class Bio::FlatFile::BufferedInputStream

Wrapper for a IO (or IO-like) object. It can input with a buffer.

Attributes

Pathname, filename or URI to open the object. Like File#path, returned value isn’t normalized.

Public Class Methods

Source

   # File lib/bio/io/flatfile/buffer.rb
32 def self.for_io(io)
33   begin
34     path = io.path
35   rescue NameError
36     path = nil
37   end
38   self.new(io, path)
39 end

Creates a new input stream wrapper from the given IO object.

new (io, path)

Source

   # File lib/bio/io/flatfile/buffer.rb
24 def initialize(io, path)
25   @io = io
26   @path = path
27   # initialize prefetch buffer
28   @buffer = String.new
29 end

Creates a new input stream wrapper

open_file (filename, *arg) { |self| ... }

Source

   # File lib/bio/io/flatfile/buffer.rb
49 def self.open_file(filename, *arg)
50   params = _parse_file_open_arg(*arg)
51   if params[:textmode] or /t/ =~ params[:fmode_string].to_s then
52     textmode = true
53   else
54     textmode = false
55   end
56   if block_given? then
57     File.open(filename, *arg) do |fobj|
58       fobj.binmode unless textmode
59       yield self.new(fobj, filename)
60     end
61   else
62     fobj = File.open(filename, *arg)
63     fobj.binmode unless textmode
64     self.new(fobj, filename)
65   end
66 end

Creates a new input stream wrapper to open file filename by using File.open. *arg is passed to File.open.

Like File.open, a block can be accepted.

Unlike File.open, the default is binary mode, unless text mode is explicity specified in mode.

open_uri (uri, *arg) { |self| ... }

Source

    # File lib/bio/io/flatfile/buffer.rb
147 def self.open_uri(uri, *arg)
148   if uri.kind_of?(URI)
149     if block_given?
150       uri.open(*arg) do |fobj|
151         yield self.new(fobj, uri.to_s)
152       end
153     else
154       fobj0 = uri.open(*arg)
155       self.new(fobj0, uri.to_s)
156     end
157   else
158     if block_given?
159       OpenURI.open_uri(uri, *arg) do |fobj|
160         yield self.new(fobj, uri)
161       end
162     else
163       fobj0 = OpenURI.open_uri(uri, *arg)
164       self.new(fobj0, uri)
165     end
166   end
167 end

Creates a new input stream wrapper from URI specified as uri. by using OpenURI.open_uri or URI#open. uri must be a String or URI object. *arg is passed to OpenURI.open_uri or URI#open.

Like OpenURI.open_uri, it can accept a block.

Public Instance Methods

close ()

Source

    # File lib/bio/io/flatfile/buffer.rb
179 def close
180   @io.close
181 end

Closes the IO object if possible

eof? ()

Source

    # File lib/bio/io/flatfile/buffer.rb
208 def eof?
209   if @buffer.size > 0
210     false
211   else
212     @io.eof?
213   end
214 end

Returns true if end-of-file. Otherwise, returns false.

Note that it returns false if internal buffer is this wrapper is not empty,

getc ()

Source

    # File lib/bio/io/flatfile/buffer.rb
268 def getc
269   if @buffer.size > 0 then
270     r = @buffer[0]
271     @buffer = @buffer[1..-1]
272   else
273     r = @io.getc
274   end
275   r
276 end

Same as IO#getc.

gets (io_rs = $/)

Source

    # File lib/bio/io/flatfile/buffer.rb
220 def gets(io_rs = $/)
221   if @buffer.size > 0
222     if io_rs == nil then
223       r = @buffer + @io.gets(nil).to_s
224       @buffer = ''
225     else
226       if io_rs == '' then # io_rs.empty?
227         sp_rs = /((?:\r?\n){2,})/n
228       else
229         sp_rs = io_rs
230       end
231       a = @buffer.split(sp_rs, 2)
232       if a.size > 1 then
233         r = a.shift
234         r += (io_rs.empty? ? a.shift : io_rs)
235         @buffer = a.shift.to_s
236       else
237         @buffer << @io.gets(io_rs).to_s
238         a = @buffer.split(sp_rs, 2)
239         if a.size > 1 then
240           r = a.shift
241           r += (io_rs.empty? ? a.shift : io_rs)
242           @buffer = a.shift.to_s
243         else
244           r = @buffer
245           @buffer = ''
246         end
247       end
248     end
249     r
250   else
251     @io.gets(io_rs)
252   end
253 end

Same as IO#gets.

Compatibility note: the bahavior of paragraph mode (io_rs = ”) may differ from that of IO#gets(”).

pos ()

Source

    # File lib/bio/io/flatfile/buffer.rb
192 def pos
193   @io.pos - @buffer.size
194 end

Returns current file position

pos= (p)

Source

    # File lib/bio/io/flatfile/buffer.rb
198 def pos=(p)
199   r = (@io.pos = p)
200   @buffer = ''
201   r
202 end

Sets current file position if possible Internal buffer in this wrapper is cleared.

prefetch_buffer ()

Source

    # File lib/bio/io/flatfile/buffer.rb
286 def prefetch_buffer
287   @buffer
288 end

Gets current prefetch buffer

prefetch_gets (*arg)

Source

    # File lib/bio/io/flatfile/buffer.rb
292 def prefetch_gets(*arg)
293   r = @io.gets(*arg)
294   @buffer << r if r
295   r
296 end

It does @io.gets, and addes returned string to the internal buffer, and returns the string.

prefetch_readpartial (*arg)

Source

    # File lib/bio/io/flatfile/buffer.rb
300 def prefetch_readpartial(*arg)
301   r = @io.readpartial(*arg)
302   @buffer << r if r
303   r
304 end

It does @io.readpartial, and addes returned string to the internal buffer, and returns the string.

rewind ()

Source

    # File lib/bio/io/flatfile/buffer.rb
185 def rewind
186   r = @io.rewind
187   @buffer = ''
188   r
189 end

Rewinds the IO object if possible Internal buffer in this wrapper is cleared.

skip_spaces ()

Source

    # File lib/bio/io/flatfile/buffer.rb
308 def skip_spaces
309   ws = { ?\s => true, ?\n => true, ?\r => true, ?\t => true }
310   while r = self.getc
311     unless ws[r] then
312       self.ungetc(r)
313       break
314     end
315   end
316   nil
317 end

Skips space characters in the stream. returns nil.

to_io ()

Source

    # File lib/bio/io/flatfile/buffer.rb
174 def to_io
175   @io.to_io
176 end

Converts to IO object if possible

ungetc (c)

Source

    # File lib/bio/io/flatfile/buffer.rb
280 def ungetc(c)
281   @buffer = sprintf("%c", c) + @buffer
282   nil
283 end

Pushes back one character into the internal buffer. Unlike IO#getc, it can be called more than one time.

ungets (str)

Source

    # File lib/bio/io/flatfile/buffer.rb
262 def ungets(str)
263   @buffer = str + @buffer
264   nil
265 end

Pushes back given str to the internal buffer. Returns nil. str must be read previously with the wrapper object.

Note that in current implementation, the str can be everything, but please don’t depend on it.