class Bio::Blast::Report::FLATFILE_SPLITTER

Flatfile splitter for NCBI BLAST XML format. It is internally used when reading BLAST XML. Normally, users do not need to use it directly.

Public Class Methods

new (klass, bstream)

Source

    # File lib/bio/appl/blast/report.rb
518 def initialize(klass, bstream)
519   super(klass, bstream)
520   @parsed_entries = []
521   @raw_unsupported = false
522 end

creates a new splitter object

Calls superclass method Bio::FlatFile::Splitter::Default::new

Public Instance Methods

entry ()

Source

    # File lib/bio/appl/blast/report.rb
563 def entry
564   raise 'not supported for new BLAST XML format' if @raw_unsupported
565   super
566 end

current raw entry as a String

Calls superclass method

entry_ended_pos ()

Source

    # File lib/bio/appl/blast/report.rb
577 def entry_ended_pos
578   if entry_pos_flag then
579     raise 'not supported for new BLAST XML format' if @raw_unsupported
580   end
581   super
582 end

(end position of the entry) + 1

Calls superclass method

entry_start_pos ()

Source

    # File lib/bio/appl/blast/report.rb
569 def entry_start_pos
570   if entry_pos_flag then
571     raise 'not supported for new BLAST XML format' if @raw_unsupported
572   end
573   super
574 end

start position of the entry

Calls superclass method

get_entry ()

Source

    # File lib/bio/appl/blast/report.rb
538 def get_entry
539   if @parsed_entries.empty? then
540     @raw_unsupported = false
541     ent = super
542     prepare_parsed_entries(ent)
543     self.parsed_entry = @parsed_entries.shift
544   else
545     raise 'not supported for new BLAST XML format'
546   end
547   ent
548 end

get an entry and return the entry as a string

Calls superclass method Bio::FlatFile::Splitter::Default#get_entry

get_parsed_entry ()

Source

    # File lib/bio/appl/blast/report.rb
551 def get_parsed_entry
552   if @parsed_entries.empty? then
553     get_entry
554   else
555     self.parsed_entry = @parsed_entries.shift
556     self.entry = nil
557     @raw_unsupported = true
558   end
559   self.parsed_entry
560 end

get an entry as a Bio::Blast::Report object

rewind ()

Source

    # File lib/bio/appl/blast/report.rb
525 def rewind
526   ret = super
527   @parsed_entries.clear
528   @raw_unsupported = false
529   ret
530 end

rewinds

Calls superclass method Bio::FlatFile::Splitter::Template#rewind

skip_leader ()

Source

    # File lib/bio/appl/blast/report.rb
533 def skip_leader
534   nil
535 end

do nothing