package jalview.bin; import java.io.File; import java.io.IOException; import java.lang.reflect.InvocationTargetException; import java.nio.file.Files; import java.util.Date; import java.util.HashSet; import java.util.Set; import javax.swing.SwingUtilities; import org.testng.Assert; import org.testng.annotations.AfterClass; import org.testng.annotations.AfterMethod; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; import jalview.gui.AlignFrame; import jalview.gui.Desktop; import jalview.gui.JvOptionPane; import jalview.util.ArrayUtils; public class CommandsTest { private static final String testfiles = "test/jalview/bin/argparser/testfiles"; @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { Cache.loadProperties("test/jalview/gui/quitProps.jvprops"); Date oneHourFromNow = new Date( System.currentTimeMillis() + 3600 * 1000); Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow); } @AfterClass(alwaysRun = true) public static void resetProps() { Cache.loadProperties("test/jalview/testProps.jvprops"); } @BeforeClass(alwaysRun = true) public void setUpJvOptionPane() { JvOptionPane.setInteractiveMode(false); JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); } @AfterMethod(alwaysRun = true) public void tearDown() { try { // occasionally we are blocked by Jmol redraws SwingUtilities.invokeAndWait(new Runnable() { @Override public void run() { Desktop.closeDesktop(); } }); } catch (Exception foo) { System.err.println("Failed during teardown with exception"); foo.printStackTrace(); } } public static void callJalviewMain(String[] args) { if (Jalview.getInstance() != null) { Jalview.getInstance().doMain(args); } else { Jalview.main(args); } } /* --setprops is currently disabled so this test won't work @Test(groups = "Functional") public void setpropsTest() { final String MOSTLY_HARMLESS = "MOSTLY_HARMLESS"; String cmdLine = "--setprop=" + MOSTLY_HARMLESS + "=Earth"; String[] args = cmdLine.split("\\s+"); Jalview.main(args); Assert.assertEquals(Cache.getDefault(MOSTLY_HARMLESS, "Magrathea"), "Earth"); } */ @Test(groups = {"Functional","testTask3"}, dataProvider = "cmdLines") public void commandsOpenTest(String cmdLine, boolean cmdArgs, int numFrames, String[] sequences) { try { String[] args = (cmdLine + " --gui").split("\\s+"); callJalviewMain(args); Commands cmds = Jalview.getInstance().getCommands(); Assert.assertNotNull(cmds); Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs, "Commands were not provided in the args"); Assert.assertEquals(cmds.argsWereParsed(), cmdArgs, "Overall command parse and operation is false"); Assert.assertEquals(Desktop.getAlignFrames().length, numFrames, "Wrong number of AlignFrames"); if (sequences != null) { Set openedSequenceNames = new HashSet<>(); AlignFrame[] afs = Desktop.getAlignFrames(); for (AlignFrame af : afs) { openedSequenceNames.addAll( af.getViewport().getAlignment().getSequenceNames()); } for (String sequence : sequences) { Assert.assertTrue(openedSequenceNames.contains(sequence), "Sequence '" + sequence + "' was not found in opened alignment files: " + cmdLine + ".\nOpened sequence names are:\n" + String.join("\n", openedSequenceNames)); } } Assert.assertFalse( lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST")); } catch (Exception x) { Assert.fail("Unexpected exception during commandsOpenTest", x); } finally { tearDown(); } } @Test( groups = { "Functional", "testTask3" }, dataProvider = "structureImageOutputFiles") public void structureImageOutputTest(String cmdLine, String[] filenames) throws IOException { cleanupFiles(filenames); String[] args = (cmdLine + " --gui").split("\\s+"); try { callJalviewMain(args); Commands cmds = Jalview.getInstance().getCommands(); Assert.assertNotNull(cmds); File lastFile = null; for (String filename : filenames) { File file = new File(filename); Assert.assertTrue(file.exists(), "File '" + filename + "' was not created by '" + cmdLine + "'"); Assert.assertTrue(file.isFile(), "File '" + filename + "' is not a file from '" + cmdLine + "'"); Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename + "' has no content from '" + cmdLine + "'"); // make sure the successive output files get bigger! if (lastFile != null) Assert.assertTrue(Files.size(file.toPath()) > Files .size(lastFile.toPath())); } } catch (Exception x) { Assert.fail("Unexpected exception during structureImageOutputTest", x); } finally { cleanupFiles(filenames); tearDown(); } } @Test(groups = "Functional", dataProvider = "argfileOutputFiles") public void argFilesGlobAndSubstitutionsTest(String cmdLine, String[] filenames) throws IOException { cleanupFiles(filenames); String[] args = (cmdLine + " --gui").split("\\s+"); try { callJalviewMain(args); Commands cmds = Jalview.getInstance().getCommands(); Assert.assertNotNull(cmds); File lastFile = null; for (String filename : filenames) { File file = new File(filename); Assert.assertTrue(file.exists(), "File '" + filename + "' was not created by '" + cmdLine + "'"); Assert.assertTrue(file.isFile(), "File '" + filename + "' is not a file from '" + cmdLine + "'"); Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename + "' has no content from '" + cmdLine + "'"); // make sure the successive output files get bigger! if (lastFile != null) Assert.assertTrue(Files.size(file.toPath()) > Files .size(lastFile.toPath())); } } catch (Exception x) { Assert.fail( "Unexpected exception during argFilesGlobAndSubstitutions", x); } finally { cleanupFiles(filenames); tearDown(); } } @DataProvider(name = "structureImageOutputFiles") public Object[][] structureImageOutputFiles() { return new Object[][] { // { "--gui --nonews --nosplash --open=./examples/test_fab41.result/sample.a2m " + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb " + "--structureimage=" + testfiles + "/structureimage1.png " + "--open=./examples/test_fab41.result/sample.a2m " + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb " + "--structureimage=" + testfiles + "/structureimage2.png --scale=1.5 " + "--open=./examples/test_fab41.result/sample.a2m " + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb " + "--structureimage=" + testfiles + "/structureimage3.png --scale=2.0 ", new String[] { testfiles + "/structureimage1.png", testfiles + "/structureimage2.png", testfiles + "/structureimage3.png" } }, { "--headless --noquit --open=./examples/test_fab41.result/sample.a2m " + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb " + "--structureimage=" + testfiles + "/structureimage1.png " + "--open=./examples/test_fab41.result/sample.a2m " + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb " + "--structureimage=" + testfiles + "/structureimage2.png --scale=1.5 " + "--open=./examples/test_fab41.result/sample.a2m " + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb " + "--structureimage=" + testfiles + "/structureimage3.png --scale=2.0 ", new String[] { testfiles + "/structureimage1.png", testfiles + "/structureimage2.png", testfiles + "/structureimage3.png" } }, /* */ // }; } @DataProvider(name = "argfileOutputFiles") public Object[][] argfileOutputFiles() { return new Object[][] { // { "--gui --argfile=" + testfiles + "/**/*.txt", new String[] { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png", testfiles + "/dir3/subdir/test0.png" } }, { "--gui --argfile=" + testfiles + "/**/argfile.txt", new String[] { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } }, { "--gui --argfile=" + testfiles + "/dir*/argfile.txt", new String[] { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } }, { "--gui --initsubstitutions --append examples/uniref50.fa --image " + testfiles + "/{basename}.png", new String[] { testfiles + "/uniref50.png" } }, { "--gui --append examples/uniref50.fa --nosubstitutions --image " + testfiles + "/{basename}.png", new String[] { testfiles + "/{basename}.png" } } // }; } @DataProvider(name = "cmdLines") public Object[][] cmdLines() { String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN", "FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" }; String[] t1 = new String[] { "TEST1" }; String[] t2 = new String[] { "TEST2" }; String[] t3 = new String[] { "TEST3" }; return new Object[][] { /* */ { "--append=examples/uniref50.fa", true, 1, someUniref50Seqs }, { "--append examples/uniref50.fa", true, 1, someUniref50Seqs }, { "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs }, // NOTE we cannot use shell expansion in tests, so list all files! { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1, someUniref50Seqs }, { "--append=[new]examples/uniref50*.fa", true, 2, someUniref50Seqs }, { "--open=examples/uniref50*.fa", true, 2, someUniref50Seqs }, { "examples/uniref50.fa", true, 1, someUniref50Seqs }, { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, ArrayUtils.concatArrays(someUniref50Seqs, t1) }, { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 }, { "--gui --argfile=" + testfiles + "/argfile0.txt", true, 1, ArrayUtils.concatArrays(t1, t3) }, { "--gui --argfile=" + testfiles + "/argfile*.txt", true, 5, ArrayUtils.concatArrays(t1, t2, t3) }, { "--gui --argfile=" + testfiles + "/argfile.autocounter", true, 3, ArrayUtils.concatArrays(t1, t2) } }; } public static boolean lookForSequenceName(String sequenceName) { AlignFrame[] afs = Desktop.getAlignFrames(); for (AlignFrame af : afs) { for (String name : af.getViewport().getAlignment().getSequenceNames()) { if (sequenceName.equals(name)) { return true; } } } return false; } public static void cleanupFiles(String[] filenames) { for (String filename : filenames) { File file = new File(filename); if (file.exists()) { file.delete(); } } } private final String deleteDir = "test/deleteAfter"; @Test( groups = "Functional", dataProvider = "allLinkedIdsData", singleThreaded = true) public void allLinkedIdsTest(String cmdLine, String[] filenames, String[] nonfilenames) { String[] args = (cmdLine + " --gui").split("\\s+"); callJalviewMain(args); Commands cmds = Jalview.getInstance().getCommands(); Assert.assertNotNull(cmds); for (String filename : filenames) { Assert.assertTrue(new File(filename).exists(), "File '" + filename + "' was not created"); } cleanupFiles(filenames); if (nonfilenames != null) { for (String nonfilename : nonfilenames) { File nonfile = new File(nonfilename); Assert.assertFalse(nonfile.exists(), "File " + nonfilename + " exists when it shouldn't!"); } } File deleteDirF = new File(deleteDir); if (deleteDirF.exists()) { deleteDirF.delete(); } } @DataProvider(name = "allLinkedIdsData") public Object[][] allLinkedIdsData() { return new Object[][] { // { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close", new String[] { "test/jalview/bin/argparser/testfiles/test1.stk", "test/jalview/bin/argparser/testfiles/test2.stk", "test/jalview/bin/argparser/testfiles/test3.stk", }, null }, { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close", new String[] { "test/jalview/bin/argparser/testfiles/test1.png", "test/jalview/bin/argparser/testfiles/test2.png", "test/jalview/bin/argparser/testfiles/test3.png", }, null }, { "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close", new String[] { "test/jalview/bin/argparser/testfiles/test1.stk", "test/jalview/bin/argparser/testfiles/test2.stk", "test/jalview/bin/argparser/testfiles/test3.stk", }, new String[] { "test/jalview/bin/argparser/testfiles/dir1/test1.stk", "test/jalview/bin/argparser/testfiles/dir1/test2.stk", "test/jalview/bin/argparser/testfiles/dir2/test1.stk", "test/jalview/bin/argparser/testfiles/dir2/test2.stk", "test/jalview/bin/argparser/testfiles/dir2/test3.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, }, { "--gui --open=test/jalview/bin/argparser/**/*.fa --all --output={dirname}/{basename}.stk --close", new String[] { "test/jalview/bin/argparser/testfiles/test1.stk", "test/jalview/bin/argparser/testfiles/test2.stk", "test/jalview/bin/argparser/testfiles/test3.stk", "test/jalview/bin/argparser/testfiles/dir1/test1.stk", "test/jalview/bin/argparser/testfiles/dir1/test2.stk", "test/jalview/bin/argparser/testfiles/dir2/test1.stk", "test/jalview/bin/argparser/testfiles/dir2/test2.stk", "test/jalview/bin/argparser/testfiles/dir2/test3.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, null }, { "--gui --open=test/jalview/bin/argparser/**/*.fa --output=*/*.stk --close", new String[] { "test/jalview/bin/argparser/testfiles/test1.stk", "test/jalview/bin/argparser/testfiles/test2.stk", "test/jalview/bin/argparser/testfiles/test3.stk", "test/jalview/bin/argparser/testfiles/dir1/test1.stk", "test/jalview/bin/argparser/testfiles/dir1/test2.stk", "test/jalview/bin/argparser/testfiles/dir2/test1.stk", "test/jalview/bin/argparser/testfiles/dir2/test2.stk", "test/jalview/bin/argparser/testfiles/dir2/test3.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, null }, { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --all --output=*/*.stk --close", new String[] { "test/jalview/bin/argparser/testfiles/dir1/test1.stk", "test/jalview/bin/argparser/testfiles/dir1/test2.stk", "test/jalview/bin/argparser/testfiles/dir2/test1.stk", "test/jalview/bin/argparser/testfiles/dir2/test2.stk", "test/jalview/bin/argparser/testfiles/dir2/test3.stk", }, new String[] { "test/jalview/bin/argparser/testfiles/test1.stk", "test/jalview/bin/argparser/testfiles/test2.stk", "test/jalview/bin/argparser/testfiles/test3.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, }, { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*/*.stk --close", new String[] { "test/jalview/bin/argparser/testfiles/dir2/test1.stk", "test/jalview/bin/argparser/testfiles/dir2/test2.stk", "test/jalview/bin/argparser/testfiles/dir2/test3.stk", }, new String[] { "test/jalview/bin/argparser/testfiles/test1.stk", "test/jalview/bin/argparser/testfiles/test2.stk", "test/jalview/bin/argparser/testfiles/test3.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, }, { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close", new String[] { "test/jalview/bin/argparser/testfiles/dir2/test1.stk", "test/jalview/bin/argparser/testfiles/dir2/test2.stk", "test/jalview/bin/argparser/testfiles/dir2/test3.stk", }, new String[] { "test/jalview/bin/argparser/testfiles/test1.stk", "test/jalview/bin/argparser/testfiles/test2.stk", "test/jalview/bin/argparser/testfiles/test3.stk", "test/jalview/bin/argparser/testfiles/dir1/test1.stk", "test/jalview/bin/argparser/testfiles/dir1/test2.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, }, { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close", new String[] { "test/jalview/bin/argparser/testfiles/dir2/test1.stk", "test/jalview/bin/argparser/testfiles/dir2/test2.stk", "test/jalview/bin/argparser/testfiles/dir2/test3.stk", }, new String[] { "test/jalview/bin/argparser/testfiles/test1.stk", "test/jalview/bin/argparser/testfiles/test2.stk", "test/jalview/bin/argparser/testfiles/test3.stk", "test/jalview/bin/argparser/testfiles/dir1/test1.stk", "test/jalview/bin/argparser/testfiles/dir1/test2.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, }, { "--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", new String[] { "test/jalview/bin/argparser/testfiles/dir1/test1.stk", "test/jalview/bin/argparser/testfiles/dir1/test2.stk", "test/jalview/bin/argparser/testfiles/dir2/test1.aln", "test/jalview/bin/argparser/testfiles/dir2/test2.aln", "test/jalview/bin/argparser/testfiles/dir2/test3.aln", }, new String[] { "test/jalview/bin/argparser/testfiles/test1.stk", "test/jalview/bin/argparser/testfiles/test2.stk", "test/jalview/bin/argparser/testfiles/test3.stk", "test/jalview/bin/argparser/testfiles/dir2/test1.stk", "test/jalview/bin/argparser/testfiles/dir2/test2.stk", "test/jalview/bin/argparser/testfiles/dir2/test3.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", "test/jalview/bin/argparser/testfiles/test1.aln", "test/jalview/bin/argparser/testfiles/test2.aln", "test/jalview/bin/argparser/testfiles/test3.aln", "test/jalview/bin/argparser/testfiles/dir1/test1.aln", "test/jalview/bin/argparser/testfiles/dir1/test2.aln", "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln", "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln", "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln", "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, }, // --mkdirs { "--headless --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output " + deleteDir + "/{dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=" + deleteDir + "/{dirname}/{basename}.aln --close --all --mkdirs", new String[] { deleteDir + "/test/jalview/bin/argparser/testfiles/dir1/test1.stk", deleteDir + "/test/jalview/bin/argparser/testfiles/dir1/test2.stk", deleteDir + "/test/jalview/bin/argparser/testfiles/dir2/test1.aln", deleteDir + "/test/jalview/bin/argparser/testfiles/dir2/test2.aln", deleteDir + "/test/jalview/bin/argparser/testfiles/dir2/test3.aln", }, new String[] { "test/jalview/bin/argparser/testfiles/test1.stk", "test/jalview/bin/argparser/testfiles/test2.stk", "test/jalview/bin/argparser/testfiles/test3.stk", "test/jalview/bin/argparser/testfiles/dir2/test1.stk", "test/jalview/bin/argparser/testfiles/dir2/test2.stk", "test/jalview/bin/argparser/testfiles/dir2/test3.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", "test/jalview/bin/argparser/testfiles/test1.aln", "test/jalview/bin/argparser/testfiles/test2.aln", "test/jalview/bin/argparser/testfiles/test3.aln", "test/jalview/bin/argparser/testfiles/dir1/test1.aln", "test/jalview/bin/argparser/testfiles/dir1/test2.aln", "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln", "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln", "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln", "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", deleteDir + "test/jalview/bin/argparser/testfiles/test1.stk", deleteDir + "test/jalview/bin/argparser/testfiles/test2.stk", deleteDir + "test/jalview/bin/argparser/testfiles/test3.stk", deleteDir + "test/jalview/bin/argparser/testfiles/dir2/test1.stk", deleteDir + "test/jalview/bin/argparser/testfiles/dir2/test2.stk", deleteDir + "test/jalview/bin/argparser/testfiles/dir2/test3.stk", deleteDir + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk", deleteDir + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk", deleteDir + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk", deleteDir + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", deleteDir + "test/jalview/bin/argparser/testfiles/test1.aln", deleteDir + "test/jalview/bin/argparser/testfiles/test2.aln", deleteDir + "test/jalview/bin/argparser/testfiles/test3.aln", deleteDir + "test/jalview/bin/argparser/testfiles/dir1/test1.aln", deleteDir + "test/jalview/bin/argparser/testfiles/dir1/test2.aln", deleteDir + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln", deleteDir + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln", deleteDir + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln", deleteDir + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, }, // }; } }