X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fbin%2FCommandsTest.java;h=36522c43836e5ab4ec5677f66e3eaec8ae199a48;hb=871535152992c147f2175c3006b6bec4615fead4;hp=91e32056fc05fd1b14acfa5c62565baf622ed00f;hpb=ad47e73ed0aaa1a24a976802084c3912422f2be7;p=jalview.git

diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java
index 91e3205..36522c4 100644
--- a/test/jalview/bin/CommandsTest.java
+++ b/test/jalview/bin/CommandsTest.java
@@ -19,15 +19,10 @@ import jalview.gui.Desktop;
 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/test2.png";
-
-  private static final String png2 = testfiles + "/dir2/test2.png";
-
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
@@ -53,15 +48,26 @@ public class CommandsTest
   @AfterMethod(alwaysRun = true)
   public void tearDown()
   {
-    if (Desktop.instance != null)
-      Desktop.instance.closeAll_actionPerformed(null);
+    Desktop.closeDesktop();
+  }
+
+  public static void callJalviewMain(String[] args)
+  {
+    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);
@@ -74,61 +80,194 @@ public class CommandsTest
   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");
+
+      if (sequences != null)
+      {
+        Set<String> 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();
 
-    Assert.assertEquals(Desktop.getAlignFrames().length, numFrames);
+    }
+  }
 
-    if (sequences != null)
+  @Test(
+    groups =
+    { "Functional", "testTask1" },
+    dataProvider = "structureImageOutputFiles")
+  public void structureImageOutputTest(String cmdLine, String[] filenames)
+          throws IOException
+  {
+    cleanupFiles(filenames);
+    String[] args = (cmdLine + " --gui").split("\\s+");
+    try
     {
-      Set<String> openedSequenceNames = new HashSet<>();
-      AlignFrame[] afs = Desktop.getAlignFrames();
-      for (AlignFrame af : afs)
+      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 --structureimagescale=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 --structureimagescale=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 --structureimagescale=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 --structureimagescale=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 = "--headless --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")
@@ -140,24 +279,28 @@ public class CommandsTest
     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 },
+        { "--append=[new]examples/uniref50*.fa", true, 2,
             someUniref50Seqs },
-        { "--open=[new]examples/uniref50*.fa", true, 2, someUniref50Seqs },
-        { "--opennew=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)
@@ -176,18 +319,195 @@ public class CommandsTest
     return false;
   }
 
-  public static void cleanupArgfilesImages()
+  public static void cleanupFiles(String[] filenames)
+  {
+    for (String filename : filenames)
+    {
+      File file = new File(filename);
+      if (file.exists())
+      {
+        file.delete();
+      }
+    }
+  }
+
+  @Test(
+    groups = "Functional",
+    dataProvider = "allLinkedIdsData",
+    singleThreaded = true)
+  public void allLinkedIdsTest(String cmdLine, String[] filenames,
+          String[] nonfilenames)
   {
-    File png1File = new File(png1);
-    File png2File = new File(png2);
-    if (png1File.exists())
+    String[] args = (cmdLine + " --gui").split("\\s+");
+    callJalviewMain(args);
+    Commands cmds = Jalview.getInstance().getCommands();
+    Assert.assertNotNull(cmds);
+    for (String filename : filenames)
     {
-      png1File.delete();
+      Assert.assertTrue(new File(filename).exists(),
+              "File '" + filename + "' was not created");
     }
-    if (png2File.exists())
+    cleanupFiles(filenames);
+    if (nonfilenames != null)
     {
-      png2File.delete();
+      for (String nonfilename : nonfilenames)
+      {
+        File nonfile = new File(nonfilename);
+        Assert.assertFalse(nonfile.exists(),
+                "File " + nonfilename + " exists when it shouldn't!");
+      }
     }
   }
 
+  @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", }, },
+        //
+    };
+  }
+
 }