Merge branch 'improvement/JAL-4262_deprecation_warning_when_old_CLI_arguments_are_pro...

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index d910819..e6c7b54 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -73,6 +73,8 @@ public class Commands
 
   private boolean argsWereParsed = false;
 
+  private List<String> errors = new ArrayList<>();
+
   public Commands(ArgParser argparser, boolean headless)
   {
     this(Desktop.instance, argparser, headless);
@@ -139,6 +141,25 @@ public class Commands
       }
 
     }
+
+    // report errors
+    StringBuilder sb = new StringBuilder();
+    for (String error : errors)
+    {
+      sb.append("- " + error);
+      sb.append("\n");
+    }
+    if (Platform.isHeadless())
+    {
+      Console.debug("All errors from command line argument commands:\n"
+              + sb.toString());
+    }
+    else
+    {
+      // scrollable dialog box
+
+    }
+
     if (argParser.getBoolean(Arg.QUIT))
     {
       Jalview.getInstance().exit(
@@ -166,7 +187,11 @@ public class Commands
     boolean theseArgsWereParsed = false;
     ArgValuesMap avm = argParser.getLinkedArgs(id);
     if (avm == null)
+    {
       return true;
+    }
+
+    boolean isError = false;
 
     // set wrap scope here so it can be applied after structures are opened
     boolean wrap = false;
@@ -219,7 +244,8 @@ public class Commands
           {
             if (!(new File(openFile)).exists())
             {
-              Console.warn("Can't find file '" + openFile + "'");
+              addError("Can't find file '" + openFile + "'");
+              isError = true;
               continue;
             }
           }
@@ -234,7 +260,8 @@ public class Commands
           format = new IdentifyFile().identify(openFile, protocol);
         } catch (FileFormatException e1)
         {
-          Console.error("Unknown file format for '" + openFile + "'");
+          addError("Unknown file format for '" + openFile + "'");
+          isError = true;
           continue;
         }
 
@@ -260,15 +287,16 @@ public class Commands
           } catch (Throwable thr)
           {
             xception = true;
-            Console.error("Couldn't open '" + openFile + "' as " + format
-                    + " " + thr.getLocalizedMessage()
+            addError("Couldn't open '" + openFile + "' as " + format + " "
+                    + thr.getLocalizedMessage()
                     + " (Enable debug for full stack trace)");
+            isError = true;
             Console.debug("Exception when opening '" + openFile + "'", thr);
           } finally
           {
             if (af == null && !xception)
             {
-              Console.info("Ignoring '" + openFile
+              addInfo("Ignoring '" + openFile
                       + "' - no alignment data found.");
               continue;
             }
@@ -285,8 +313,7 @@ public class Commands
 
             if (cs == null && !"None".equals(colour))
             {
-              Console.warn(
-                      "Couldn't parse '" + colour + "' as a colourscheme.");
+              addWarn("Couldn't parse '" + colour + "' as a colourscheme.");
             }
             else
             {
@@ -350,7 +377,8 @@ public class Commands
                       "examples/testdata/uniref50_test_tree", treefile);
             } catch (IOException e)
             {
-              Console.warn("Couldn't add tree " + treefile, e);
+              addError("Couldn't add tree " + treefile, e);
+              isError = true;
             }
           }
 
@@ -421,7 +449,7 @@ public class Commands
         }
         else
         {
-          Console.warn("No more files to open");
+          Console.info("No more files to open");
         }
       }
       if (progressBarSet && desktop != null)
@@ -451,10 +479,8 @@ public class Commands
 
           if (seq == null)
           {
-            Console.warn("Could not find sequence for argument "
+            addWarn("Could not find sequence for argument "
                     + Arg.STRUCTURE.argString() + "=" + val);
-            // you probably want to continue here, not break
-            // break;
             continue;
           }
           File structureFile = null;
@@ -487,14 +513,14 @@ public class Commands
 
           if (structureFile == null)
           {
-            Console.warn("Not provided structure file with '" + val + "'");
+            addWarn("Not provided structure file with '" + val + "'");
             continue;
           }
 
           if (!structureFile.exists())
           {
-            Console.warn("Structure file '"
-                    + structureFile.getAbsoluteFile() + "' not found.");
+            addWarn("Structure file '" + structureFile.getAbsoluteFile()
+                    + "' not found.");
             continue;
           }
 
@@ -526,7 +552,7 @@ public class Commands
             } catch (IOException e)
             {
               paeFilepath = paeFile.getAbsolutePath();
-              Console.warn("Problem with the PAE file path: '"
+              addWarn("Problem with the PAE file path: '"
                       + paeFile.getPath() + "'");
             }
           }
@@ -569,7 +595,7 @@ public class Commands
                 if (it.hasNext())
                   sb.append(", ");
               }
-              Console.warn(sb.toString());
+              addWarn(sb.toString());
             }
           }
 
@@ -586,7 +612,8 @@ public class Commands
 
           if (sv == null)
           {
-            Console.error("Failed to import and open structure view.");
+            addError("Failed to import and open structure view for file '"
+                    + structureFile + "'.");
             continue;
           }
           try
@@ -604,13 +631,15 @@ public class Commands
             }
             if (tries == 0 && sv.isBusy())
             {
-              Console.warn(
-                      "Gave up waiting for structure viewer to load. Something may have gone wrong.");
+              addWarn("Gave up waiting for structure viewer to load file '"
+                      + structureFile
+                      + "'. Something may have gone wrong.");
             }
           } catch (Exception x)
           {
-            Console.warn("Exception whilst waiting for structure viewer "
+            addError("Exception whilst waiting for structure viewer "
                     + structureFilepath, x);
+            isError = true;
           }
 
           // add StructureViewer to svMap list
@@ -659,7 +688,7 @@ public class Commands
                       typeS.toUpperCase(Locale.ROOT));
             } catch (IllegalArgumentException e)
             {
-              Console.warn("Do not know image format '" + typeS
+              addWarn("Do not know image format '" + typeS
                       + "', using PNG");
               imageType = TYPE.PNG;
             }
@@ -676,6 +705,18 @@ public class Commands
                 AppJmol jmol = (AppJmol) sview;
                 try
                 {
+                  whatNext wn = this.checksBeforeWritingToFile(avm, subVals,
+                          false, structureImageFilename, "structure image");
+                  if (wn == whatNext.ERROR)
+                  {
+                    isError = true;
+                    continue;
+                  }
+                  else if (wn == whatNext.CONTINUE)
+                  {
+                    continue;
+                  }
+
                   Console.debug("Rendering image to " + structureImageFile);
                   jmol.makePDBImage(structureImageFile, imageType, renderer,
                           userBis);
@@ -684,16 +725,18 @@ public class Commands
 
                 } catch (ImageOutputException ioexc)
                 {
-                  Console.warn("Unexpected error whilst exporting image to "
+                  addError("Unexpected error whilst exporting image to "
                           + structureImageFile, ioexc);
+                  isError = true;
+                  continue;
                 }
 
               }
               break;
             default:
-              Console.warn("Cannot export image for structure viewer "
+              addWarn("Cannot export image for structure viewer "
                       + sv.getViewerType() + " yet");
-              break;
+              continue;
             }
           }
         }
@@ -726,7 +769,7 @@ public class Commands
     }
     */
 
-    return theseArgsWereParsed;
+    return theseArgsWereParsed && !isError;
   }
 
   protected void processGroovyScript(String id)
@@ -736,7 +779,7 @@ public class Commands
 
     if (af == null)
     {
-      Console.warn("Did not have an alignment window for id=" + id);
+      addWarn("Did not have an alignment window for id=" + id);
       return;
     }
 
@@ -760,10 +803,11 @@ public class Commands
 
     if (af == null)
     {
-      Console.warn("Did not have an alignment window for id=" + id);
+      addWarn("Did not have an alignment window for id=" + id);
       return false;
     }
 
+    boolean isError = false;
     if (avm.containsArg(Arg.IMAGE))
     {
       for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
@@ -804,6 +848,19 @@ public class Commands
         Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
 
         Console.info("Writing " + file);
+
+        whatNext wn = this.checksBeforeWritingToFile(avm, subVal, false,
+                fileName, "image");
+        if (wn == whatNext.ERROR)
+        {
+          isError = true;
+          continue;
+        }
+        else if (wn == whatNext.CONTINUE)
+        {
+          continue;
+        }
+
         try
         {
           switch (type)
@@ -851,17 +908,19 @@ public class Commands
             break;
 
           default:
-            Console.warn(Arg.IMAGE.argString() + " type '" + type
+            addWarn(Arg.IMAGE.argString() + " type '" + type
                     + "' not known. Ignoring");
             break;
           }
         } catch (Exception ioex)
         {
-          Console.warn("Unexpected error during export", ioex);
+          addError("Unexpected error during export to '" + fileName + "'",
+                  ioex);
+          isError = true;
         }
       }
     }
-    return true;
+    return !isError;
   }
 
   protected boolean processOutput(String id)
@@ -871,10 +930,12 @@ public class Commands
 
     if (af == null)
     {
-      Console.warn("Did not have an alignment window for id=" + id);
+      addWarn("Did not have an alignment window for id=" + id);
       return false;
     }
 
+    boolean isError = false;
+
     if (avm.containsArg(Arg.OUTPUT))
     {
       for (ArgValue av : avm.getArgValueList(Arg.OUTPUT))
@@ -884,24 +945,6 @@ public class Commands
         String fileName = subVals.getContent();
         boolean stdout = ArgParser.STDOUTFILENAME.equals(fileName);
         File file = new File(fileName);
-        boolean overwrite = ArgParser.getFromSubValArgOrPref(avm,
-                Arg.OVERWRITE, subVals, null, "OVERWRITE_OUTPUT", false);
-        // backups. Use the Arg.BACKUPS or subval "backups" setting first,
-        // otherwise if headless assume false, if not headless use the user
-        // preference with default true.
-        boolean backups = ArgParser.getFromSubValArgOrPref(avm, Arg.BACKUPS,
-                subVals, null,
-                Platform.isHeadless() ? null : BackupFiles.ENABLED,
-                !Platform.isHeadless());
-
-        // if backups is not true then --overwrite must be specified
-        if (file.exists() && !(overwrite || backups || stdout))
-        {
-          Console.error("Won't overwrite file '" + fileName + "' without "
-                  + Arg.OVERWRITE.argString() + " or "
-                  + Arg.BACKUPS.argString() + " set");
-          return false;
-        }
 
         String name = af.getName();
         String format = ArgParser.getValueFromSubValOrArg(avm, av,
@@ -951,41 +994,49 @@ public class Commands
               validSB.append(")");
             }
 
-            Jalview.exit("No valid format specified for "
+            addError("No valid format specified for "
                     + Arg.OUTPUT.argString() + ". Valid formats are "
-                    + validSB.toString() + ".", ExitCode.INVALID_FORMAT);
-            // this return really shouldn't happen
-            return false;
+                    + validSB.toString() + ".");
+            continue;
           }
         }
 
-        String savedBackupsPreference = Cache
-                .getDefault(BackupFiles.ENABLED, null);
-        Console.debug("Setting backups to " + backups);
-        Cache.applicationProperties.put(BackupFiles.ENABLED,
-                Boolean.toString(backups));
+        whatNext wn = this.checksBeforeWritingToFile(avm, subVals, true,
+                fileName, ff.getName());
+        if (wn == whatNext.ERROR)
+        {
+          isError = true;
+          continue;
+        }
+        else if (wn == whatNext.CONTINUE)
+        {
+          continue;
+        }
+
+        boolean backups = ArgParser.getFromSubValArgOrPref(avm, Arg.BACKUPS,
+                subVals, null,
+                Platform.isHeadless() ? null : BackupFiles.ENABLED,
+                !Platform.isHeadless());
 
         Console.info("Writing " + fileName);
 
-        af.saveAlignment(fileName, ff, stdout);
-        Console.debug("Returning backups to " + savedBackupsPreference);
-        if (savedBackupsPreference != null)
-          Cache.applicationProperties.put(BackupFiles.ENABLED,
-                  savedBackupsPreference);
+        af.saveAlignment(fileName, ff, stdout, backups);
         if (af.isSaveAlignmentSuccessful())
         {
           Console.debug("Written alignment '" + name + "' in "
-                  + ff.getName() + " format to " + file);
+                  + ff.getName() + " format to '" + file + "'");
         }
         else
         {
-          Console.warn("Error writing file " + file + " in " + ff.getName()
+          addError("Error writing file '" + file + "' in " + ff.getName()
                   + " format!");
+          isError = true;
+          continue;
         }
 
       }
     }
-    return true;
+    return !isError;
   }
 
   private SequenceI getSpecifiedSequence(AlignFrame af, ArgValuesMap avm,
@@ -1051,4 +1102,78 @@ public class Commands
     }
     return svs;
   }
+
+  private void addInfo(String errorMessage)
+  {
+    Console.info(errorMessage);
+    errors.add(errorMessage);
+  }
+
+  private void addWarn(String errorMessage)
+  {
+    Console.warn(errorMessage);
+    errors.add(errorMessage);
+  }
+
+  private void addError(String errorMessage)
+  {
+    addError(errorMessage, null);
+  }
+
+  private void addError(String errorMessage, Exception e)
+  {
+    Console.error(errorMessage, e);
+    errors.add(errorMessage);
+  }
+
+  private enum whatNext
+  {
+    OKAY, CONTINUE, ERROR;
+  }
+
+  private whatNext checksBeforeWritingToFile(ArgValuesMap avm,
+          SubVals subVal, boolean includeBackups, String filename,
+          String adjective)
+  {
+    File file = new File(filename);
+
+    boolean overwrite = ArgParser.getFromSubValArgOrPref(avm, Arg.OVERWRITE,
+            subVal, null, "OVERWRITE_OUTPUT", false);
+    boolean stdout = false;
+    boolean backups = false;
+    if (includeBackups)
+    {
+      stdout = ArgParser.STDOUTFILENAME.equals(filename);
+      // backups. Use the Arg.BACKUPS or subval "backups" setting first,
+      // otherwise if headless assume false, if not headless use the user
+      // preference with default true.
+      backups = ArgParser.getFromSubValArgOrPref(avm, Arg.BACKUPS, subVal,
+              null, Platform.isHeadless() ? null : BackupFiles.ENABLED,
+              !Platform.isHeadless());
+    }
+
+    if (file.exists() && !(overwrite || backups || stdout))
+    {
+      addWarn("Won't overwrite file '" + filename + "' without "
+              + Arg.OVERWRITE.argString()
+              + (includeBackups ? " or " + Arg.BACKUPS.argString() : "")
+              + " set");
+      return whatNext.CONTINUE;
+    }
+
+    boolean mkdirs = ArgParser.getFromSubValArgOrPref(avm, Arg.MKDIRS,
+            subVal, null, "MKDIRS_OUTPUT", false);
+
+    if (!FileUtils.checkParentDir(file, mkdirs))
+    {
+      addError("Directory '"
+              + FileUtils.getParentDir(file).getAbsolutePath()
+              + "' does not exist for " + adjective + " file '" + filename
+              + "'."
+              + (mkdirs ? "" : "  Try using " + Arg.MKDIRS.argString()));
+      return whatNext.ERROR;
+    }
+
+    return whatNext.OKAY;
+  }
 }

diff --git a/src/jalview/bin/argparser/Arg.java b/src/jalview/bin/argparser/Arg.java
index 2bd8e26..9dd5c93 100644 (file)
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -68,14 +68,15 @@ public enum Arg
           true, Opt.BOOLEAN, Opt.BOOTSTRAP, Opt.NOACTION, Opt.SECRET),
   P(Type.CONFIG, "Set a Jalview preference value for this session.",
           Opt.PREFIXKEV, Opt.PRESERVECASE, Opt.STRING, Opt.BOOTSTRAP,
-          Opt.MULTIVALUE, Opt.NOACTION, Opt.SECRET), // keep this secret for now.
+          Opt.MULTIVALUE, Opt.NOACTION, Opt.SECRET), // keep this secret for
+                                                     // now.
 
   // Opening an alignment
   OPEN(Type.OPENING,
           "Opens one or more alignment files or URLs in new alignment windows.",
-          Opt.STRING, Opt.LINKED, Opt.INCREMENTDEFAULTCOUNTER, Opt.MULTIVALUE,
-          Opt.GLOB, Opt.ALLOWSUBSTITUTIONS, Opt.INPUT, Opt.STORED,
-          Opt.PRIMARY),
+          Opt.STRING, Opt.LINKED, Opt.INCREMENTDEFAULTCOUNTER,
+          Opt.MULTIVALUE, Opt.GLOB, Opt.ALLOWSUBSTITUTIONS, Opt.INPUT,
+          Opt.STORED, Opt.PRIMARY),
   APPEND(Type.OPENING,
           "Appends one or more alignment files or URLs to the open alignment window (or opens a new alignment if none already open).",
           Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.GLOB,
@@ -146,8 +147,9 @@ public enum Arg
           Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWMULTIID),
   NOTEMPFAC(Type.STRUCTURE,
           "Do not show the temperature factor annotation for the preceding --structure.",
-          Opt.UNARY, Opt.LINKED, Opt.ALLOWMULTIID, Opt.SECRET), // keep this secret
-                                                            // until it works!
+          Opt.UNARY, Opt.LINKED, Opt.ALLOWMULTIID, Opt.SECRET), // keep this
+                                                                // secret
+  // until it works!
   SHOWSSANNOTATIONS(Type.STRUCTURE, null, Opt.BOOLEAN, Opt.LINKED,
           Opt.ALLOWMULTIID),
 
@@ -224,11 +226,15 @@ public enum Arg
   CLOSE(Type.OPENING,
           "Close the current open alignment window. This occurs after other output arguments. This applies to the current open alignment.  To apply to all ‑‑output and ‑‑image files, use after ‑‑all.",
           Opt.UNARY, Opt.LINKED, Opt.ALLOWMULTIID),
+  MKDIRS(Type.OUTPUT,
+          "Automatically create directories when outputting a file to a new directory.",
+          Opt.UNARY, Opt.LINKED, Opt.ALLOWMULTIID),
 
   // controlling flow of arguments
   NEW(Type.FLOW,
           "Move on to a new alignment window. This will ensure --append will start a new alignment window and other linked arguments will apply to the new alignment window.",
-          Opt.UNARY, Opt.MULTIVALUE, Opt.NOACTION, Opt.INCREMENTDEFAULTCOUNTER),
+          Opt.UNARY, Opt.MULTIVALUE, Opt.NOACTION,
+          Opt.INCREMENTDEFAULTCOUNTER),
   SUBSTITUTIONS(Type.FLOW,
           "The following argument values allow (or don't allow) subsituting filename parts. This is initially true. Valid substitutions are:\n"
                   + "{basename} - the filename-without-extension of the currently --opened file (or first --appended file),\n"
@@ -269,7 +275,8 @@ public enum Arg
           "Allow specific stdout information.  For testing purposes only.",
           Opt.UNARY, Opt.BOOTSTRAP, Opt.SECRET), // do not show this to the user
   SETPROP(Type.CONFIG, "Set an individual Java System property.",
-          Opt.STRING, Opt.MULTIVALUE, Opt.BOOTSTRAP, Opt.SECRET), // not in use yet
+          Opt.STRING, Opt.MULTIVALUE, Opt.BOOTSTRAP, Opt.SECRET), // not in use
+                                                                  // yet
   NIL(Type.FLOW,
           "This argument does nothing on its own, but can be used with linkedIds.",
           Opt.UNARY, Opt.LINKED, Opt.MULTIVALUE, Opt.NOACTION, Opt.SECRET),

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index dba400e..f3cb012 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1252,10 +1252,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   public void saveAlignment(String file, FileFormatI format)
   {
-    saveAlignment(file, format, false);
+    saveAlignment(file, format, false, false);
   }
 
-  public void saveAlignment(String file, FileFormatI format, boolean stdout)
+  public void saveAlignment(String file, FileFormatI format, boolean stdout,
+          boolean forceBackup)
   {
     lastSaveSuccessful = true;
     if (!stdout)
@@ -1308,7 +1309,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       else
       {
         // create backupfiles object and get new temp filename destination
-        boolean doBackup = BackupFiles.getEnabled() && !stdout;
+        boolean doBackup = forceBackup
+                || (BackupFiles.getEnabled() && !stdout);
         BackupFiles backupfiles = null;
         if (doBackup)
         {

diff --git a/src/jalview/util/FileUtils.java b/src/jalview/util/FileUtils.java
index 79cac0a..983ba75 100644 (file)
--- a/src/jalview/util/FileUtils.java
+++ b/src/jalview/util/FileUtils.java
@@ -17,6 +17,8 @@ import java.util.EnumSet;
 import java.util.List;
 import java.util.stream.Collectors;
 
+import jalview.bin.Console;
+
 public class FileUtils
 {
   /*
@@ -226,4 +228,47 @@ public class FileUtils
     }
     return path.toString();
   }
+
+  public static File getParentDir(File file)
+  {
+    if (file == null)
+    {
+      return null;
+    }
+    File parentDir = file.getAbsoluteFile().getParentFile();
+    return parentDir;
+  }
+
+  public static boolean checkParentDir(File file, boolean mkdirs)
+  {
+    if (file == null)
+    {
+      return false;
+    }
+    File parentDir = getParentDir(file);
+    if (parentDir.exists())
+    {
+      // already exists, nothing to do so nothing to worry about!
+      return true;
+    }
+
+    if (!mkdirs)
+    {
+      return false;
+    }
+
+    Path path = file.toPath();
+    for (int i = 0; i < path.getNameCount(); i++)
+    {
+      Path p = path.getName(i);
+      if ("..".equals(p.toString()))
+      {
+        Console.warn("Cautiously not running mkdirs on " + file.toString()
+                + " because the path to be made contains '..'");
+        return false;
+      }
+    }
+
+    return parentDir.mkdirs();
+  }
 }

diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java
index 36522c4..66250d8 100644 (file)
--- a/test/jalview/bin/CommandsTest.java
+++ b/test/jalview/bin/CommandsTest.java
@@ -331,6 +331,8 @@ public class CommandsTest
     }
   }
 
+  private final String deleteDir = "test/deleteAfter";
+
   @Test(
     groups = "Functional",
     dataProvider = "allLinkedIdsData",
@@ -357,6 +359,12 @@ public class CommandsTest
                 "File " + nonfilename + " exists when it shouldn't!");
       }
     }
+
+    File deleteDirF = new File(deleteDir);
+    if (deleteDirF.exists())
+    {
+      deleteDirF.delete();
+    }
   }
 
   @DataProvider(name = "allLinkedIdsData")
@@ -506,6 +514,81 @@ public class CommandsTest
                 "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", }, },
         //
     };
   }