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 b739144..0c525ad 100644 (file)
--- a/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb
@@ -292,17 +292,16 @@ module Evoruby
                 per_species_counter = 0
               end
               puts " " + species_counter.to_s +  ":" + current_species + " [" + my_readlink + "]"
-              log << species_counter.to_s +  ": " + current_species + " [" + my_readlink + "]" + Constants::LINE_DELIMITER
+              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
+            log << "   " << seq_name << Constants::LINE_DELIMITER
             per_species_counter = per_species_counter + 1
             seq = nil
 
             indices = current_msa.find_by_name_start( seq_name, true )
             if indices.size == 1
-              seq =  current_msa.get_sequence( indices[ 0 ] )
+              seq = current_msa.get_sequence( indices[ 0 ] )
             elsif indices.size == 0
               # Not found, try finding by partial match.
               begin
@@ -314,21 +313,6 @@ module Evoruby
               Util.fatal_error( PRG_NAME, "error: seq name \"" + seq_name + "\" not unique"  )
             end
 
-            # if current_msa.find_by_name_start( seq_name, true ).size > 0
-            #   begin
-            #     seq = current_msa.get_by_name_start( seq_name, true ).copy
-            #   rescue ArgumentError => e
-            #     Util.fatal_error( PRG_NAME, "error: " + e.to_s )
-            #   end
-            # else
-            #   # Not found, try finding by partial match.
-            #   begin
-            #     seq = current_msa.get_by_name( seq_name, true, true )
-            #   rescue ArgumentError => e
-            #     Util.fatal_error( PRG_NAME, "error: " + e.to_s )
-            #   end
-            # end
-
             normalized_id = per_species_counter.to_s( 16 ).upcase +
              "_" + current_species
 
@@ -536,8 +520,8 @@ module Evoruby
     end
 
     def print_counts( per_species_counter, log, ld )
-      puts "   [sum: " + per_species_counter.to_s + "]"
-      log << "   [sum: " + per_species_counter.to_s + "]" + ld
+      puts "   sum: " + per_species_counter.to_s
+      log << "   sum: " + per_species_counter.to_s + ld
     end
 
     def read_fasta_file( input )
@@ -552,7 +536,7 @@ module Evoruby
       rescue Exception => e
         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
       end
-      if @seqs <= 10000000
+      if @seqs <= 400000
         @file_to_msa[ input ] = msa
         @seqs += msa.get_number_of_seqs
         puts "   total seqs in memory: " + @seqs.to_s