# File lib/bio/io/flatfile/indexer.rb, line 275 def initialize(pri_name = nil, sec_names = nil) super() self.format = 'fasta' self.dbclass = Bio::FastaFormat self.set_primary_namespace((pri_name or PRIMARY)) unless sec_names then sec_names = self.class::SECONDARY end self.add_secondary_namespaces(*sec_names) end
# File lib/bio/io/flatfile/indexer.rb, line 285 def open_flatfile(fileid, file) super @count = 1 @flatfilename_base = File.basename(@flatfilename) @flatfile.pos = 0 begin pos = @flatfile.pos line = @flatfile.gets end until (!line or line =~ /^\>/) @flatfile.pos = pos end
# File lib/bio/io/flatfile/indexer.rb, line 262 def parse_primary if p = self.primary.proc then r = p.call(@entry) unless r.is_a?(String) and r.length > 0 #@fatal = true raise 'primary id must be a non-void string (skipped this entry)' end r else unique_primary_key end end
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