class Bio::FlatFile::Splitter::LineOriented

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.

Public Class Methods

new (klass, bstream)

Source

    # File lib/bio/io/flatfile/splitter.rb
215 def initialize(klass, bstream)
216   super(klass, bstream)
217   self.flag_to_fetch_header = true
218 end

Creates a new splitter.

klass: database class
bstream: input stream. It must be a BufferedInputStream object.

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

Public Instance Methods

get_entry ()

Source

    # File lib/bio/io/flatfile/splitter.rb
226 def get_entry
227   if e = get_parsed_entry then
228     entry
229   else
230     e
231   end
232 end

get an entry and return the entry as a string

get_parsed_entry ()

Source

    # File lib/bio/io/flatfile/splitter.rb
235 def get_parsed_entry
236   p0 = stream_pos()
237   ent = @dbclass.new()
238 
239   lines = []
240   line_overrun = nil
241 
242   if flag_to_fetch_header then
243     while line = stream.gets("\n")
244       unless ent.add_header_line(line) then
245         line_overrun = line
246         break
247       end
248       lines.push line
249     end
250     stream.ungets(line_overrun) if line_overrun
251     line_overrun = nil
252     self.flag_to_fetch_header = false
253   end
254       
255   while line = stream.gets("\n")
256     unless ent.add_line(line) then
257       line_overrun = line
258       break
259     end
260     lines.push line
261   end
262   stream.ungets(line_overrun) if line_overrun
263   p1 = stream_pos()
264 
265   return nil if lines.empty?
266 
267   self.entry_start_pos = p0
268   self.entry = lines.join('')
269   self.parsed_entry = ent
270   self.entry_ended_pos = p1
271 
272   return ent
273 end

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

rewind ()

Source

    # File lib/bio/io/flatfile/splitter.rb
276 def rewind
277   ret = super
278   self.flag_to_fetch_header = true
279   ret
280 end

rewinds the stream

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

skip_leader ()

Source

    # File lib/bio/io/flatfile/splitter.rb
221 def skip_leader
222   nil
223 end

do nothing