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

Methods

new   open_flatfile  

Constants

NAMESTYLE = NameSpaces.new( NameSpace.new( 'QUERY', Proc.new { |x| x.query_def } ), NameSpace.new( 'query_id', Proc.new { |x| a = Bio::FastaDefline.new(x.query_def.to_s).id_strings
PRIMARY = 'QUERY'
SECONDARY = [ 'query_id', 'hit' ]

Public Class methods

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

[Source]

     # File lib/bio/io/flatfile/indexer.rb, line 392
392:           def initialize(klass, pri_name = nil, sec_names = nil)
393:             super()
394:             self.format = 'raw'
395:             self.dbclass = klass
396:             self.set_primary_namespace((pri_name or PRIMARY))
397:             unless sec_names then
398:               sec_names = []
399:               @namestyle.each_value do |x|
400:                 sec_names << x.name if x.name != self.primary.name
401:               end
402:             end
403:             self.add_secondary_namespaces(*sec_names)
404:           end

Public Instance methods

open_flatfile(fileid, file)

[Source]

     # File lib/bio/io/flatfile/indexer.rb, line 405
405:           def open_flatfile(fileid, file)
406:             super
407:             @flatfile.rewind
408:             @flatfile.dbclass = nil
409:             @flatfile.autodetect
410:             @flatfile.dbclass = self.dbclass unless @flatfile.dbclass
411:             @flatfile.rewind
412:             begin
413:               pos = @flatfile.pos
414:               line = @flatfile.gets
415:             end until (!line or line =~ /^T?BLAST/)
416:             @flatfile.pos = pos
417:           end

[Validate]