/* * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.bin; import java.awt.image.BufferedImage; import java.io.File; import java.io.IOException; import java.nio.file.Files; import java.util.Date; import java.util.HashSet; import java.util.Set; import javax.imageio.ImageIO; 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) { callJalviewMain(args, false); } public static void callJalviewMain(String[] args, boolean newJalview) { if (Jalview.getInstance() != null && !newJalview) { 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", singleThreaded = true) 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.getDesktopAlignFrames().length, numFrames, "Wrong number of AlignFrames"); if (sequences != null) { 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)); } } 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", singleThreaded = true) public void structureImageOutputTest(String cmdLine, String[] filenames) throws IOException { cleanupFiles(filenames); String[] args = (cmdLine).split("\\s+"); try { callJalviewMain(args, true); Commands cmds = Jalview.getInstance().getCommands(); Assert.assertNotNull(cmds); verifyIncreasingSize(cmdLine, filenames); } catch (Exception x) { Assert.fail("Unexpected exception during structureImageOutputTest", x); } finally { // cleanupFiles(filenames); tearDown(); } } /** * given two command lines, compare the output files produced - they should * exist and be equal in size */ @Test( groups = { "Functional", "testTask3" }, dataProvider = "compareHeadlessAndGUIOps", singleThreaded = true) public void headlessOrGuiImageOutputTest(String[] cmdLines, String[] filenames) throws IOException { cleanupFiles(filenames); try { for (String cmdLine : cmdLines) { CommandLineOperations.Worker runner = CommandLineOperations .getJalviewDesktopRunner(false, cmdLine, 1000); long timeOut = 10000; while (runner.isAlive() && timeOut > 0) { Thread.sleep(25); timeOut -= 25; } } /* * larger margin between IDs and alignment/annotations when in --gui mode * verifyOrderedFileSet(cmdLines[0] + " vs " + cmdLines[1], filenames, false); */ verifySimilarEnoughImages(cmdLines[0] + " vs " + cmdLines[1], filenames, 0.6f, 0f); } catch (Exception x) { Assert.fail("Unexpected exception during structureImageOutputTest", x); } finally { cleanupFiles(filenames); tearDown(); } } @DataProvider(name = "compareHeadlessAndGUIOps") public Object[][] compareHeadlessAndGUIOps() { return new Object[][] { new Object[] { new String[] { "--open examples/uniref50.fa " + "--structure [seqid=FER1_SPIOL,tempfac=plddt,showssannotations,structureviewer=jmol]" + "examples/AlphaFold/AF-P00221-F1-model_v4.pdb " + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json --image=" + testfiles + "/" + "test-al-pae-ss-gui.png --overwrite --gui --quit", "--open examples/uniref50.fa " + "--structure [seqid=FER1_SPIOL,tempfac=plddt,showssannotations,structureviewer=jmol]" + "examples/AlphaFold/AF-P00221-F1-model_v4.pdb " + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json --image=" + testfiles + "/" + "test-al-pae-ss-nogui.png --overwrite --nogui" }, new String[] { testfiles + "/test-al-pae-ss-gui.png", testfiles + "/test-al-pae-ss-nogui.png", } } }; } private static void verifyIncreasingSize(String cmdLine, String[] filenames) throws Exception { verifyOrderedFileSet(cmdLine, filenames, true); } private static void verifyOrderedFileSet(String cmdLine, String[] filenames, boolean increasingSize) throws Exception { 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) { waitForLastWrite(file, 25); if (increasingSize) { Assert.assertTrue( Files.size(file.toPath()) > Files.size(lastFile.toPath()), "Expected " + file.toPath() + " to be larger than " + lastFile.toPath()); } else { Assert.assertEquals(Files.size(file.toPath()), Files.size(lastFile.toPath()), "New file " + file.toPath() + " (actual size) not same as last file's size " + lastFile.toString()); } } // remember it for next file lastFile = file; } } private static void verifySimilarEnoughImages(String cmdLine, String[] filenames, float w_tolerance_pc, float h_tolerance_pc) throws Exception { int min_w = -1; int max_w = -1; int min_h = -1; int max_h = -1; 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 + "'"); BufferedImage img = ImageIO.read(file); if (img.getWidth() < min_w || min_w == -1) { min_w = img.getWidth(); } if (img.getWidth() > max_w || max_w == -1) { max_w = img.getWidth(); } if (img.getHeight() < min_h || min_h == -1) { min_h = img.getHeight(); } if (img.getHeight() > max_h || max_h == -1) { max_h = img.getHeight(); } } Assert.assertTrue(min_w > 0, "Minimum width is not positive (" + min_w + ")"); Assert.assertTrue(max_w > 0, "Maximum width is not positive (" + max_w + ")"); Assert.assertTrue(min_h > 0, "Minimum height is not positive (" + min_h + ")"); Assert.assertTrue(max_h > 0, "Maximum height is not positive (" + max_h + ")"); // tolerance Assert.assertTrue(100 * (max_w - min_w) / min_w < w_tolerance_pc, "Width variation (" + (max_w - min_w) + " not within tolerance of minimum width (" + min_w + ")"); if (max_w != min_w) { System.out.println("Widths within tolerance (" + w_tolerance_pc + "%), min_w=" + min_w + " < max_w=" + max_w); } Assert.assertTrue(100 * (max_h - min_h) / min_h < w_tolerance_pc, "Height variation (" + (max_h - min_h) + " not within tolerance of minimum height (" + min_h + ")"); if (max_h != min_h) { System.out.println("Heights within tolerance (" + h_tolerance_pc + "%), min_h=" + min_h + " < max_h=" + max_h); } } private static long waitForLastWrite(File file, int i) throws IOException { long lastSize, stableSize = Files.size(file.toPath()); // wait around until we are sure the file has been completely written. do { lastSize = stableSize; try { Thread.sleep(i); } catch (Exception x) { } stableSize = Files.size(file.toPath()); } while (stableSize != lastSize); return stableSize; } @Test( groups = "Functional", dataProvider = "argfileOutputFiles", singleThreaded = true) 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())); System.out.println("this file: " + file + " +" + Files.size(file.toPath()) + " greater than " + Files.size(lastFile.toPath())); } // remember it for next file lastFile = file; } } 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 + "/structureimage0-1.png " + "--open=./examples/test_fab41.result/sample.a2m " + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb " + "--structureimage=" + testfiles + "/structureimage0-2.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 + "/structureimage0-3.png --scale=2.0 ", new String[] { testfiles + "/structureimage0-1.png", testfiles + "/structureimage0-2.png", testfiles + "/structureimage0-3.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 + "/structureimage1-1.png " + "--open=./examples/test_fab41.result/sample.a2m " + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb " + "--structureimage=" + testfiles + "/structureimage1-2.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 + "/structureimage1-3.png --scale=2.0 ", new String[] { testfiles + "/structureimage1-1.png", testfiles + "/structureimage1-2.png", testfiles + "/structureimage1-3.png" } }, { "--gui --nonews --nosplash --open examples/1gaq.txt --append ./examples/3W5V.pdb " + "--structure examples/1gaq.txt --seqid \"1GAQ|A\" " + "--structureimage " + testfiles + "/structureimage2-1gaq.png --structure examples/3W5V.pdb " + "--seqid \"3W5V|A\" --structureimage " + testfiles + "/structureimage2-3w5v.png --overwrite", new String[] { testfiles + "/structureimage2-3w5v.png", testfiles + "/structureimage2-1gaq.png", } }, { "--headless --noquit --open ./examples/1gaq.txt --append ./examples/3W5V.pdb " + "--structure examples/1gaq.txt --seqid \"1GAQ|A\" " + "--structureimage " + testfiles + "/structureimage3-1gaq.png --structure examples/3W5V.pdb " + "--seqid \"3W5V|A\" --structureimage " + testfiles + "/structureimage3-3w5v.png --overwrite", new String[] { testfiles + "/structureimage3-3w5v.png", testfiles + "/structureimage3-1gaq.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.getDesktopAlignFrames(); 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", }, }, // }; } @Test( groups = { "Functional", "testTask3" }, dataProvider = "structureImageAnnotationsOutputFiles", singleThreaded = true) public void structureImageAnnotationsOutputTest(String cmdLine, String filename, int height) throws IOException { cleanupFiles(new String[] { filename }); String[] args = (cmdLine).split("\\s+"); callJalviewMain(args, true); // Create new instance of Jalview each time for // linkedIds BufferedImage img = ImageIO.read(new File(filename)); Assert.assertEquals(height, img.getHeight(), "Output image '" + filename + "' is not in the expected height range, possibly because of the wrong number of annotations"); cleanupFiles(new String[] { filename }); tearDown(); } @DataProvider(name = "structureImageAnnotationsOutputFiles") public Object[][] structureImageAnnotationsOutputFiles() { String filename = "test/jalview/bin/argparser/testfiles/test_annotations.png"; return new Object[][] { // MUST use --noquit with --headless to avoid a System.exit() { "--noquit --headless --nonews --nosplash --open=./examples/uniref50.fa " + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb " + "--seqid=FER1_SPIOL --structureviewer=jmol " + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json " + "--image=" + filename + " " + "--tempfac=plddt " + "--overwrite " // + "--noshowssannotations " + "--noshowannotations", // filename, // 252 }, // { "--noquit --headless --nonews --nosplash --open=./examples/uniref50.fa " + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb " + "--seqid=FER1_SPIOL --structureviewer=jmol " + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json " + "--image=" + filename + " " + "--tempfac=plddt " + "--overwrite " // + "--showssannotations " + "--noshowannotations", // filename, // 368 }, // { "--noquit --headless --nonews --nosplash --open=./examples/uniref50.fa " + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb " + "--seqid=FER1_SPIOL --structureviewer=jmol " + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json " + "--image=" + filename + " " + "--tempfac=plddt " + "--overwrite " // + "--noshowssannotations " + "--showannotations", // filename, // 524 }, // { "--noquit --headless --nonews --nosplash --open=./examples/uniref50.fa " + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb " + "--seqid=FER1_SPIOL --structureviewer=jmol " + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json " + "--image=" + filename + " " + "--tempfac=plddt " + "--overwrite " // + "--showssannotations " + "--showannotations", // filename, // 660 }, // { "--gui --nonews --nosplash --open=./examples/uniref50.fa " + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb " + "--seqid=FER1_SPIOL --structureviewer=jmol " + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json " + "--image=" + filename + " " + "--tempfac=plddt " + "--overwrite " // + "--noshowssannotations " + "--noshowannotations", // filename, // 252 }, // { "--gui --nonews --nosplash --open=./examples/uniref50.fa " + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb " + "--seqid=FER1_SPIOL --structureviewer=jmol " + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json " + "--image=" + filename + " " + "--tempfac=plddt " + "--overwrite " // + "--showssannotations " + "--noshowannotations", // filename, // 368 }, // { "--gui --nonews --nosplash --open=./examples/uniref50.fa " + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb " + "--seqid=FER1_SPIOL --structureviewer=jmol " + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json " + "--image=" + filename + " " + "--tempfac=plddt " + "--overwrite " // + "--noshowssannotations " + "--showannotations", // filename, // 524 }, // { "--gui --nonews --nosplash --open=./examples/uniref50.fa " + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb " + "--seqid=FER1_SPIOL --structureviewer=jmol " + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json " + "--image=" + filename + " " + "--tempfac=plddt " + "--overwrite " // + "--showssannotations " + "--showannotations", // filename, // 660 }, // }; } }