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