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 jalview.gui.JvOptionPane;
import jalview.util.ArrayUtils;
-@Test(singleThreaded = true)
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
{
}
@AfterMethod(alwaysRun = true)
- public void tearDown()
+ 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 (Desktop.instance != null)
- Desktop.instance.closeAll_actionPerformed(null);
+ if (Jalview.getInstance() != null)
+ {
+ Jalview.getInstance().doMain(args);
+ }
+ else
+ {
+ Jalview.main(args);
+ }
}
- /* --setprop currently disabled
+ /* --setprops is currently disabled so this test won't work
@Test(groups = "Functional")
public void setpropsTest()
{
- String MOSTLY_HARMLESS = "MOSTLY_HARMLESS";
+ final String MOSTLY_HARMLESS = "MOSTLY_HARMLESS";
String cmdLine = "--setprop=" + MOSTLY_HARMLESS + "=Earth";
String[] args = cmdLine.split("\\s+");
Jalview.main(args);
}
*/
- @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);
+ Assert.assertEquals(Desktop.getDesktopAlignFrames().length, numFrames,
+ "Wrong number of AlignFrames");
+
+ if (sequences != null)
+ {
+ Set<String> 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));
+ }
+ }
- if (sequences != null)
+ Assert.assertFalse(
+ lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
+ } catch (Exception x)
{
- Set<String> openedSequenceNames = new HashSet<>();
- AlignFrame[] afs = Desktop.getAlignFrames();
- for (AlignFrame af : afs)
+ 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)
{
- openedSequenceNames
- .addAll(af.getViewport().getAlignment().getSequenceNames());
+ 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()));
}
- for (String sequence : sequences)
+ } 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)
{
- 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 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" } },
+ /*
+ */
+ //
+ };
- Assert.assertFalse(
- lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
}
- @Test(groups = "Functional")
- public void argFilesGlobAndSubstitutionsTest() throws IOException
+ @DataProvider(name = "argfileOutputFiles")
+ public Object[][] argfileOutputFiles()
{
- cleanupArgfilesImages();
- String cmdLine = "--argfile=" + testfiles + "/dir*/argfile.txt";
- String[] args = cmdLine.split("\\s+");
- Jalview.main(args);
- Commands cmds = Jalview.getInstance().getCommands();
- File file1 = new File(png1);
- File file2 = new File(png2);
- Assert.assertTrue(file1.exists(),
- "Did not make file " + png1 + " from argfile");
- Assert.assertTrue(file2.exists(),
- "Did not make file " + png2 + " from argfile");
- long size1 = Files.size(file1.toPath());
- long size2 = Files.size(file2.toPath());
- Assert.assertTrue(file1.isFile() && size1 > 0);
- Assert.assertTrue(file2.isFile() && size2 > 0);
- Assert.assertTrue(size2 > size1); // png2 has three sequences, png1 has 2
- cleanupArgfilesImages();
+ 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")
String[] t2 = new String[] { "TEST2" };
String[] t3 = new String[] { "TEST3" };
return new Object[][] {
- { "--open=examples/uniref50.fa", true, 1, someUniref50Seqs },
- { "--open examples/uniref50.fa", true, 1, someUniref50Seqs },
- { "--open=examples/uniref50*.fa", true, 1, someUniref50Seqs },
+ /*
+ */
+ { "--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!
- { "--open examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
+ { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
someUniref50Seqs },
- { "--open=[new]examples/uniref50*.fa", true, 2, someUniref50Seqs },
- { "--opennew=examples/uniref50*.fa", true, 2, 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 },
- { "--argfile=" + testfiles + "/argfile0.txt", true, 1,
+ { "--gui --argfile=" + testfiles + "/argfile0.txt", true, 1,
ArrayUtils.concatArrays(t1, t3) },
- { "--argfile=" + testfiles + "/argfile*.txt", true, 4,
+ { "--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())
return false;
}
- public static void cleanupArgfilesImages()
+ public static void cleanupFiles(String[] filenames)
{
- File png1File = new File(png1);
- File png2File = new File(png2);
- if (png1File.exists())
+ for (String filename : filenames)
{
- png1File.delete();
+ File file = new File(filename);
+ if (file.exists())
+ {
+ file.delete();
+ }
}
- if (png2File.exists())
+ }
+
+ 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)
{
- png2File.delete();
+ 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", }, },
+ //
+ };
}
}