From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Wed, 16 Jan 2013 22:27:30 +0000 (+0000)
Subject: inprogress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=4a28a6795c9170f35eb1bf698055d5a730d7839a;p=jalview.git

inprogress
---

diff --git a/forester/ruby/evoruby/exe/select_same_gn.rb b/forester/ruby/evoruby/exe/select_same_gn.rb
index e3d5132..97887a9 100755
--- a/forester/ruby/evoruby/exe/select_same_gn.rb
+++ b/forester/ruby/evoruby/exe/select_same_gn.rb
@@ -25,6 +25,7 @@ module Evoruby
   end
 
   all_names = Set.new
+  all_seqs = Set.new
   gn_to_seqs = Hash.new
   unique_genes_msa = Msa.new
   longest_non_unique_genes_msa = Msa.new
@@ -38,11 +39,18 @@ module Evoruby
     seq = msa.get_sequence( i )
     name = seq.get_name
     if all_names.include?( name )
-      puts "error: " + name + " is not unique"
+      puts "error: " + name + " is not unique (#" + i + ")"
+      exit
     else
       all_names << name
     end
-
+    mol_seq = seq.get_sequence_as_string.upcase
+    if all_seqs.include?( mol_seq )
+      puts "error: sequence of " + name + " is not unique (#" + i + ")"
+      exit
+    else
+      all_seqs << mol_seq
+    end
 
     if fragment_re.match( name )
       puts "ignored because fragment: " + name