inprogress

[jalview.git] / forester / ruby / evoruby / lib / evo / tool / phylogenies_decorator.rb

diff --git a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
index 953f924..b2d5a87 100644 (file)
--- a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
@@ -101,32 +101,9 @@ module Evoruby
         Util.fatal_error( PRG_NAME, 'logfile [' + LOG_FILE + '] already exists' )
       end
 
-      allowed_opts = Array.new
-      allowed_opts.push( IDS_ONLY_OPTION )
-      allowed_opts.push( DOMAINS_ONLY_OPTION )
-
-      disallowed = cla.validate_allowed_options_as_str( allowed_opts )
-      if ( disallowed.length > 0 )
-        Util.fatal_error( PRG_NAME, "unknown option(s): " + disallowed )
-      end
-
-      ids_only = false
-      domains_only = false
-
       in_suffix = cla.get_file_name( 0 )
       out_suffix = cla.get_file_name( 1 )
 
-      if cla.is_option_set?( IDS_ONLY_OPTION )
-        ids_only = true
-      end
-      if cla.is_option_set?( DOMAINS_ONLY_OPTION )
-        domains_only = true
-      end
-
-      if ( ids_only && domains_only )
-        Util.fatal_error( PRG_NAME, 'attempt to use ids only and domains only at the same time' )
-      end
-
       log = String.new
 
       now = DateTime.now
@@ -189,7 +166,8 @@ module Evoruby
           log << counter.to_s + ': ' + phylogeny_file + ' -> ' +  outfile + NL
 
           phylogeny_id = get_id( phylogeny_file )
-
+          puts "id:" + phylogeny_id
+          
           ids_mapfile_name = nil
           domains_mapfile_name = nil
           seqs_file_name = nil
@@ -259,33 +237,25 @@ module Evoruby
 
 
     def get_id( phylogeny_file_name )
-      phylogeny_file_name =~ /^([^_]+)/
+      phylogeny_file_name =~ /^(.+?)__/
       $1
     end
 
     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 ) &&
              file !~ /^\./ &&
              file !~ /^00/ &&
-             file =~ /^#{phylogeny_id}.*#{suffix_pattern}$/ )
+             file =~ /^#{phylogeny_id}#{suffix_pattern}$/ )
           matching_files << file
         end
-        if ( !File.directory?( file ) &&
-             file !~ /^\./ &&
-             file !~ /^00/ &&
-             file =~ /#{suffix_pattern}$/ )
-          matching_suffix_files << file
-        end
       }
-      if matching_files.length < 1 && matching_suffix_files.length == 1
-        return matching_suffix_files[ 0 ]
-      end
+    
 
-      if matching_files.length < 1 && matching_suffix_files.length < 1
+      if matching_files.length < 1
         Util.fatal_error( PRG_NAME, 'no file matching [' + phylogeny_id +
            '_] [' + suffix_pattern + '] present in current directory' )
       end
@@ -307,7 +277,6 @@ module Evoruby
              file =~ /^#{phylogeny_id}.+\d$/ )
           matching_files << file
         end
-
       }
 
       if matching_files.length < 1