lib/genevalidator/tabular_parser.rb in genevalidator-1.6.2 vs lib/genevalidator/tabular_parser.rb in genevalidator-1.6.3

@@ -1,11 +1,11 @@
 require 'csv'
 require 'forwardable'
 
-require 'genevalidator/sequences'
-require 'genevalidator/hsp'
 require 'genevalidator/exceptions'
+require 'genevalidator/hsp'
+require 'genevalidator/query'
 
 #
 module GeneValidator
   TabularEntry = Struct.new(:filename, :type, :title, :footer, :xtitle,
                             :ytitle, :aux1, :aux2)
@@ -50,11 +50,10 @@
       loop do
         entry = @rows.peek['qseqid']
         @rows.next
         break unless entry == current_entry
       end
-      # rescue StopIteration
     end
 
     alias move_to_next_query next
 
     ##
@@ -77,10 +76,10 @@
       hits = tab_results.partition { |h| h['qseqid'] == current_id }[0]
       hit_list = []
       grouped_hits = hits.group_by { |row| row['sseqid'] }
 
       grouped_hits.each do |query_id, row|
-        hit_seq = Sequence.new
+        hit_seq = Query.new
         hit_seq.init_tabular_attribute(row[0])
 
         initialise_all_hsps(query_id, hits, hit_seq)
 
         hit_seq.type = :protein