X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FFileUtils.java;fp=src%2Fjalview%2Futil%2FFileUtils.java;h=9b56c6438a746518a62605e228db9b34634be346;hb=6125140c3ea968b79423882d1191a897af9d76be;hp=f5b370116c7a753e32001e289b7c970188530502;hpb=be6f655652936ae635f212f4f2daac505d63a0bb;p=jalview.git

diff --git a/src/jalview/util/FileUtils.java b/src/jalview/util/FileUtils.java
index f5b3701..9b56c64 100644
--- a/src/jalview/util/FileUtils.java
+++ b/src/jalview/util/FileUtils.java
@@ -164,7 +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(