primary[R]
# File lib/bio/io/flatfile/indexer.rb, line 98 def add_secondary_namespaces(*names) DEBUG.print "add_secondary_namespaces: #{names.inspect}\n" names.each do |x| unless x.is_a?(NameSpace) then y = @namestyle[x] raise 'unknown secondary namespace' unless y @secondary << y end end true end
# File lib/bio/io/flatfile/indexer.rb, line 164 def close_flatfile DEBUG.print "close flatfile #{@flatfilename.inspect}\n" @flatfile.close end
# File lib/bio/io/flatfile/indexer.rb, line 122 def each @flatfile.each do |x| @entry = x pos = @flatfile.entry_start_pos len = @flatfile.entry_ended_pos - @flatfile.entry_start_pos begin yield pos, len rescue RuntimeError, NameError => evar DEBUG.print "Caught error: #{evar.inspect}\n" DEBUG.print "in #{@flatfilename.inspect} position #{pos}\n" DEBUG.print "===begin===\n" DEBUG.print @flatfile.entry_raw.to_s.chomp DEBUG.print "\n===end===\n" @errorlog << [ evar, @flatfilename, pos ] if @fatal then DEBUG.print "Fatal error occurred, stop creating index...\n" raise evar else DEBUG.print "This entry shall be incorrectly indexed.\n" end end #rescue end end
administration of a single flatfile
# File lib/bio/io/flatfile/indexer.rb, line 111 def open_flatfile(fileid, file) @fileid = fileid @flatfilename = file DEBUG.print "fileid=#{fileid} file=#{@flatfilename.inspect}\n" @flatfile = Bio::FlatFile.open(@dbclass, file, 'rb') @flatfile.raw = nil @flatfile.entry_pos_flag = true @entry = nil end
# File lib/bio/io/flatfile/indexer.rb, line 146 def parse_primary r = self.primary.proc.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 end
# File lib/bio/io/flatfile/indexer.rb, line 155 def parse_secondary self.secondary.each do |x| p = x.proc.call(@entry) p.each do |y| yield x.name, y if y.length > 0 end end end
# File lib/bio/io/flatfile/indexer.rb, line 87 def set_primary_namespace(name) DEBUG.print "set_primary_namespace: #{name.inspect}\n" if name.is_a?(NameSpace) then @primary = name else @primary = @namestyle[name] end raise 'unknown primary namespace' unless @primary @primary end
Generated with the Darkfish Rdoc Generator 2.