X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FFileUtils.java;h=e62a7d600892584996bed6bdff1aee8aec075757;hb=a7169b1c72607f3c9357195b4999869650a2a891;hp=63af0bc4d96e8840d4fa52200f73d096ce8f066c;hpb=988d7abeef3e08d01ff8ebb918325d95caae70b7;p=jalview.git

diff --git a/src/jalview/util/FileUtils.java b/src/jalview/util/FileUtils.java
index 63af0bc..e62a7d6 100644
--- a/src/jalview/util/FileUtils.java
+++ b/src/jalview/util/FileUtils.java
@@ -12,10 +12,13 @@ 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;
 
+import jalview.bin.Console;
+
 public class FileUtils
 {
   /*
@@ -65,10 +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>()
@@ -106,6 +110,7 @@ public class FileUtils
         files.add(f);
       }
     }
+    Collections.sort(files);
 
     return files;
   }
@@ -123,4 +128,65 @@ public class FileUtils
             ? System.getProperty("user.home") + path.substring(1)
             : path;
   }
+
+  /*
+   * This method returns the basename of File file
+   */
+  public static String getBasename(File file)
+  {
+    return getBasenameOrExtension(file, false);
+  }
+
+  /*
+   * This method returns the extension of File file.
+   */
+  public static String getExtension(File file)
+  {
+    return getBasenameOrExtension(file, true);
+  }
+
+  public static String getBasenameOrExtension(File file, boolean extension)
+  {
+    if (file == null)
+      return null;
+
+    String value = null;
+    String filename = file.getName();
+    int lastDot = filename.lastIndexOf('.');
+    if (lastDot > 0) // don't truncate if starts with '.'
+    {
+      value = extension ? filename.substring(lastDot + 1)
+              : filename.substring(0, lastDot);
+    }
+    else
+    {
+      value = extension ? "" : filename;
+    }
+    return 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)
+  {
+    if (file == null)
+      return null;
+
+    String dirname = null;
+    try
+    {
+      File p = file.getParentFile();
+      File d = new File(substituteHomeDir(p.getPath()));
+      dirname = d.getCanonicalPath();
+    } catch (IOException e)
+    {
+      Console.debug(
+              "Exception when getting dirname of '" + file.getPath() + "'",
+              e);
+      dirname = "";
+    }
+    return dirname;
+  }
 }