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

@@ -19,34 +19,39 @@
 
         # Module to fetch a line from GFF3 file and returns a parsed 
         # record
         module SeekRec
           # Fetch a record using fh and file seek position
-          def SeekRec::fetch(fh,fpos)
+          def SeekRec::fetch(fh,fpos,parser)
             return nil if fh==nil or fpos==nil
             fh.seek(fpos)
-            GFF::GFF3::FileRecord.new(fpos, fh.gets)
+            if parser == :bioruby 
+              GFF::GFF3::BioRubyFileRecord.new(fpos, fh.gets)
+            else
+              GFF::GFF3::FastParserFileRecord.new(fpos, fh.gets)
+            end
           end
         end
 
         # Helper class which gives Hash-like access to the 
         # no-cache GFF3 file
         class SeekRecList 
-          def initialize fh
+          def initialize fh, parser
             @fh = fh
             @h = {}
+            @parser = parser
           end
 
           def []= id, rec
             raise "id #{id} occurs twice!" if @h[id]
             fpos = rec.io_seek
             @h[id] = fpos
           end
 
           def [](id)
             fpos = @h[id]
-            SeekRec::fetch(@fh,fpos)
+            SeekRec::fetch(@fh,fpos,@parser)
           end
 
           def each 
             @h.each do | id,fpos |
               yield id, self[id]
@@ -54,11 +59,11 @@
           end
         end
 
         # List of ids
         class SeekLinkedRecs < Hash
-          include Helpers::Error
+          include Helpers::Logger
           def add id, rec
             info "Adding #{rec.feature_type} <#{id}>"
             self[id] = [] if self[id] == nil
             self[id] << rec.io_seek
           end
@@ -89,18 +94,26 @@
         # rather than the records themselves
         def parse
           info "---- Digest DB and store data in mRNA Hash (NoCache)"
           @count_ids          = Counter.new   # Count ids
           @count_seqnames     = Counter.new   # Count seqnames
-          @componentlist      = SeekRecList.new(@iter.fh) # Store containers, like genes, contigs
+          @componentlist      = SeekRecList.new(@iter.fh,@options[:parser]) # Store containers, like genes, contigs
           @orflist            = SeekLinkedRecs.new   # Store linked gene records
           @mrnalist           = SeekLinkedRecs.new   # Store linked mRNA records
           @cdslist            = SeekLinkedRecs.new
           @exonlist           = SeekLinkedRecs.new
           @sequencelist       = {}
           @unrecognized_features = {}
-          @iter.each_rec do | id, rec |
+          @iter.each_rec do |fpos, line|
+            rec = case @options[:parser]
+              when :bioruby
+                Bio::GFF::GFF3::BioRubyFileRecord.new(fpos, line)
+              when :line
+                Bio::GFF::GFF3::FastParserFileRecord.new(fpos, line)
+              else
+                raise 'Unknown parser'
+            end
             store_record(rec)
           end
           @iter.each_sequence do | id, bioseq |
             @sequencelist[id] = bioseq.to_s
           end
@@ -115,14 +128,20 @@
           # p list.class
           fh = @iter.fh
           list.each do | id, io_seeklist |
             recs = []
             io_seeklist.each do | fpos |
-              recs << SeekRec::fetch(fh,fpos)
+              recs << SeekRec::fetch(fh,fpos,@options[:parser])
             end
             seqid = recs[0].seqname
             component = find_component(recs[0])
-            yield id, recs, component
+            if @options[:no_assemble]
+              recs.each do | rec |
+                yield id, [rec], component
+              end
+            else
+              yield id, recs, component
+            end
           end
         end
         
       end
     end