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