X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fruby%2Fevoruby%2Flib%2Fevo%2Ftool%2Fmulti_sequence_extractor.rb;h=40b1211ffca6858fe65d39692eeef35a7e0ac934;hb=d3f81733e02dfcf4f74b450da5a34f467093433c;hp=b4355661f248f98f08e785e0a7528afa9f1a3e04;hpb=90d29ca20f3e7c5007a21e9e8ca7f44d57b4ce67;p=jalview.git

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..40b1211 100644
--- 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
@@ -550,10 +552,10 @@ module Evoruby
       rescue Exception => e
         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
       end
-      if @seqs <= 10000000
+      if @seqs <= 100000000
         @file_to_msa[ input ] = msa
         @seqs += msa.get_number_of_seqs
-        puts "total seqs in memory: " + @seqs.to_str
+        puts "   total seqs in memory: " + @seqs.to_s
       end
       msa
     end