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)

Source

    # File lib/bio/io/flatfile/splitter.rb
129 def initialize(klass, bstream)
130   super(klass, bstream)
131 
132   @delimiter = klass::DELIMITER rescue nil
133   @header = klass::FLATFILE_HEADER rescue nil
134   # for specific classes' benefit
135   unless header
136     if (defined?(Bio::GenBank) and klass == Bio::GenBank) or
137         (defined?(Bio::GenPept) and klass == Bio::GenPept)
138       @header = 'LOCUS '
139     end
140   end
141   @delimiter_overrun = klass::DELIMITER_OVERRUN rescue nil
142 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
181 def get_entry
182   p0 = stream_pos()
183   e  = stream.gets(@delimiter)
184   if e and @delimiter_overrun then
185     if e[-@delimiter.size, @delimiter.size ] == @delimiter then
186       overrun = e[-@delimiter_overrun, @delimiter_overrun]
187       e[-@delimiter_overrun, @delimiter_overrun] = ''
188       stream.ungets(overrun)
189     end
190   end
191   p1 = stream_pos()
192   self.entry_start_pos = p0
193   self.entry = e
194   self.entry_ended_pos = p1
195   return entry
196 end

gets a entry

skip_leader ()

Source

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

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.