inprogress

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

diff --git a/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb b/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb
index b435566..08c034b 100644 (file)
--- a/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb
@@ -249,6 +249,7 @@ module Evoruby
       puts basename
 
       File.open( input_file ) do | file |
+        species_counter = 1
         while line = file.gets
           line.strip!
           if !Util.is_string_empty?( line ) && !(line =~ /\s*#/ )
@@ -290,8 +291,9 @@ module Evoruby
                 print_counts( per_species_counter, log, Constants::LINE_DELIMITER )
                 per_species_counter = 0
               end
-              puts " " + current_species + " [" + my_readlink + "]"
-              log << current_species + " [" + my_readlink + "]" + Constants::LINE_DELIMITER
+              puts " " + species_counter.to_s +  ": " + current_species + " [" + my_readlink + "]"
+              log << species_counter.to_s +  ": " + current_species + " [" + my_readlink + "]" + Constants::LINE_DELIMITER
+              species_counter += 1
             end
             puts "   " + seq_name
             log << "   " + seq_name + Constants::LINE_DELIMITER