inprogress

diff --git a/forester/ruby/evoruby/exe/select_same_gn.rb b/forester/ruby/evoruby/exe/select_same_gn.rb
index 1ecd373..e3d5132 100755 (executable)
--- a/forester/ruby/evoruby/exe/select_same_gn.rb
+++ b/forester/ruby/evoruby/exe/select_same_gn.rb
@@ -12,7 +12,7 @@ module Evoruby
 
   input = ARGV[ 0 ]
   f = MsaFactory.new()
 
   input = ARGV[ 0 ]
   f = MsaFactory.new()

-  
+

   IGNORE_SEQS_LACKING_GN = false
 
   msa = nil
   IGNORE_SEQS_LACKING_GN = false
 
   msa = nil

@@ -37,19 +37,19 @@ module Evoruby
   for i in 0 ... msa.get_number_of_seqs()
     seq = msa.get_sequence( i )
     name = seq.get_name
   for i in 0 ... msa.get_number_of_seqs()
     seq = msa.get_sequence( i )
     name = seq.get_name

-    if all_names.has?( name )
-     puts "error: " + name + " is not unique"
-    else      
-      all_names.put( name )
+    if all_names.include?( name )
+      puts "error: " + name + " is not unique"
+    else
+      all_names << name

     end
     end

-    
-    
+
+

     if fragment_re.match( name )
       puts "ignored because fragment: " + name
       frag_counter += 1
       next
     end
     if fragment_re.match( name )
       puts "ignored because fragment: " + name
       frag_counter += 1
       next
     end

-    
+

     gn_match = gn_re.match( name )
     if IGNORE_SEQS_LACKING_GN
       unless gn_match
     gn_match = gn_re.match( name )
     if IGNORE_SEQS_LACKING_GN
       unless gn_match

@@ -62,7 +62,7 @@ module Evoruby
         puts "no GN=: " + name
       end
     end
         puts "no GN=: " + name
       end
     end

-    
+

     gn =nil
     if gn_match
       gn = gn_match[1]
     gn =nil
     if gn_match
       gn = gn_match[1]

@@ -72,8 +72,8 @@ module Evoruby
         exit
       end
       gn = name
         exit
       end
       gn = name

-    end  
-    
+    end
+

     unless gn_to_seqs.has_key?(gn)
       gn_to_seqs[gn] = Msa.new
     end
     unless gn_to_seqs.has_key?(gn)
       gn_to_seqs[gn] = Msa.new
     end