X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fbin%2FCommandsTest.java;h=de6185c40b2e181dffd4616f4beebc3f68ae8c82;hb=b122ba188c2ffcbb302809bafc02058e355643ee;hp=57c4d0d07632cff890e5feab05ec90479a33b788;hpb=b9e759d4f273ff99675c6c1fc7fd91d791948b93;p=jalview.git diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java index 57c4d0d..de6185c 100644 --- a/test/jalview/bin/CommandsTest.java +++ b/test/jalview/bin/CommandsTest.java @@ -2,11 +2,14 @@ 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; @@ -14,21 +17,15 @@ import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; -import jalview.bin.argparser.Arg; import jalview.gui.AlignFrame; import jalview.gui.Desktop; import jalview.gui.JvOptionPane; import jalview.util.ArrayUtils; -@Test public class CommandsTest { private static final String testfiles = "test/jalview/bin/argparser/testfiles"; - private static final String png1 = testfiles + "/dir1/test1.png"; - - private static final String png2 = testfiles + "/dir2/test1.png"; - @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { @@ -52,10 +49,38 @@ public class CommandsTest } @AfterMethod(alwaysRun = true) - public void tearDown() + public void tearDown() { - if (Desktop.instance != null) - Desktop.instance.closeAll_actionPerformed(null); + 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 @@ -71,43 +96,93 @@ public class CommandsTest } */ - @Test(groups = "Functional", dataProvider = "cmdLines") + @Test(groups = {"Functional","testTask3"}, dataProvider = "cmdLines") public void commandsOpenTest(String cmdLine, boolean cmdArgs, int numFrames, String[] sequences) { - String[] args = cmdLine.split("\\s+"); - Jalview.main(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"); + 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"); + Assert.assertEquals(Desktop.getDesktopAlignFrames().length, numFrames, + "Wrong number of AlignFrames"); - if (sequences != null) - { - Set openedSequenceNames = new HashSet<>(); - AlignFrame[] afs = Desktop.getAlignFrames(); - for (AlignFrame af : afs) + if (sequences != null) { - openedSequenceNames - .addAll(af.getViewport().getAlignment().getSequenceNames()); + Set openedSequenceNames = new HashSet<>(); + AlignFrame[] afs = Desktop.getDesktopAlignFrames(); + 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)); + } } - for (String sequence : sequences) + + 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) { - Assert.assertTrue(openedSequenceNames.contains(sequence), - "Sequence '" + sequence - + "' was not found in opened alignment files: " - + cmdLine + ".\nOpened sequence names are:\n" - + String.join("\n", openedSequenceNames)); + 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(); } - - Assert.assertFalse( - lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST")); } @Test(groups = "Functional", dataProvider = "argfileOutputFiles") @@ -115,48 +190,104 @@ public class CommandsTest String[] filenames) throws IOException { cleanupFiles(filenames); - String[] args = cmdLine.split("\\s+"); - Jalview.main(args); - Commands cmds = Jalview.getInstance().getCommands(); - Assert.assertNotNull(cmds); - File lastFile = null; - for (String filename : filenames) + String[] args = (cmdLine + " --gui").split("\\s+"); + try { - 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())); + 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(); } - 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[][] { - { "--argfile=" + testfiles + "/**/*.txt", new String[] + // + { "--gui --argfile=" + testfiles + "/**/*.txt", new String[] { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png", testfiles + "/dir3/subdir/test0.png" } }, - { "--argfile=" + testfiles + "/**/argfile.txt", new String[] + { "--gui --argfile=" + testfiles + "/**/argfile.txt", new String[] { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } }, - { "--argfile=" + testfiles + "/dir*/argfile.txt", new String[] + { "--gui --argfile=" + testfiles + "/dir*/argfile.txt", new String[] { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } }, - { "--initsubstitutions --append examples/uniref50.fa --image " + { "--gui --initsubstitutions --append examples/uniref50.fa --image " + testfiles + "/{basename}.png", new String[] { testfiles + "/uniref50.png" } }, - { "--append examples/uniref50.fa --image " + testfiles - + "/{basename}.png", + { "--gui --append examples/uniref50.fa --nosubstitutions --image " + + testfiles + "/{basename}.png", new String[] - { testfiles + "/{basename}.png" } } }; + { testfiles + "/{basename}.png" } } + // + }; + } @DataProvider(name = "cmdLines") @@ -183,18 +314,18 @@ public class CommandsTest { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, ArrayUtils.concatArrays(someUniref50Seqs, t1) }, { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 }, - { "--argfile=" + testfiles + "/argfile0.txt", true, 1, + { "--gui --argfile=" + testfiles + "/argfile0.txt", true, 1, ArrayUtils.concatArrays(t1, t3) }, - { "--argfile=" + testfiles + "/argfile*.txt", true, 5, + { "--gui --argfile=" + testfiles + "/argfile*.txt", true, 5, ArrayUtils.concatArrays(t1, t2, t3) }, - { "--argfile=" + testfiles + "/argfile.autocounter", true, 3, + { "--gui --argfile=" + testfiles + "/argfile.autocounter", true, 3, ArrayUtils.concatArrays(t1, t2) } }; } public static boolean lookForSequenceName(String sequenceName) { - AlignFrame[] afs = Desktop.getAlignFrames(); + AlignFrame[] afs = Desktop.getDesktopAlignFrames(); for (AlignFrame af : afs) { for (String name : af.getViewport().getAlignment().getSequenceNames()) @@ -220,11 +351,17 @@ public class CommandsTest } } - @Test(groups = "Functional", dataProvider = "allLinkedIdsData") - public void allLinkedIdsTest(String cmdLine, Arg a, String[] filenames) + 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.split("\\s+"); - Jalview.main(args); + String[] args = (cmdLine + " --gui").split("\\s+"); + callJalviewMain(args); Commands cmds = Jalview.getInstance().getCommands(); Assert.assertNotNull(cmds); for (String filename : filenames) @@ -233,6 +370,21 @@ public class CommandsTest "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") @@ -240,18 +392,223 @@ public class CommandsTest { return new Object[][] { // - /* - { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --allframes --output={dirname}/{basename}.stk --close", - Arg.OUTPUT, new String[] + { "--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", } }, - */ - { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --allframes --image={dirname}/{basename}.png --close", - Arg.IMAGE, new String[] + "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", } }, + "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", }, }, // }; }