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 (Jalview.getInstance() != null && !newJalview)
 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).split("\\s+");
 189     try
 190     {
 191       callJalviewMain(args, true);
 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       /*
 233        *  larger margin between IDs and alignment/annotations when in --gui mode
 234        *
 235       verifyOrderedFileSet(cmdLines[0] + " vs " + cmdLines[1], filenames, false);
 236        */
 237
 238       verifySimilarEnoughImages(cmdLines[0] + " vs " + cmdLines[1],
 239               filenames, 0.6f, 0f);
 240     } catch (Exception x)
 241     {
 242       Assert.fail("Unexpected exception during structureImageOutputTest",
 243               x);
 244     } finally
 245     {
 246       cleanupFiles(filenames);
 247       tearDown();
 248     }
 249   }
 250
 251   @DataProvider(name = "compareHeadlessAndGUIOps")
 252   public Object[][] compareHeadlessAndGUIOps()
 253   {
 254     return new Object[][] {
 255         new Object[]
 256         { new String[] { "--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-gui.png --overwrite --gui --quit",
 262             "--open examples/uniref50.fa "
 263                     + "--structure [seqid=FER1_SPIOL,tempfac=plddt,showssannotations,structureviewer=jmol]"
 264                     + "examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
 265                     + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json --image="
 266                     + testfiles + "/"
 267                     + "test-al-pae-ss-nogui.png --overwrite --nogui" },
 268             new String[]
 269             { testfiles + "/test-al-pae-ss-gui.png",
 270                 testfiles + "/test-al-pae-ss-nogui.png", } } };
 271   }
 272
 273   private static void verifyIncreasingSize(String cmdLine,
 274           String[] filenames) throws Exception
 275   {
 276     verifyOrderedFileSet(cmdLine, filenames, true);
 277   }
 278
 279   private static void verifyOrderedFileSet(String cmdLine,
 280           String[] filenames, boolean increasingSize) throws Exception
 281   {
 282     File lastFile = null;
 283     for (String filename : filenames)
 284     {
 285       File file = new File(filename);
 286       Assert.assertTrue(file.exists(), "File '" + filename
 287               + "' was not created by '" + cmdLine + "'");
 288       Assert.assertTrue(file.isFile(), "File '" + filename
 289               + "' is not a file from '" + cmdLine + "'");
 290       Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
 291               + "' has no content from '" + cmdLine + "'");
 292       // make sure the successive output files get bigger!
 293       if (lastFile != null)
 294       {
 295         waitForLastWrite(file, 25);
 296
 297         if (increasingSize)
 298         {
 299           Assert.assertTrue(
 300                   Files.size(file.toPath()) > Files.size(lastFile.toPath()),
 301                   "Expected " + file.toPath() + " to be larger than "
 302                           + lastFile.toPath());
 303         }
 304         else
 305         {
 306           Assert.assertEquals(Files.size(file.toPath()),
 307                   Files.size(lastFile.toPath()),
 308                   "New file " + file.toPath()
 309                           + " (actual size) not same as last file's size "
 310                           + lastFile.toString());
 311         }
 312       }
 313       // remember it for next file
 314       lastFile = file;
 315     }
 316
 317   }
 318
 319   private static void verifySimilarEnoughImages(String cmdLine,
 320           String[] filenames, float w_tolerance_pc, float h_tolerance_pc)
 321           throws Exception
 322   {
 323     int min_w = -1;
 324     int max_w = -1;
 325     int min_h = -1;
 326     int max_h = -1;
 327     for (String filename : filenames)
 328     {
 329       File file = new File(filename);
 330       Assert.assertTrue(file.exists(), "File '" + filename
 331               + "' was not created by '" + cmdLine + "'");
 332       Assert.assertTrue(file.isFile(), "File '" + filename
 333               + "' is not a file from '" + cmdLine + "'");
 334       Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
 335               + "' has no content from '" + cmdLine + "'");
 336
 337       BufferedImage img = ImageIO.read(file);
 338       if (img.getWidth() < min_w || min_w == -1)
 339       {
 340         min_w = img.getWidth();
 341       }
 342       if (img.getWidth() > max_w || max_w == -1)
 343       {
 344         max_w = img.getWidth();
 345       }
 346       if (img.getHeight() < min_h || min_h == -1)
 347       {
 348         min_h = img.getHeight();
 349       }
 350       if (img.getHeight() > max_h || max_h == -1)
 351       {
 352         max_h = img.getHeight();
 353       }
 354     }
 355     Assert.assertTrue(min_w > 0,
 356             "Minimum width is not positive (" + min_w + ")");
 357     Assert.assertTrue(max_w > 0,
 358             "Maximum width is not positive (" + max_w + ")");
 359     Assert.assertTrue(min_h > 0,
 360             "Minimum height is not positive (" + min_h + ")");
 361     Assert.assertTrue(max_h > 0,
 362             "Maximum height is not positive (" + max_h + ")");
 363     // tolerance
 364     Assert.assertTrue(100 * (max_w - min_w) / min_w < w_tolerance_pc,
 365             "Width variation (" + (max_w - min_w)
 366                     + " not within tolerance of minimum width (" + min_w
 367                     + ")");
 368     if (max_w != min_w)
 369     {
 370       System.out.println("Widths within tolerance (" + w_tolerance_pc
 371               + "%), min_w=" + min_w + " < max_w=" + max_w);
 372     }
 373     Assert.assertTrue(100 * (max_h - min_h) / min_h < w_tolerance_pc,
 374             "Height variation (" + (max_h - min_h)
 375                     + " not within tolerance of minimum height (" + min_h
 376                     + ")");
 377     if (max_h != min_h)
 378     {
 379       System.out.println("Heights within tolerance (" + h_tolerance_pc
 380               + "%), min_h=" + min_h + " < max_h=" + max_h);
 381     }
 382   }
 383
 384   private static long waitForLastWrite(File file, int i) throws IOException
 385   {
 386     long lastSize, stableSize = Files.size(file.toPath());
 387     // wait around until we are sure the file has been completely written.
 388     do
 389     {
 390       lastSize = stableSize;
 391       try
 392       {
 393         Thread.sleep(i);
 394       } catch (Exception x)
 395       {
 396       }
 397       stableSize = Files.size(file.toPath());
 398     } while (stableSize != lastSize);
 399     return stableSize;
 400   }
 401
 402   @Test(
 403     groups = "Functional",
 404     dataProvider = "argfileOutputFiles",
 405     singleThreaded = true)
 406
 407   public void argFilesGlobAndSubstitutionsTest(String cmdLine,
 408           String[] filenames) throws IOException
 409   {
 410     cleanupFiles(filenames);
 411     String[] args = (cmdLine + " --gui").split("\\s+");
 412     try
 413     {
 414       callJalviewMain(args);
 415       Commands cmds = Jalview.getInstance().getCommands();
 416       Assert.assertNotNull(cmds);
 417       File lastFile = null;
 418       for (String filename : filenames)
 419       {
 420         File file = new File(filename);
 421         Assert.assertTrue(file.exists(), "File '" + filename
 422                 + "' was not created by '" + cmdLine + "'");
 423         Assert.assertTrue(file.isFile(), "File '" + filename
 424                 + "' is not a file from '" + cmdLine + "'");
 425         Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
 426                 + "' has no content from '" + cmdLine + "'");
 427         // make sure the successive output files get bigger!
 428         if (lastFile != null)
 429         {
 430           Assert.assertTrue(Files.size(file.toPath()) > Files
 431                   .size(lastFile.toPath()));
 432           System.out.println("this file: " + file + " +"
 433                   + Files.size(file.toPath()) + " greater than "
 434                   + Files.size(lastFile.toPath()));
 435         }
 436         // remember it for next file
 437         lastFile = file;
 438       }
 439     } catch (Exception x)
 440     {
 441       Assert.fail(
 442               "Unexpected exception during argFilesGlobAndSubstitutions",
 443               x);
 444     } finally
 445     {
 446       cleanupFiles(filenames);
 447       tearDown();
 448     }
 449   }
 450
 451   @DataProvider(name = "structureImageOutputFiles")
 452   public Object[][] structureImageOutputFiles()
 453   {
 454     return new Object[][] {
 455         //
 456         /*
 457                 */
 458         { "--gui --nonews --nosplash --open=./examples/test_fab41.result/sample.a2m "
 459                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 460                 + "--structureimage=" + testfiles
 461                 + "/structureimage0-1.png "
 462                 + "--open=./examples/test_fab41.result/sample.a2m "
 463                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 464                 + "--structureimage=" + testfiles
 465                 + "/structureimage0-2.png --scale=1.5 "
 466                 + "--open=./examples/test_fab41.result/sample.a2m "
 467                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 468                 + "--structureimage=" + testfiles
 469                 + "/structureimage0-3.png --scale=2.0 ",
 470             new String[]
 471             { testfiles + "/structureimage0-1.png",
 472                 testfiles + "/structureimage0-2.png",
 473                 testfiles + "/structureimage0-3.png" } },
 474         { "--headless --noquit --open=./examples/test_fab41.result/sample.a2m "
 475                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 476                 + "--structureimage=" + testfiles
 477                 + "/structureimage1-1.png "
 478                 + "--open=./examples/test_fab41.result/sample.a2m "
 479                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 480                 + "--structureimage=" + testfiles
 481                 + "/structureimage1-2.png --scale=1.5 "
 482                 + "--open=./examples/test_fab41.result/sample.a2m "
 483                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
 484                 + "--structureimage=" + testfiles
 485                 + "/structureimage1-3.png --scale=2.0 ",
 486             new String[]
 487             { testfiles + "/structureimage1-1.png",
 488                 testfiles + "/structureimage1-2.png",
 489                 testfiles + "/structureimage1-3.png" } },
 490         { "--gui --nonews --nosplash --open examples/1gaq.txt --append ./examples/3W5V.pdb "
 491                 + "--structure examples/1gaq.txt --seqid \"1GAQ|A\" "
 492                 + "--structureimage " + testfiles
 493                 + "/structureimage2-1gaq.png --structure examples/3W5V.pdb "
 494                 + "--seqid \"3W5V|A\" --structureimage " + testfiles
 495                 + "/structureimage2-3w5v.png --overwrite",
 496
 497             new String[]
 498             { testfiles + "/structureimage2-3w5v.png",
 499                 testfiles + "/structureimage2-1gaq.png", } },
 500         { "--headless --noquit --open ./examples/1gaq.txt --append ./examples/3W5V.pdb "
 501                 + "--structure examples/1gaq.txt --seqid \"1GAQ|A\" "
 502                 + "--structureimage " + testfiles
 503                 + "/structureimage3-1gaq.png --structure examples/3W5V.pdb "
 504                 + "--seqid \"3W5V|A\" --structureimage " + testfiles
 505                 + "/structureimage3-3w5v.png --overwrite",
 506
 507             new String[]
 508             { testfiles + "/structureimage3-3w5v.png",
 509                 testfiles + "/structureimage3-1gaq.png", } }
 510         /*
 511                 */
 512         //
 513     };
 514
 515   }
 516
 517   @DataProvider(name = "argfileOutputFiles")
 518   public Object[][] argfileOutputFiles()
 519   {
 520     return new Object[][] {
 521         //
 522         { "--gui --argfile=" + testfiles + "/**/*.txt", new String[]
 523         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
 524             testfiles + "/dir3/subdir/test0.png" } },
 525         { "--gui --argfile=" + testfiles + "/**/argfile.txt", new String[]
 526         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
 527         { "--gui --argfile=" + testfiles + "/dir*/argfile.txt", new String[]
 528         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
 529         { "--gui --initsubstitutions --append examples/uniref50.fa --image "
 530                 + testfiles + "/{basename}.png",
 531             new String[]
 532             { testfiles + "/uniref50.png" } },
 533         { "--gui --append examples/uniref50.fa --nosubstitutions --image "
 534                 + testfiles + "/{basename}.png",
 535             new String[]
 536             { testfiles + "/{basename}.png" } }
 537         //
 538     };
 539
 540   }
 541
 542   @DataProvider(name = "cmdLines")
 543   public Object[][] cmdLines()
 544   {
 545     String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN",
 546         "FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" };
 547     String[] t1 = new String[] { "TEST1" };
 548     String[] t2 = new String[] { "TEST2" };
 549     String[] t3 = new String[] { "TEST3" };
 550     return new Object[][] {
 551         /*
 552         */
 553         { "--append=examples/uniref50.fa", true, 1, someUniref50Seqs },
 554         { "--append examples/uniref50.fa", true, 1, someUniref50Seqs },
 555         { "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs },
 556         // NOTE we cannot use shell expansion in tests, so list all files!
 557         { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
 558             someUniref50Seqs },
 559         { "--append=[new]examples/uniref50*.fa", true, 2,
 560             someUniref50Seqs },
 561         { "--open=examples/uniref50*.fa", true, 2, someUniref50Seqs },
 562         { "examples/uniref50.fa", true, 1, someUniref50Seqs },
 563         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
 564             ArrayUtils.concatArrays(someUniref50Seqs, t1) },
 565         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
 566         { "--gui --argfile=" + testfiles + "/argfile0.txt", true, 1,
 567             ArrayUtils.concatArrays(t1, t3) },
 568         { "--gui --argfile=" + testfiles + "/argfile*.txt", true, 5,
 569             ArrayUtils.concatArrays(t1, t2, t3) },
 570         { "--gui --argfile=" + testfiles + "/argfile.autocounter", true, 3,
 571             ArrayUtils.concatArrays(t1, t2) } };
 572
 573   }
 574
 575   public static boolean lookForSequenceName(String sequenceName)
 576   {
 577     AlignFrame[] afs = Desktop.getDesktopAlignFrames();
 578     for (AlignFrame af : afs)
 579     {
 580       for (String name : af.getViewport().getAlignment().getSequenceNames())
 581       {
 582         if (sequenceName.equals(name))
 583         {
 584           return true;
 585         }
 586       }
 587     }
 588     return false;
 589   }
 590
 591   public static void cleanupFiles(String[] filenames)
 592   {
 593     for (String filename : filenames)
 594     {
 595       File file = new File(filename);
 596       if (file.exists())
 597       {
 598         file.delete();
 599       }
 600     }
 601   }
 602
 603   private final String deleteDir = "test/deleteAfter";
 604
 605   @Test(
 606     groups = "Functional",
 607     dataProvider = "allLinkedIdsData",
 608     singleThreaded = true)
 609   public void allLinkedIdsTest(String cmdLine, String[] filenames,
 610           String[] nonfilenames)
 611   {
 612     String[] args = (cmdLine + " --gui").split("\\s+");
 613     callJalviewMain(args);
 614     Commands cmds = Jalview.getInstance().getCommands();
 615     Assert.assertNotNull(cmds);
 616     for (String filename : filenames)
 617     {
 618       Assert.assertTrue(new File(filename).exists(),
 619               "File '" + filename + "' was not created");
 620     }
 621     cleanupFiles(filenames);
 622     if (nonfilenames != null)
 623     {
 624       for (String nonfilename : nonfilenames)
 625       {
 626         File nonfile = new File(nonfilename);
 627         Assert.assertFalse(nonfile.exists(),
 628                 "File " + nonfilename + " exists when it shouldn't!");
 629       }
 630     }
 631
 632     File deleteDirF = new File(deleteDir);
 633     if (deleteDirF.exists())
 634     {
 635       deleteDirF.delete();
 636     }
 637   }
 638
 639   @DataProvider(name = "allLinkedIdsData")
 640   public Object[][] allLinkedIdsData()
 641   {
 642     return new Object[][] {
 643         //
 644         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
 645             new String[]
 646             { "test/jalview/bin/argparser/testfiles/test1.stk",
 647                 "test/jalview/bin/argparser/testfiles/test2.stk",
 648                 "test/jalview/bin/argparser/testfiles/test3.stk", },
 649             null },
 650         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
 651             new String[]
 652             { "test/jalview/bin/argparser/testfiles/test1.png",
 653                 "test/jalview/bin/argparser/testfiles/test2.png",
 654                 "test/jalview/bin/argparser/testfiles/test3.png", },
 655             null },
 656         { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
 657             new String[]
 658             { "test/jalview/bin/argparser/testfiles/test1.stk",
 659                 "test/jalview/bin/argparser/testfiles/test2.stk",
 660                 "test/jalview/bin/argparser/testfiles/test3.stk", },
 661             new String[]
 662             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 663                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 664                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 665                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 666                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 667                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 668                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 669                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 670                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 671         { "--gui --open=test/jalview/bin/argparser/**/*.fa --all --output={dirname}/{basename}.stk --close",
 672             new String[]
 673             { "test/jalview/bin/argparser/testfiles/test1.stk",
 674                 "test/jalview/bin/argparser/testfiles/test2.stk",
 675                 "test/jalview/bin/argparser/testfiles/test3.stk",
 676                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 677                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 678                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 679                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 680                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 681                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 682                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 683                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 684                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
 685             null },
 686         { "--gui --open=test/jalview/bin/argparser/**/*.fa --output=*/*.stk --close",
 687             new String[]
 688             { "test/jalview/bin/argparser/testfiles/test1.stk",
 689                 "test/jalview/bin/argparser/testfiles/test2.stk",
 690                 "test/jalview/bin/argparser/testfiles/test3.stk",
 691                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 692                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 693                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 694                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 695                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 696                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 697                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 698                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 699                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", },
 700             null },
 701         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --all --output=*/*.stk --close",
 702             new String[]
 703             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 704                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 705                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 706                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 707                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 708             new String[]
 709             { "test/jalview/bin/argparser/testfiles/test1.stk",
 710                 "test/jalview/bin/argparser/testfiles/test2.stk",
 711                 "test/jalview/bin/argparser/testfiles/test3.stk",
 712                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 713                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 714                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 715                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 716         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*/*.stk --close",
 717             new String[]
 718             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 719                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 720                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 721             new String[]
 722             { "test/jalview/bin/argparser/testfiles/test1.stk",
 723                 "test/jalview/bin/argparser/testfiles/test2.stk",
 724                 "test/jalview/bin/argparser/testfiles/test3.stk",
 725                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 726                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 727                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 728                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 729         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
 730             new String[]
 731             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 732                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 733                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 734             new String[]
 735             { "test/jalview/bin/argparser/testfiles/test1.stk",
 736                 "test/jalview/bin/argparser/testfiles/test2.stk",
 737                 "test/jalview/bin/argparser/testfiles/test3.stk",
 738                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 739                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 740                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 741                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 742                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 743                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 744         { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
 745             new String[]
 746             { "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 747                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 748                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
 749             new String[]
 750             { "test/jalview/bin/argparser/testfiles/test1.stk",
 751                 "test/jalview/bin/argparser/testfiles/test2.stk",
 752                 "test/jalview/bin/argparser/testfiles/test3.stk",
 753                 "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 754                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 755                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 756                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 757                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 758                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, },
 759         { "--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",
 760             new String[]
 761             { "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 762                 "test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 763                 "test/jalview/bin/argparser/testfiles/dir2/test1.aln",
 764                 "test/jalview/bin/argparser/testfiles/dir2/test2.aln",
 765                 "test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
 766             new String[]
 767             { "test/jalview/bin/argparser/testfiles/test1.stk",
 768                 "test/jalview/bin/argparser/testfiles/test2.stk",
 769                 "test/jalview/bin/argparser/testfiles/test3.stk",
 770                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 771                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 772                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 773                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 774                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 775                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 776                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
 777                 "test/jalview/bin/argparser/testfiles/test1.aln",
 778                 "test/jalview/bin/argparser/testfiles/test2.aln",
 779                 "test/jalview/bin/argparser/testfiles/test3.aln",
 780                 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 781                 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 782                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 783                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 784                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 785                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
 786         // --mkdirs
 787         { "--headless --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output "
 788                 + deleteDir
 789                 + "/{dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output="
 790                 + deleteDir
 791                 + "/{dirname}/{basename}.aln --close --all --mkdirs",
 792             new String[]
 793             { deleteDir
 794                     + "/test/jalview/bin/argparser/testfiles/dir1/test1.stk",
 795                 deleteDir
 796                         + "/test/jalview/bin/argparser/testfiles/dir1/test2.stk",
 797                 deleteDir
 798                         + "/test/jalview/bin/argparser/testfiles/dir2/test1.aln",
 799                 deleteDir
 800                         + "/test/jalview/bin/argparser/testfiles/dir2/test2.aln",
 801                 deleteDir
 802                         + "/test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
 803             new String[]
 804             { "test/jalview/bin/argparser/testfiles/test1.stk",
 805                 "test/jalview/bin/argparser/testfiles/test2.stk",
 806                 "test/jalview/bin/argparser/testfiles/test3.stk",
 807                 "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 808                 "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 809                 "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 810                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 811                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 812                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 813                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
 814                 "test/jalview/bin/argparser/testfiles/test1.aln",
 815                 "test/jalview/bin/argparser/testfiles/test2.aln",
 816                 "test/jalview/bin/argparser/testfiles/test3.aln",
 817                 "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 818                 "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 819                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 820                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 821                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 822                 "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln",
 823                 deleteDir
 824                         + "test/jalview/bin/argparser/testfiles/test1.stk",
 825                 deleteDir
 826                         + "test/jalview/bin/argparser/testfiles/test2.stk",
 827                 deleteDir
 828                         + "test/jalview/bin/argparser/testfiles/test3.stk",
 829                 deleteDir
 830                         + "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
 831                 deleteDir
 832                         + "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
 833                 deleteDir
 834                         + "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
 835                 deleteDir
 836                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
 837                 deleteDir
 838                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
 839                 deleteDir
 840                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
 841                 deleteDir
 842                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
 843                 deleteDir
 844                         + "test/jalview/bin/argparser/testfiles/test1.aln",
 845                 deleteDir
 846                         + "test/jalview/bin/argparser/testfiles/test2.aln",
 847                 deleteDir
 848                         + "test/jalview/bin/argparser/testfiles/test3.aln",
 849                 deleteDir
 850                         + "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
 851                 deleteDir
 852                         + "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
 853                 deleteDir
 854                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
 855                 deleteDir
 856                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
 857                 deleteDir
 858                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
 859                 deleteDir
 860                         + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
 861         //
 862     };
 863   }
 864
 865   @Test(
 866     groups =
 867     { "Functional", "testTask3" },
 868     dataProvider = "structureImageAnnotationsOutputFiles",
 869     singleThreaded = true)
 870   public void structureImageAnnotationsOutputTest(String cmdLine,
 871           String filename, int height) throws IOException
 872   {
 873     cleanupFiles(new String[] { filename });
 874     String[] args = (cmdLine).split("\\s+");
 875     callJalviewMain(args, true); // Create new instance of Jalview each time for
 876                                  // linkedIds
 877     BufferedImage img = ImageIO.read(new File(filename));
 878     Assert.assertEquals(height, img.getHeight(), "Output image '" + filename
 879             + "' is not in the expected height range, possibly because of the wrong number of annotations");
 880
 881     cleanupFiles(new String[] { filename });
 882     tearDown();
 883   }
 884
 885   @DataProvider(name = "structureImageAnnotationsOutputFiles")
 886   public Object[][] structureImageAnnotationsOutputFiles()
 887   {
 888     String filename = "test/jalview/bin/argparser/testfiles/test_annotations.png";
 889     return new Object[][] {
 890         // MUST use --noquit with --headless to avoid a System.exit()
 891         { "--noquit --headless --nonews --nosplash --open=./examples/uniref50.fa "
 892                 + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
 893                 + "--seqid=FER1_SPIOL --structureviewer=jmol "
 894                 + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 895                 + "--image=" + filename + " " + "--tempfac=plddt "
 896                 + "--overwrite " //
 897                 + "--noshowssannotations " + "--noshowannotations", //
 898             filename, //
 899             252 }, //
 900         { "--noquit --headless --nonews --nosplash --open=./examples/uniref50.fa "
 901                 + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
 902                 + "--seqid=FER1_SPIOL --structureviewer=jmol "
 903                 + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 904                 + "--image=" + filename + " " + "--tempfac=plddt "
 905                 + "--overwrite " //
 906                 + "--showssannotations " + "--noshowannotations", //
 907             filename, //
 908             368 }, //
 909         { "--noquit --headless --nonews --nosplash --open=./examples/uniref50.fa "
 910                 + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
 911                 + "--seqid=FER1_SPIOL --structureviewer=jmol "
 912                 + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 913                 + "--image=" + filename + " " + "--tempfac=plddt "
 914                 + "--overwrite " //
 915                 + "--noshowssannotations " + "--showannotations", //
 916             filename, //
 917             524 }, //
 918         { "--noquit --headless --nonews --nosplash --open=./examples/uniref50.fa "
 919                 + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
 920                 + "--seqid=FER1_SPIOL --structureviewer=jmol "
 921                 + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 922                 + "--image=" + filename + " " + "--tempfac=plddt "
 923                 + "--overwrite " //
 924                 + "--showssannotations " + "--showannotations", //
 925             filename, //
 926             660 }, //
 927         { "--gui --nonews --nosplash --open=./examples/uniref50.fa "
 928                 + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
 929                 + "--seqid=FER1_SPIOL --structureviewer=jmol "
 930                 + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 931                 + "--image=" + filename + " " + "--tempfac=plddt "
 932                 + "--overwrite " //
 933                 + "--noshowssannotations " + "--noshowannotations", //
 934             filename, //
 935             252 }, //
 936         { "--gui --nonews --nosplash --open=./examples/uniref50.fa "
 937                 + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
 938                 + "--seqid=FER1_SPIOL --structureviewer=jmol "
 939                 + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 940                 + "--image=" + filename + " " + "--tempfac=plddt "
 941                 + "--overwrite " //
 942                 + "--showssannotations " + "--noshowannotations", //
 943             filename, //
 944             368 }, //
 945         { "--gui --nonews --nosplash --open=./examples/uniref50.fa "
 946                 + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
 947                 + "--seqid=FER1_SPIOL --structureviewer=jmol "
 948                 + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 949                 + "--image=" + filename + " " + "--tempfac=plddt "
 950                 + "--overwrite " //
 951                 + "--noshowssannotations " + "--showannotations", //
 952             filename, //
 953             524 }, //
 954         { "--gui --nonews --nosplash --open=./examples/uniref50.fa "
 955                 + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
 956                 + "--seqid=FER1_SPIOL --structureviewer=jmol "
 957                 + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
 958                 + "--image=" + filename + " " + "--tempfac=plddt "
 959                 + "--overwrite " //
 960                 + "--showssannotations " + "--showannotations", //
 961             filename, //
 962             660 }, //
 963     };
 964   }
 965
 966 }