lib/bio/db/gff/gffcomponent.rb in bio-gff3-0.8.5 vs lib/bio/db/gff/gffcomponent.rb in bio-gff3-0.8.6

@@ -5,17 +5,19 @@
 #              Pjotr Prins <[e-mail]>
 # License::    The Ruby License
 #
 # Fetch information from a GFF file
 
+require 'set'
+
 module Bio
   module GFFbrowser
 
     module Helpers
 
       module Record
-        include Error
+        include Logger
         # Format a record ID by, first, getting the ID attribute. If that fails
         # the seqname is used with the start/stop positions.
         def Record::formatID rec  
           id = rec.id if rec.id
           if !id
@@ -31,15 +33,15 @@
         end
       end
 
       module Gff3Component
 
-        include Error
+        include Logger
 
-        COMPONENT_TYPES = %w{
+        COMPONENT_TYPES = Set.new(%w{
           gene SO:0000704 contig transcript Component region
-        }
+        })
  
         # Walk the component list to find a matching component/container for a
         # record. First use the parent ID. If that is missing go by sequence
         # name.
         def find_component rec
@@ -78,16 +80,16 @@
       end
 
       module Gff3Features
 
         # Ignore the following features (case sensitive?)
-        IGNORE_FEATURES = Gff3Component::COMPONENT_TYPES + %w{
+        IGNORE_FEATURES = Gff3Component::COMPONENT_TYPES + Set.new(%w{
           transposon Match similarity UTR
           TF_binding_site intronSO:0000188 polyA_sequence SO:0000610
           polyA_site SO:0000553
           five_prime_UTR SO:0000204 three_prime_UTR SO:0000205
           exon SO:0000147
-        }
+        })
       end
 
     end
   end
 end