showssannotations,structureviewer=jmol]"
 258                     + "examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
 259                     + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json --image="
 260                     + testfiles
 261                     + "test-al-pae-ss-nogui.png --overwrite --nogui"
 262
 263         }, new String[] { testfiles + "test-al-pae-ss-gui.png",
 264             testfiles + "test-al-pae-ss-nogui.png", } } };
 265   }
 266
 267   private static void verifyIncreasingSize(String cmdLine,
 268           String[] filenames) throws Exception
 269   {
 270     verifyOrderedFileSet(cmdLine, filenames, true);
 271   }
 272
 273   private static void verifyOrderedFileSet(String cmdLine,
 274           String[] filenames, boolean increasingSize) throws Exception
 275   {
 276     File lastFile = null;
 277     for (String filename : filenames)
 278     {
 279       File file = new File(filename);
 280       Assert.assertTrue(file.exists(), "File '" + filename
 281               + "' was not created by '" + cmdLine + "'");
 282       Assert.assertTrue(file.isFile(), "File '" + filename
 283               + "' is not a file from '" + cmdLine + "'");
 284       Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
 285               + "' has no content from '" + cmdLine + "'");
 286       // make sure the successive output files get bigger!
 287       if (lastFile != null)
 288       {
 289         waitForLastWrite(file, 25);
 290
 291         if (increasingSize)
 292         {
 293           Assert.assertTrue(
 294                   Files.size(file.toPath()) > Files.size(lastFile.toPath()),
 295                   "Expected " + file.toPath() + " to be larger than "
 296                           + lastFile.toPath());
 297         }
 298         else
 299         {
 300           Assert.assertEquals(Files.size(file.toPath()),
 301                   Files.size(lastFile.toPath()),
 302                   "New file " + file.toPath()
 303                           + " (actual size) not same as last file's size "
 304                           + lastFile.toString());
 305         }
 306       }
 307       // remember it for next file
 308       lastFile = file;
 309     }
 310
 311   }
 312
 313   private static long waitForLastWrite(File file, int i) throws IOException
 314   {
 315     long lastSize, stableSize = Files.size(file.toPath());
 316     // wait around until we are sure the file has been completely written.
 317     do
 318     {
 319       lastSize = stableSize;
 320       try
 321       {
 322         Thread.sleep(i);
 323       } catch (Exception x)
 324       {
 325       }
 326       stableSize = Files.size(file.toPath());
 327     } while (stableSize != lastSize);
 328     return stableSize;
 329   }
 330
 331   @Test(
 332     groups = "Functional",
 333     dataProvider = "argfileOutputFiles",
 334     singleThreaded = true)
 335
 336   public void argFilesGlobAndSubstitutionsTest(String cmdLine,
 337           String[] filenames) throws IOException
 338   {
 339     cleanupFiles(filenames);
 340     String[] args = (cmdLine + " --gui").split("\\s+");
 341     try
 342     {
 343       callJalviewMain(args);
 344       Commands cmds = Jalview.getInstance().getCommands();
 345       Assert.assertNotNull(cmds);
 346       File lastFile = null;
 347       for (String filename : filenames)
 348       {
 349         File file = new File(filename);
 350         Assert.assertTrue(file.exists(), "File '" + filename
 351                 + "' was not created by '" + cmdLine + "'");
 352         Assert.assertTrue(file.isFile(), "File '" + filename
 353                 + "' is not a file from '" + cmdLine + "'");
 354         Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
 355                 + "' has no content from '" + cmdLine + "'");
 356         // make sure the successive output files get bigger!
 357         if (lastFile != null)
 358         {
 359           Assert.assertTrue(Files.size(file.toPath()) > Files
 360                   .size(lastFile.toPath()));
 361           System.out.println("this file: " + file + " +"
 362                   + Files.size(file.toPath()) + " greater than "
 363                   + Files.size(lastFile.toPath()));
 364         }
 365         // remember it for next file
 366         lastFile = file;
 367       }
 368     } catch (Exception x)
 369     {
 370       Assert.fail(
 371               "Unexpected exception during argFilesGlobAndSubstitutions",
 372               x);
 373     } finally
 374     {
 375       cleanupFiles(filenames);
 376       tearDown();
 377     }
 378   }
 379
 380   @DataProvider(name = "structureImageOutputFiles")
 381   public Object[][] structureImageOutputFiles()
 382   {
 383     return new Object[][] {
 384         //
 385         { "--gui --nonews --nosplash --open=./examples/test_fab41.result/sample.a2m "
 386                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 387                 + "--structureimage=" + testfiles + "/structureimage1.png "
 388                 + "--open=./examples/test_fab41.result/sample.a2m "
 389                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 390                 + "--structureimage=" + testfiles
 391                 + "/structureimage2.png --scale=1.5 "
 392                 + "--open=./examples/test_fab41.result/sample.a2m "
 393                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 394                 + "--structureimage=" + testfiles
 395                 + "/structureimage3.png --scale=2.0 ",
 396             new String[]
 397             { testfiles + "/structureimage1.png",
 398                 testfiles + "/structureimage2.png",
 399                 testfiles + "/structureimage3.png" } },
 400         { "--headless --noquit --open=./examples/test_fab41.result/sample.a2m "
 401                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 402                 + "--structureimage=" + testfiles + "/structureimage1.png "
 403                 + "--open=./examples/test_fab41.result/sample.a2m "
 404                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 405                 + "--structureimage=" + testfiles
 406                 + "/structureimage2.png --scale=1.5 "
 407                 + "--open=./examples/test_fab41.result/sample.a2m "
 408                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 409                 + "--structureimage=" + testfiles
 410                 + "/structureimage3.png --scale=2.0 ",
 411             new String[]
 412             { testfiles + "/structureimage1.png",
 413                 testfiles + "/structureimage2.png",
 414                 testfiles + "/structureimage3.png" } },
 415         { "--gui --nonews --nosplash --open examples/1gaq.txt --append ./examples/3W5V.pdb "
 416                 + "--structure examples/1gaq.txt --seqid \"1GAQ|A\" "
 417                 + "--structureimage " + testfiles
 418                 + "/1gaq.png --structure examples/3W5V.pdb "
 419                 + "--seqid \"3W5V|A\" --structureimage " + testfiles
 420                 + "/3w5v.png --overwrite",
 421
 422             new String[]
 423             { testfiles + "/1gaq.png",
 424                 testfiles + "/3w5v.png" } },
 425         { "--headless --noquit --open ./examples/1gaq.txt --append ./examples/3W5V.pdb "
 426                 + "--structure examples/1gaq.txt --seqid \"1GAQ|A\" "
 427                 + "--structureimage " + testfiles
 428                 + "/1gaq.png --structure examples/3W5V.pdb "
 429                 + "--seqid \"3W5V|A\" --structureimage " + testfiles
 430                 + "/3w5v.png --overwrite",
 431
 432             new String[]
 433             { testfiles + "/1gaq.png", testfiles + "/3w5v.png" } }
 434
 435         /*
 436                 */
 437         //
 438     };
 439
 440   }
 441
 442   @DataProvider(name = "argfileOutputFiles")
 443   public Object[][] argfileOutputFiles()
 444   {
 445     return new Object[][] {
 446         //
 447         { "--gui --argfile=" + testfiles + "/**/*.txt", new String[]
 448         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
 449             testfiles + "/dir3/subdir/test0.png" } },
 450         { "--gui --argfile=" + testfiles + "/**/argfile.txt", new String[]
 451         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
 452         { "--gui --argfile=" + testfiles + "/dir*/argfile.txt", new String[]
 453         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
 454         { "--gui --initsubstitutions --append examples/uniref50.fa --image "
 455                 + testfiles + "/{basename}.png",
 456             new String[]
 457             { testfiles + "/uniref50.png" } },
 458         { "--gui --append examples/uniref50.fa --nosubstitutions --image "
 459                 + testfiles + "/{basename}.png",
 460             new String[]
 461             { testfiles + "/{basename}.png" } }
 462         //
 463     };
 464
 465   }
 466
 467   @DataProvider(name = "cmdLines")
 468   public Object[][] cmdLines()
 469   {
 470     String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN",
 471         "FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" };
 472     String[] t1 = new String[] { "TEST1" };
 473     String[] t2 = new String[] { "TEST2" };
 474     String[] t3 = new String[] { "TEST3" };
 475     return new Object[][] {
 476         /*
 477         */
 478         { "--append=examples/uniref50.fa", true, 1, someUniref50Seqs },
 479         { "--append examples/uniref50.fa", true, 1, someUniref50Seqs },
 480         { "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs },
 481         // NOTE we cannot use shell expansion in tests, so list all files!
 482         { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
 483             someUniref50Seqs },
 484         { "--append=[new]examples/uniref50*.fa", true, 2,
 485             someUniref50Seqs },
 486         { "--open=examples/uniref50*.fa", true, 2, someUniref50Seqs },
 487         { "examples/uniref50.fa", true, 1, someUniref50Seqs },
 488         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
 489             ArrayUtils.concatArrays(someUniref50Seqs, t1) },
 490         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
 491         { "--gui --argfile=" + testfiles + "/argfile0.txt", true, 1,
 492             ArrayUtils.concatArrays(t1, t3) },
 493         { "--gui --argfile=" + testfiles + "/argfile*.txt", true, 5,
 494             ArrayUtils.concatArrays(t1, t2, t3) },
 495         { "--gui --argfile=" + testfiles + "/argfile.autocounter", true, 3,
 496             ArrayUtils.concatArrays(t1, t2) } };
 497
 498   }
 499
 500   public static boolean lookForSequenceName(String sequenceName)
 501   {
 502     AlignFrame[] afs = Desktop.getDesktopAlignFrames();
 503     for (AlignFrame af : afs)
 504     {
 505       for (String name : af.getViewport().getAlignment().getSequenceNames())
 506       {
 507         if (sequenceName.equals(name))
 508         {
 509           return true;
 510         }
 511       }
 512     }
 513     return false;
 514   }
 515
 516   public static void cleanupFiles(String[] filenames)
 517   {
 518     for (String filename : filenames)
 519     {
 520       File file = new File(filename);
 521       if (file.exists())
 522       {
 523         file.delete();
 524       }
 525     }
 526   }
 527
 528   private final String deleteDir = "test/deleteAfter";
 529
 530   @Test(
 531     groups = "Functional",
 532     dataProvider = "allLinkedIdsData",
 533     singleThreaded = true)
 534   public void allLinkedIdsTest(String cmdLine, String[] filenames,
 535           String[] nonfilenames)
 536   {
 537     String[] args = (cmdLine + " --gui").split("\\s+");
 538     callJalviewMain(args);
 539     Commands cmds = Jalview.getInstance().getCommands();
 540     Assert.assertNotNull(cmds);
 541     for (String filename : filenames)
 542     {
 543       Assert.assertTrue(new File(filename).exists(),
 544               "File '" + filename + "' was not created");
 545     }
 546     cleanupFiles(filenames);
 547     if (nonfilenames != null)
 548     {
 549       for (String nonfilename : nonfilenames)
 550       {
 551         File nonfile = new File(nonfilename);
 552         Assert.assertFalse(nonfile.exists(),
 553                 "File " + nonfilename + " exists when it shouldn't!");
 554       }
 555     }
 556
 557     File deleteDirF = new File(deleteDir);
 558     if (deleteDirF.exists())
 559     {
 560       deleteDirF.delete();
 561     }
 562   }
 563
 564   @DataProvider(name = "allLinkedIdsData")
 565   public Object[][] allLinkedIdsData()
 566   {
 567     return new Object[][] {
 568         //
 569         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
 570             new String[]
 571             { "test/jalview/bin/argparser/testfiles/test1.stk",
 572                 "test/jalview/bin/argparser/testfiles/test2.stk",
 573                 "test/jalview/bin/argparser/testfiles/test3.stk", },
 574             null },
 575         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
 576             new String[]
 577             { "test/jalview/bin/argparser/testfiles/test1.png",
 578                 "test/jalview/bin/argparser/testfiles/test2.png",
 579                 "test/jalview/bin/argparser/testfiles/test3.png", },
 580             null },
 581         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
 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             new String[]
 587             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 588                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 589                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 590                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 591                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 592                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 593                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 594                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 595                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 596         { "--gui --open=test/jalview/bin/argparser/**/*.fa --all --output={dirname}/{basename}.stk --close",
 597             new String[]
 598             { "test/jalview/bin/argparser/testfiles/test1.stk",
 599                 "test/jalview/bin/argparser/testfiles/test2.stk",
 600                 "test/jalview/bin/argparser/testfiles/test3.stk",
 601                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 602                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 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                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 607                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 608                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 609                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
 610             null },
 611         { "--gui --open=test/jalview/bin/argparser/**/*.fa --output=*/*.stk --close",
 612             new String[]
 613             { "test/jalview/bin/argparser/testfiles/test1.stk",
 614                 "test/jalview/bin/argparser/testfiles/test2.stk",
 615                 "test/jalview/bin/argparser/testfiles/test3.stk",
 616                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 617                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 618                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 619                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 620                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 621                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 622                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 623                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 624                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
 625             null },
 626         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --all --output=*/*.stk --close",
 627             new String[]
 628             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 629                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 630                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 631                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 632                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 633             new String[]
 634             { "test/jalview/bin/argparser/testfiles/test1.stk",
 635                 "test/jalview/bin/argparser/testfiles/test2.stk",
 636                 "test/jalview/bin/argparser/testfiles/test3.stk",
 637                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 638                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 639                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 640                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 641         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*/*.stk --close",
 642             new String[]
 643             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 644                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 645                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 646             new String[]
 647             { "test/jalview/bin/argparser/testfiles/test1.stk",
 648                 "test/jalview/bin/argparser/testfiles/test2.stk",
 649                 "test/jalview/bin/argparser/testfiles/test3.stk",
 650                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 651                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 652                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 653                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 654         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
 655             new String[]
 656             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 657                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 658                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 659             new String[]
 660             { "test/jalview/bin/argparser/testfiles/test1.stk",
 661                 "test/jalview/bin/argparser/testfiles/test2.stk",
 662                 "test/jalview/bin/argparser/testfiles/test3.stk",
 663                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 664                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 665                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 666                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 667                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 668                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 669         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
 670             new String[]
 671             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 672                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 673                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 674             new String[]
 675             { "test/jalview/bin/argparser/testfiles/test1.stk",
 676                 "test/jalview/bin/argparser/testfiles/test2.stk",
 677                 "test/jalview/bin/argparser/testfiles/test3.stk",
 678                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 679                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 680                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 681                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 682                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 683                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 684         { "--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",
 685             new String[]
 686             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 687                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 688                 "test/jalview/bin/argparser/testfiles/dir2/test1.aln",
 689                 "test/jalview/bin/argparser/testfiles/dir2/test2.aln",
 690                 "test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
 691             new String[]
 692             { "test/jalview/bin/argparser/testfiles/test1.stk",
 693                 "test/jalview/bin/argparser/testfiles/test2.stk",
 694                 "test/jalview/bin/argparser/testfiles/test3.stk",
 695                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 696                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 697                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 698                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 699                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 700                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 701                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
 702                 "test/jalview/bin/argparser/testfiles/test1.aln",
 703                 "test/jalview/bin/argparser/testfiles/test2.aln",
 704                 "test/jalview/bin/argparser/testfiles/test3.aln",
 705                 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 706                 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 707                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 708                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 709                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 710                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
 711         // --mkdirs
 712         { "--headless --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output "
 713                 + deleteDir
 714                 + "/{dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output="
 715                 + deleteDir
 716                 + "/{dirname}/{basename}.aln --close --all --mkdirs",
 717             new String[]
 718             { deleteDir
 719                     + "/test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 720                 deleteDir
 721                         + "/test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 722                 deleteDir
 723                         + "/test/jalview/bin/argparser/testfiles/dir2/test1.aln",
 724                 deleteDir
 725                         + "/test/jalview/bin/argparser/testfiles/dir2/test2.aln",
 726                 deleteDir
 727                         + "/test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
 728             new String[]
 729             { "test/jalview/bin/argparser/testfiles/test1.stk",
 730                 "test/jalview/bin/argparser/testfiles/test2.stk",
 731                 "test/jalview/bin/argparser/testfiles/test3.stk",
 732                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 733                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 734                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 735                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 736                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 737                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 738                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
 739                 "test/jalview/bin/argparser/testfiles/test1.aln",
 740                 "test/jalview/bin/argparser/testfiles/test2.aln",
 741                 "test/jalview/bin/argparser/testfiles/test3.aln",
 742                 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 743                 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 744                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 745                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 746                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 747                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln",
 748                 deleteDir
 749                         + "test/jalview/bin/argparser/testfiles/test1.stk",
 750                 deleteDir
 751                         + "test/jalview/bin/argparser/testfiles/test2.stk",
 752                 deleteDir
 753                         + "test/jalview/bin/argparser/testfiles/test3.stk",
 754                 deleteDir
 755                         + "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 756                 deleteDir
 757                         + "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 758                 deleteDir
 759                         + "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 760                 deleteDir
 761                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 762                 deleteDir
 763                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 764                 deleteDir
 765                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 766                 deleteDir
 767                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
 768                 deleteDir
 769                         + "test/jalview/bin/argparser/testfiles/test1.aln",
 770                 deleteDir
 771                         + "test/jalview/bin/argparser/testfiles/test2.aln",
 772                 deleteDir
 773                         + "test/jalview/bin/argparser/testfiles/test3.aln",
 774                 deleteDir
 775                         + "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 776                 deleteDir
 777                         + "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 778                 deleteDir
 779                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 780                 deleteDir
 781                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 782                 deleteDir
 783                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 784                 deleteDir
 785                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
 786         //
 787     };
 788   }
 789
 790   @Test(
 791     groups =
 792     { "Functional", "testTask3" },
 793     dataProvider = "structureImageAnnotationsOutputFiles",
 794     singleThreaded = true)
 795   public void structureImageAnnotationsOutputTest(String cmdLine,
 796           String filename, int height) throws IOException
 797   {
 798     cleanupFiles(new String[] { filename });
 799     String[] args = (cmdLine).split("\\s+");
 800     callJalviewMain(args, true); // Create new instance of Jalview each time for
 801                                  // linkedIds
 802
 803     BufferedImage img = ImageIO.read(new File(filename));
 804     Assert.assertEquals(height, img.getHeight(), "Output image '" + filename
 805             + "' is not in the expected height range, possibly because of the wrong number of annotations");
 806
 807     cleanupFiles(new String[] { filename });
 808     tearDown();
 809   }
 810
 811   @DataProvider(name = "structureImageAnnotationsOutputFiles")
 812   public Object[][] structureImageAnnotationsOutputFiles()
 813   {
 814     String filename = "test/jalview/bin/argparser/testfiles/test_annotations.png";
 815     return new Object[][] {
 816         //
 817         { "--headless --nonews --nosplash --overwrite --open=./examples/uniref50.fa "
 818                 + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
 819                 + "--seqid=FER1_SPIOL --structureviewer=jmol "
 820                 + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 821                 + "--image=" + filename + " " + "--tempfac=plddt "
 822                 + "--noshowssannotations " + "--noshowannotations", //
 823             filename, //
 824             252 }, //
 825         { "--headless --nonews --nosplash --overwrite --open=./examples/uniref50.fa "
 826                 + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
 827                 + "--seqid=FER1_SPIOL --structureviewer=jmol "
 828                 + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 829                 + "--image=" + filename + " " + "--tempfac=plddt "
 830                 + "--showssannotations " + "--noshowannotations", //
 831             filename, //
 832             368 }, //
 833         { "--headless --nonews --nosplash --overwrite --open=./examples/uniref50.fa "
 834                 + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
 835                 + "--seqid=FER1_SPIOL --structureviewer=jmol "
 836                 + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 837                 + "--image=" + filename + " " + "--tempfac=plddt "
 838                 + "--noshowssannotations " + "--showannotations", //
 839             filename, //
 840             524 }, //
 841         { "--headless --nonews --nosplash --overwrite --open=./examples/uniref50.fa "
 842                 + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
 843                 + "--seqid=FER1_SPIOL --structureviewer=jmol "
 844                 + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 845                 + "--image=" + filename + " " + "--tempfac=plddt "
 846                 + "--showssannotations " + "--showannotations", //
 847             filename, //
 848             660 }, //
 849         { "--gui --nonews --nosplash --overwrite --open=./examples/uniref50.fa "
 850                 + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
 851                 + "--seqid=FER1_SPIOL --structureviewer=jmol "
 852                 + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 853                 + "--image=" + filename + " " + "--tempfac=plddt "
 854                 + "--noshowssannotations " + "--noshowannotations", //
 855             filename, //
 856             252 }, //
 857         { "--gui --nonews --nosplash --overwrite --open=./examples/uniref50.fa "
 858                 + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
 859                 + "--seqid=FER1_SPIOL --structureviewer=jmol "
 860                 + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 861                 + "--image=" + filename + " " + "--tempfac=plddt "
 862                 + "--showssannotations " + "--noshowannotations", //
 863             filename, //
 864             368 }, //
 865         { "--gui --nonews --nosplash --overwrite --open=./examples/uniref50.fa "
 866                 + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
 867                 + "--seqid=FER1_SPIOL --structureviewer=jmol "
 868                 + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 869                 + "--image=" + filename + " " + "--tempfac=plddt "
 870                 + "--noshowssannotations " + "--showannotations", //
 871             filename, //
 872             524 }, //
 873         { "--gui --nonews --nosplash --overwrite --open=./examples/uniref50.fa "
 874                 + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
 875                 + "--seqid=FER1_SPIOL --structureviewer=jmol "
 876                 + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 877                 + "--image=" + filename + " " + "--tempfac=plddt "
 878                 + "--showssannotations " + "--showannotations", //
 879             filename, //
 880             660 }, //
 881     };
 882   }
 883
 884 }