From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Fri, 12 Apr 2013 02:16:50 +0000 (+0000)
Subject: inprogress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8a293e9c405a3937f9d0ae598ed4408daafac644;p=jalview.git

inprogress
---

diff --git a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
index 4e26acb..af48cc5 100644
--- a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
@@ -271,6 +271,7 @@ module Evoruby
 
     def get_file( files_in_dir, phylogeny_id, suffix_pattern )
       matching_files = Array.new
+      matching_suffix_files = Array.new
       files_in_dir.each { | file |
 
         if ( !File.directory?( file ) &&
@@ -279,11 +280,22 @@ module Evoruby
              file =~ /^#{phylogeny_id}.*#{suffix_pattern}$/ )
           matching_files << file
         end
+        if ( !File.directory?( file ) &&
+             file !~ /^\./ &&
+             file !~ /^00/ &&
+             file =~ /#{suffix_pattern}$/ )
+          matching_suffix_files << file
+        end
       }
-      if matching_files.length < 1
+      if matching_files.length < 1 && matching_suffix_files.length == 1
+        return matching_suffix_files[ 0 ]
+      end  
+      
+      if matching_files.length < 1 && matching_suffix_files.length < 1
         Util.fatal_error( PRG_NAME, 'no file matching [' + phylogeny_id +
            '_] [' + suffix_pattern + '] present in current directory' )
-      elsif matching_files.length > 1
+      end  
+      if matching_files.length > 1
         Util.fatal_error( PRG_NAME, 'more than one file matching [' + phylogeny_id +
            '_] [' + suffix_pattern + '] present in current directory' )
       end