in progress

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

diff --git a/forester/ruby/evoruby/lib/evo/apps/multi_sequence_extractor.rb b/forester/ruby/evoruby/lib/evo/apps/multi_sequence_extractor.rb
index 12706a5..0e6d1e7 100644 (file)
--- a/forester/ruby/evoruby/lib/evo/apps/multi_sequence_extractor.rb
+++ b/forester/ruby/evoruby/lib/evo/apps/multi_sequence_extractor.rb
@@ -226,6 +226,7 @@ module Evoruby
                         domain_ranges = nil
                         if ( values.length > 3 )        
                           domain_ranges_block = values[ 3 ]
+                          puts "domain_ranges_bloc=" + domain_ranges_block
                           domain_ranges = domain_ranges_block.split( "/" )
                         end
                         if ( species != current_species )
@@ -293,13 +294,13 @@ module Evoruby
                         
                         if  domain_ranges != nil 
                             domain_ranges.each { |range| 
-                            puts range + "\n"  
-                                if range != nil
+                                puts "reange:" + range + ":\n"  
+                                if range != nil && range.length > 0
                                     s= range.split("-")
                                     from = s[ 0 ]
                                     to = s[ 1 ]
                                     puts from + "-" + to
-                                    new_msa_domains.add_sequence( Sequence.new( orig_name + "/" + from + "-" + to + " [" + basename + "] [" + current_species + "]", seq.get_sequence_as_string[from..to] ) )
+                                    new_msa_domains.add_sequence( Sequence.new( orig_name + "/" + from + "-" + to + " [" + basename + "] [" + current_species + "]", seq.get_sequence_as_string[from.to_i..to.to_i] ) )
                                 end   
                             }
                         end