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) click to toggle source

creates a new splitter object

Calls superclass method Bio::FlatFile::Splitter::Default.new
# File lib/bio/appl/blast/report.rb, line 486
def initialize(klass, bstream)
  super(klass, bstream)
  @parsed_entries = []
  @raw_unsupported = false
end

Public Instance Methods

entry() click to toggle source

current raw entry as a String

Calls superclass method
# File lib/bio/appl/blast/report.rb, line 531
def entry
  raise 'not supported for new BLAST XML format' if @raw_unsupported
  super
end
entry_ended_pos() click to toggle source

(end position of the entry) + 1

Calls superclass method
# 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
entry_start_pos() click to toggle source

start position of the entry

Calls superclass method
# 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_entry() click to toggle source

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_parsed_entry() click to toggle source

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
    get_entry
  else
    self.parsed_entry = @parsed_entries.shift
    self.entry = nil
    @raw_unsupported = true
  end
  self.parsed_entry
end
rewind() click to toggle source

rewinds

# File lib/bio/appl/blast/report.rb, line 493
def rewind
  ret = super
  @parsed_entries.clear
  @raw_unsupported = false
  ret
end
skip_leader() click to toggle source

do nothing

# File lib/bio/appl/blast/report.rb, line 501
def skip_leader
  nil
end