X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fbin%2FCommandsTest.java;h=e42cc5462d583dc928c3f69a5a828026d7b38796;hb=refs%2Fheads%2Fbug%2FJAL-4290_headless_alignment_figure_with_sse;hp=e4fea7b18c2803c24106f64735d3e8f371ac3e8a;hpb=5afaa80bd2cddc6651867f86a04affffa0896f89;p=jalview.git

diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java
index e4fea7b..e42cc54 100644
--- a/test/jalview/bin/CommandsTest.java
+++ b/test/jalview/bin/CommandsTest.java
@@ -1,103 +1,750 @@
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.bin;
 
 import java.io.File;
 import java.io.IOException;
-import java.lang.management.ManagementFactory;
+import java.lang.reflect.InvocationTargetException;
+import java.nio.file.Files;
+import java.util.Date;
+import java.util.HashSet;
+import java.util.Set;
 
-import org.testng.annotations.BeforeTest;
+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 io.github.classgraph.ClassGraph;
+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";
 
-  private static final int SETUP_TIMEOUT = 30000;
+  @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);
+  }
 
-  private static class Worker extends Thread
+  @AfterClass(alwaysRun = true)
+  public static void resetProps()
   {
-    private final Process process;
+    Cache.loadProperties("test/jalview/testProps.jvprops");
+  }
 
-    private Integer exit;
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
 
-    private Worker(Process process)
+  @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)
     {
-      this.process = process;
+      System.err.println("Failed during teardown with exception");
+      foo.printStackTrace();
     }
 
-    @Override
-    public void run()
+  }
+
+  public static void callJalviewMain(String[] args)
+  {
+    if (Jalview.getInstance() != null)
     {
-      try
-      {
-        exit = process.waitFor();
-      } catch (InterruptedException ignore)
+      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)
       {
-        return;
+        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));
+        }
       }
+
+      Assert.assertFalse(
+              lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
+    } catch (Exception x)
+    {
+      Assert.fail("Unexpected exception during commandsOpenTest", x);
+    } finally
+    {
+      tearDown();
+
     }
   }
 
-  private static ClassGraph scanner = null;
-
-  private static String classpath = null;
+  @Test(
+    groups =
+    { "Functional", "testTask3" },
+    dataProvider = "structureImageOutputFiles",    singleThreaded = true)
+  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);
+      verifyIncreasingSize(cmdLine, filenames);
+    } catch (Exception x)
+    {
+      Assert.fail("Unexpected exception during structureImageOutputTest",
+              x);
+    } finally
+    {
+      cleanupFiles(filenames);
+      tearDown();
+    }
+  }
 
-  private static String modules = null;
+  /**
+   * 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;
+        }
+      }
+      verifyOrderedFileSet(cmdLines[0] + " vs " + cmdLines[1], filenames,
+              false);
+    } 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"
 
-  private static String java_exe = null;
+        }, 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;
+    }
 
-  public synchronized static String getClassPath()
+  }
+  private static long waitForLastWrite(File file, int i) throws IOException
   {
-    java_exe = System.getProperty("java.home") + File.separator + "bin"
-            + File.separator + "java";
-    classpath = ManagementFactory.getRuntimeMXBean().getClassPath();
-    return classpath;
+    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;
   }
 
-  private Worker getJalviewDesktopRunner(boolean withAwt, String cmd,
-          int timeout)
+  @Test(groups = "Functional", dataProvider = "argfileOutputFiles", singleThreaded = true)
+
+  public void argFilesGlobAndSubstitutionsTest(String cmdLine,
+          String[] filenames) throws IOException
   {
-    // Note: JAL-3065 - don't include quotes for lib/* because the arguments are
-    // not expanded by the shell
-    String classpath = getClassPath();
-    String _cmd = java_exe + " "
-            + (withAwt ? "-Djava.awt.headless=true" : "") + " -classpath "
-            + classpath + " jalview.bin.Jalview ";
-    Process ls2_proc = null;
-    Worker worker = null;
+    cleanupFiles(filenames);
+    String[] args = (cmdLine + " --gui").split("\\s+");
     try
     {
-      ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
-    } catch (Throwable e1)
+      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
     {
-      e1.printStackTrace();
+      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" } },
+        { "--gui --nonews --nosplash --open examples/1gaq.txt --append ./examples/3W5V.pdb "+"--structure examples/1gaq.txt --seqid \"1GAQ|A\" "+"--structureimage "+testfiles+"/1gaq.png --structure examples/3W5V.pdb "+"--seqid \"3W5V|A\" --structureimage "+testfiles+"/3w5v.png --overwrite",
+                	
+                new String[] {
+                		testfiles+"/1gaq.png",testfiles+"/3w5v.png"
+                }
+        },
+        { "--headless --noquit --open ./examples/1gaq.txt --append ./examples/3W5V.pdb "+"--structure examples/1gaq.txt --seqid \"1GAQ|A\" "+"--structureimage "+testfiles+"/1gaq.png --structure examples/3W5V.pdb "+"--seqid \"3W5V|A\" --structureimage "+testfiles+"/3w5v.png --overwrite",
+        	
+            new String[] {
+            		testfiles+"/1gaq.png",testfiles+"/3w5v.png"
+            }
     }
-    if (ls2_proc != null)
+
+        /*
+                */
+        //
+    };
+
+  }
+
+  @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)
     {
-      worker = new Worker(ls2_proc);
-      worker.start();
-      try
+      for (String name : af.getViewport().getAlignment().getSequenceNames())
       {
-        worker.join(timeout);
-      } catch (InterruptedException e)
+        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())
       {
-        System.err.println("Thread interrupted");
+        file.delete();
       }
     }
-    return worker;
   }
 
-  @BeforeTest(alwaysRun = true)
-  public void initialize()
+  private final String deleteDir = "test/deleteAfter";
+
+  @Test(
+    groups = "Functional",
+    dataProvider = "allLinkedIdsData",
+    singleThreaded = true)
+  public void allLinkedIdsTest(String cmdLine, String[] filenames,
+          String[] nonfilenames)
   {
-    new CommandsTest();
+    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();
+    }
   }
 
-  @Test(groups = "Functional")
-  public void setUpForHeadlessCommandsTest() throws IOException
+  @DataProvider(name = "allLinkedIdsData")
+  public Object[][] allLinkedIdsData()
   {
-    String cmds = "--open=./examples/uniref50.fa";
-    Worker worker = getJalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
+    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", }, },
+        //
+    };
   }
 
 }