Class: Bio::FlatFile::Splitter::LineOriented

Inherits:
Template show all
Defined in:
lib/bio/io/flatfile/splitter.rb

Overview

A splitter for line oriented text data.

The given class’s object must have following methods.

Klass#add_header_line(line)
Klass#add_line(line)

where ‘line’ is a string. They normally returns self. If the line is not suitable to add to the current entry, nil or false should be returned. Then, the line is treated as (for add_header_line) the entry data or (for add_line) the next entry’s data.

Instance Attribute Summary

Attributes inherited from Template

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

Instance Method Summary collapse

Constructor Details

#initialize(klass, bstream) ⇒ LineOriented

Creates a new splitter.

klass

database class

bstream

input stream. It must be a BufferedInputStream object.



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# File 'lib/bio/io/flatfile/splitter.rb', line 214

def initialize(klass, bstream)
  super(klass, bstream)
  self.flag_to_fetch_header = true
end

Instance Method Details

#get_entry ⇒ Object

get an entry and return the entry as a string



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# File 'lib/bio/io/flatfile/splitter.rb', line 225

def get_entry
  if e = get_parsed_entry then
    entry
  else
    e
  end
end

#get_parsed_entry ⇒ Object

get an entry and return the entry as a data class object



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# File 'lib/bio/io/flatfile/splitter.rb', line 234

def get_parsed_entry
  p0 = stream_pos()
  ent = @dbclass.new()

  lines = []
  line_overrun = nil

  if flag_to_fetch_header then
    while line = stream.gets("\n")
      unless ent.add_header_line(line) then
        line_overrun = line
        break
      end
      lines.push line
    end
    stream.ungets(line_overrun) if line_overrun
    line_overrun = nil
    self.flag_to_fetch_header = false
  end
      
  while line = stream.gets("\n")
    unless ent.add_line(line) then
      line_overrun = line
      break
    end
    lines.push line
  end
  stream.ungets(line_overrun) if line_overrun
  p1 = stream_pos()

  return nil if lines.empty?

  self.entry_start_pos = p0
  self.entry = lines.join('')
  self.parsed_entry = ent
  self.entry_ended_pos = p1

  return ent
end

#rewind ⇒ Object

rewinds the stream



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# File 'lib/bio/io/flatfile/splitter.rb', line 275

def rewind
  ret = super
  self.flag_to_fetch_header = true
  ret
end

#skip_leader ⇒ Object

do nothing



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# File 'lib/bio/io/flatfile/splitter.rb', line 220

def skip_leader
  nil
end