Flatfile splitter for NCBI BLAST XML format. It is internally used when reading BLAST XML. Normally, users do not need to use it directly.
current raw entry as a String
# File lib/bio/appl/blast/report.rb, line 531 def entry raise 'not supported for new BLAST XML format' if @raw_unsupported super end
(end position of the entry) + 1
# File lib/bio/appl/blast/report.rb, line 545 def entry_ended_pos if entry_pos_flag then raise 'not supported for new BLAST XML format' if @raw_unsupported end super end
start position of the entry
# File lib/bio/appl/blast/report.rb, line 537 def entry_start_pos if entry_pos_flag then raise 'not supported for new BLAST XML format' if @raw_unsupported end super end
get an entry and return the entry as a string
# File lib/bio/appl/blast/report.rb, line 506 def get_entry if @parsed_entries.empty? then @raw_unsupported = false ent = super prepare_parsed_entries(ent) self.parsed_entry = @parsed_entries.shift else raise 'not supported for new BLAST XML format' end ent end
get an entry as a Bio::Blast::Report object
# File lib/bio/appl/blast/report.rb, line 519 def get_parsed_entry if @parsed_entries.empty? then ent = get_entry else self.parsed_entry = @parsed_entries.shift self.entry = nil @raw_unsupported = true end self.parsed_entry end
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