Class Bio::FlatFileIndex::Indexer::Parser::PDBChemicalComponentParser
In: lib/bio/io/flatfile/indexer.rb
Parent: TemplateParser

Methods

new   open_flatfile  

Constants

NAMESTYLE = NameSpaces.new( NameSpace.new( 'UNIQUE', Proc.new { |x| x.entry_id } )
PRIMARY = 'UNIQUE'

Public Class methods

new(klass, pri_name = nil, sec_names = nil)

[Source]

     # File lib/bio/io/flatfile/indexer.rb, line 425
425:           def initialize(klass, pri_name = nil, sec_names = nil)
426:             super()
427:             self.format = 'raw'
428:             self.dbclass = Bio::PDB::ChemicalComponent
429:             self.set_primary_namespace((pri_name or PRIMARY))
430:             unless sec_names then
431:               sec_names = []
432:               @namestyle.each_value do |x|
433:                 sec_names << x.name if x.name != self.primary.name
434:               end
435:             end
436:             self.add_secondary_namespaces(*sec_names)
437:           end

Public Instance methods

open_flatfile(fileid, file)

[Source]

     # File lib/bio/io/flatfile/indexer.rb, line 438
438:           def open_flatfile(fileid, file)
439:             super
440:             @flatfile.pos = 0
441:             begin
442:               pos = @flatfile.pos
443:               line = @flatfile.gets
444:             end until (!line or line =~ /^RESIDUE /)
445:             @flatfile.pos = pos
446:           end

[Validate]