JAL-629 Change --open to --append and --opennew to --open. Make --open(new) part...

[jalview.git] / src / jalview / util / FileUtils.java

diff --git a/src/jalview/util/FileUtils.java b/src/jalview/util/FileUtils.java
index b6f4e90..4d35cd2 100644 (file)
--- a/src/jalview/util/FileUtils.java
+++ b/src/jalview/util/FileUtils.java
@@ -12,6 +12,7 @@ import java.nio.file.Paths;
 import java.nio.file.SimpleFileVisitor;
 import java.nio.file.attribute.BasicFileAttributes;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.EnumSet;
 import java.util.List;
 import java.util.stream.Collectors;
@@ -67,10 +68,11 @@ public class FileUtils
           String glob = "glob:" + parentDir.toString() + File.separator
                   + rest;
           PathMatcher pm = FileSystems.getDefault().getPathMatcher(glob);
-          int maxDepth = rest.contains("**") ? Integer.MAX_VALUE
+          int maxDepth = rest.contains("**") ? 1028
                   : (int) (rest.chars()
                           .filter(ch -> ch == File.separatorChar).count())
                           + 1;
+
           Files.walkFileTree(parentDir,
                   EnumSet.of(FileVisitOption.FOLLOW_LINKS), maxDepth,
                   new SimpleFileVisitor<Path>()
@@ -108,6 +110,7 @@ public class FileUtils
         files.add(f);
       }
     }
+    Collections.sort(files);
 
     return files;
   }
@@ -127,7 +130,7 @@ public class FileUtils
   }
 
   /*
-   * This method returns the basename of the first --open or --opennew value. 
+   * This method returns the basename of the first --append or --open value. 
    * Used primarily for substitutions in output filenames.
    */
   public static String getBasename(File file)
@@ -150,7 +153,7 @@ public class FileUtils
   }
 
   /*
-   * This method returns the dirname of the first --open or --opennew value. 
+   * This method returns the dirname of the first --append or --open value. 
    * Used primarily for substitutions in output filenames.
    */
   public static String getDirname(File file)
@@ -161,7 +164,9 @@ public class FileUtils
     String dirname = null;
     try
     {
-      dirname = file.getParentFile().getCanonicalPath();
+      File p = file.getParentFile();
+      File d = new File(substituteHomeDir(p.getPath()));
+      dirname = d.getCanonicalPath();
     } catch (IOException e)
     {
       Console.debug(