Class: Bio::Fasta::Report::FastaFormat10Splitter

Inherits:
Bio::FlatFile::Splitter::Template show all
Defined in:
lib/bio/appl/fasta/format10.rb

Overview

Splitter for Bio::FlatFile

Instance Attribute Summary

Attributes inherited from Bio::FlatFile::Splitter::Template

#entry, #entry_ended_pos, #entry_pos_flag, #entry_start_pos, #parsed_entry

Instance Method Summary collapse

Methods inherited from Bio::FlatFile::Splitter::Template

#get_parsed_entry, #rewind

Constructor Details

#initialize(klass, bstream) ⇒ FastaFormat10Splitter

creates a new splitter object



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# File 'lib/bio/appl/fasta/format10.rb', line 23

def initialize(klass, bstream)
  super(klass, bstream)
  @delimiter = '>>>'
  @real_delimiter = /^\s*\d+\>\>\>\z/
end

Instance Method Details

#get_entry ⇒ Object

gets an entry



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# File 'lib/bio/appl/fasta/format10.rb', line 35

def get_entry
  p0 = stream_pos()
  pieces = []
  overrun = nil
  first = true
  while e = stream.gets(@delimiter)
    pieces.push e
    if @real_delimiter =~ e then
      if first then
        first = nil
      else
        overrun = $&
        break
      end
    end
  end

  ent = (pieces.empty? ? nil : pieces.join(''))
  if ent and overrun then
    ent[-overrun.length, overrun.length] = ''
    stream.ungets(overrun)
  end

  p1 = stream_pos()
  self.entry_start_pos = p0
  self.entry = ent
  self.entry_ended_pos = p1
  return ent
end

#skip_leader ⇒ Object

do nothing and returns nil



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# File 'lib/bio/appl/fasta/format10.rb', line 30

def skip_leader
  nil
end