X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fbin%2FCommandsTest.java;h=81f0e1f3858865ee3b732efa78b47bc365a7af9d;hb=6723fff70de0a8576fab9196e99ece7ae67f3dbf;hp=bd67ded0e32da5f6d2a150580c329bd24aa9e430;hpb=128a6aca2330923c3e47de8ec4013c8f4ceef47e;p=jalview.git

diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java
index bd67ded..81f0e1f 100644
--- a/test/jalview/bin/CommandsTest.java
+++ b/test/jalview/bin/CommandsTest.java
@@ -1,8 +1,14 @@
 package jalview.bin;
 
+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 org.testng.Assert;
+import org.testng.annotations.AfterClass;
 import org.testng.annotations.AfterMethod;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
@@ -11,10 +17,12 @@ import org.testng.annotations.Test;
 import jalview.gui.AlignFrame;
 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";
+
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
@@ -24,6 +32,12 @@ public class CommandsTest
     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()
   {
@@ -34,44 +48,446 @@ public class CommandsTest
   @AfterMethod(alwaysRun = true)
   public void tearDown()
   {
-    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);
+    }
   }
 
-  @Test(groups = "Functional", dataProvider = "cmdLines")
-  public void commandsOpenTest(String cmdLine, String sequence)
+  /* --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);
-    ArgParser argparser = new ArgParser(args);
-    boolean commandsSuccess = Commands.processArgs(argparser, false);
-    Assert.assertTrue(commandsSuccess, "Overall commandsSuccess is false");
+    Assert.assertEquals(Cache.getDefault(MOSTLY_HARMLESS, "Magrathea"),
+            "Earth");
+  }
+  */
 
-    if (sequence != null)
+  @Test(groups = "Functional", dataProvider = "cmdLines")
+  public void commandsOpenTest(String cmdLine, boolean cmdArgs,
+          int numFrames, String[] sequences)
+  {
+    try
     {
-      AlignFrame[] afs = Desktop.getAlignFrames();
-      boolean found = false;
-      ALIGNFRAME: for (AlignFrame af : afs)
+      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)
       {
-        for (String name : af.getViewport().getAlignment()
-                .getSequenceNames())
+        Set<String> openedSequenceNames = new HashSet<>();
+        AlignFrame[] afs = Desktop.getAlignFrames();
+        for (AlignFrame af : afs)
+        {
+          openedSequenceNames.addAll(
+                  af.getViewport().getAlignment().getSequenceNames());
+        }
+        for (String sequence : sequences)
         {
-          if (sequence.equals(name))
-          {
-            found = true;
-            break ALIGNFRAME;
-          }
+          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.assertTrue(found, "Sequence '" + sequence
-              + "' was not found in opened alignment files: " + cmdLine);
+
+      Assert.assertFalse(
+              lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
+    } catch (Exception x)
+    {
+      Assert.fail("Unexpected exception during commandsOpenTest", x);
+    } finally
+    {
+      tearDown();
+
+    }
+  }
+
+  @Test(groups = "Functional", dataProvider = "structureImageOutputFiles")
+  public void structureImageOutputTest(String cmdLine, String[] filenames)
+          throws IOException
+  {
+    cleanupFiles(filenames);
+    String[] args = (cmdLine + " --gui").split("\\s+");
+    try
+    {
+      callJalviewMain(args);
+      Commands cmds = Jalview.getInstance().getCommands();
+      Assert.assertNotNull(cmds);
+      File lastFile = null;
+      for (String filename : filenames)
+      {
+        File file = new File(filename);
+        Assert.assertTrue(file.exists(), "File '" + filename
+                + "' was not created by '" + cmdLine + "'");
+        Assert.assertTrue(file.isFile(), "File '" + filename
+                + "' is not a file from '" + cmdLine + "'");
+        Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
+                + "' has no content from '" + cmdLine + "'");
+        // make sure the successive output files get bigger!
+        if (lastFile != null)
+          Assert.assertTrue(Files.size(file.toPath()) > Files
+                  .size(lastFile.toPath()));
+      }
+    } catch (Exception x)
+    {
+      Assert.fail("Unexpected exception during structureImageOutputTest",
+              x);
+    } finally
+    {
+      cleanupFiles(filenames);
+      tearDown();
     }
   }
 
+  @Test(groups = "Functional", dataProvider = "argfileOutputFiles")
+  public void argFilesGlobAndSubstitutionsTest(String cmdLine,
+          String[] filenames) throws IOException
+  {
+    cleanupFiles(filenames);
+    String[] args = (cmdLine + " --gui").split("\\s+");
+    try {
+    callJalviewMain(args);
+    Commands cmds = Jalview.getInstance().getCommands();
+    Assert.assertNotNull(cmds);
+    File lastFile = null;
+    for (String filename : filenames)
+    {
+      File file = new File(filename);
+      Assert.assertTrue(file.exists(), "File '" + filename
+              + "' was not created by '" + cmdLine + "'");
+      Assert.assertTrue(file.isFile(), "File '" + filename
+              + "' is not a file from '" + cmdLine + "'");
+      Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
+              + "' has no content from '" + cmdLine + "'");
+      // make sure the successive output files get bigger!
+      if (lastFile != null)
+        Assert.assertTrue(
+                Files.size(file.toPath()) > Files.size(lastFile.toPath()));
+    }
+    } catch (Exception x)
+    {
+      Assert.fail("Unexpected exception during argFilesGlobAndSubstitutions",
+              x);
+    } finally
+    {
+      cleanupFiles(filenames);
+      tearDown();
+    }
+  }
+
+  @DataProvider(name = "structureImageOutputFiles")
+  public Object[][] structureImageOutputFiles()
+  {
+    return new Object[][] {
+        //
+        { "--gui --nonews --nosplash --open=./examples/test_fab41.result/sample.a2m "
+                + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
+                + "--structureimage=" + testfiles + "/structureimage1.png "
+                + "--open=./examples/test_fab41.result/sample.a2m "
+                + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
+                + "--structureimage=" + testfiles
+                + "/structureimage2.png --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" } },
+                */
+        //
+    };
+
+  }
+
+  @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()
   {
-    return new Object[][] { { "--open=examples/uniref50.fa", "FER1_SPIOL" },
-        { "--argfile=test/jalview/bin/argparser/argfile0.txt", null } };
+    String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN",
+        "FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" };
+    String[] t1 = new String[] { "TEST1" };
+    String[] t2 = new String[] { "TEST2" };
+    String[] t3 = new String[] { "TEST3" };
+    return new Object[][] {
+        /*
+        */
+        { "--append=examples/uniref50.fa", true, 1, someUniref50Seqs },
+        { "--append examples/uniref50.fa", true, 1, someUniref50Seqs },
+        { "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs },
+        // NOTE we cannot use shell expansion in tests, so list all files!
+        { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
+            someUniref50Seqs },
+        { "--append=[new]examples/uniref50*.fa", true, 2,
+            someUniref50Seqs },
+        { "--open=examples/uniref50*.fa", true, 2, someUniref50Seqs },
+        { "examples/uniref50.fa", true, 1, someUniref50Seqs },
+        { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
+            ArrayUtils.concatArrays(someUniref50Seqs, t1) },
+        { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
+        { "--gui --argfile=" + testfiles + "/argfile0.txt", true, 1,
+            ArrayUtils.concatArrays(t1, t3) },
+        { "--gui --argfile=" + testfiles + "/argfile*.txt", true, 5,
+            ArrayUtils.concatArrays(t1, t2, t3) },
+        { "--gui --argfile=" + testfiles + "/argfile.autocounter", true, 3,
+            ArrayUtils.concatArrays(t1, t2) } };
+
+  }
+
+  public static boolean lookForSequenceName(String sequenceName)
+  {
+    AlignFrame[] afs = Desktop.getAlignFrames();
+    for (AlignFrame af : afs)
+    {
+      for (String name : af.getViewport().getAlignment().getSequenceNames())
+      {
+        if (sequenceName.equals(name))
+        {
+          return true;
+        }
+      }
+    }
+    return false;
+  }
+
+  public static void cleanupFiles(String[] filenames)
+  {
+    for (String filename : filenames)
+    {
+      File file = new File(filename);
+      if (file.exists())
+      {
+        file.delete();
+      }
+    }
+  }
+
+  @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!");
+      }
+    }
+  }
+
+  @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 --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=open*.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 --opened --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 open*.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.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", }, },
+        //
+    };
   }
 
 }