class Bio::FlatFile::Splitter::Default

Default splitter. It sees following constants in the given class.

DELIMITER: (String) delimiter indicates the end of a entry.
FLATFILE_HEADER: (String) start of a entry, located on head of a line.
DELIMITER_OVERRUN: (Integer) excess read size included in DELIMITER.

Attributes

delimiter[RW]

(String) delimiter indicates the end of a entry.

delimiter_overrun[RW]

(Integer) excess read data size included in delimiter.

header[RW]

(String) start of a entry, located on head of a line.

Public Class Methods

new(klass, bstream) click to toggle source

Creates a new splitter.

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

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

    # File lib/bio/io/flatfile/splitter.rb
128 def initialize(klass, bstream)
129   super(klass, bstream)
130 
131   @delimiter = klass::DELIMITER rescue nil
132   @header = klass::FLATFILE_HEADER rescue nil
133   # for specific classes' benefit
134   unless header
135     if (defined?(Bio::GenBank) and klass == Bio::GenBank) or
136         (defined?(Bio::GenPept) and klass == Bio::GenPept)
137       @header = 'LOCUS '
138     end
139   end
140   @delimiter_overrun = klass::DELIMITER_OVERRUN rescue nil
141 end

Public Instance Methods

get_entry() click to toggle source

gets a entry

    # File lib/bio/io/flatfile/splitter.rb
180 def get_entry
181   p0 = stream_pos()
182   e  = stream.gets(@delimiter)
183   if e and @delimiter_overrun then
184     if e[-@delimiter.size, @delimiter.size ] == @delimiter then
185       overrun = e[-@delimiter_overrun, @delimiter_overrun]
186       e[-@delimiter_overrun, @delimiter_overrun] = ''
187       stream.ungets(overrun)
188     end
189   end
190   p1 = stream_pos()
191   self.entry_start_pos = p0
192   self.entry = e
193   self.entry_ended_pos = p1
194   return entry
195 end

skip_leader() click to toggle source

Skips leader of the entry.

If @header is not nil, it reads till the contents of @header comes at the head of a line. If correct FLATFILE_HEADER is found, returns true. Otherwise, returns nil.

    # File lib/bio/io/flatfile/splitter.rb
158 def skip_leader
159   if @header then
160     data = ''
161     while s = stream.gets(@header)
162       data << s
163       if data.split(/[\r\n]+/)[-1] == @header then
164         stream.ungets(@header)
165         return true
166       end
167     end
168     # @header was not found. For safety,
169     # pushes back data with removing white spaces in the head.
170     data.sub(/\A\s+/, '')
171     stream.ungets(data)
172     return nil
173   else
174     stream.skip_spaces
175     return nil
176   end
177 end