[BioRuby-cvs] bioruby/lib/bio/appl/blast format0.rb,1.13,1.14

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/appl/blast
In directory pub.open-bio.org:/tmp/cvs-serv32104/blast

Modified Files:
	format0.rb 
Log Message:
added references to document.
added #:nodoc: to Bio, Bio::Blast, Bio::Blast::Default.


Index: format0.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/format0.rb,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** format0.rb	26 Oct 2005 09:12:06 -0000	1.13
--- format0.rb	31 Oct 2005 11:07:05 -0000	1.14
***************
*** 6,9 ****
--- 6,10 ----
  # License:: LGPL
  #
+ #--
  #  This library is free software; you can redistribute it and/or
  #  modify it under the terms of the GNU Lesser General Public
***************
*** 19,25 ****
--- 20,37 ----
  #  License along with this library; if not, write to the Free Software
  #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+ #++
  #
  #  $Id$
  #
+ # NCBI BLAST default (-m 0 option) output parser.
+ #
+ # == References
+ #
+ # * Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
+ #   Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
+ #   "Gapped BLAST and PSI-BLAST: a new generation of protein database search
+ #   programs", Nucleic Acids Res. 25:3389-3402.
+ # * http://www.ncbi.nlm.nih.gov/blast/ 
+ #
  
  begin
***************
*** 29,38 ****
  require 'singleton'
  
  #require 'bio/db'
  require 'bio/io/flatfile'
  
! module Bio
!   class Blast
!     module Default
  
        # Bio::Blast::Default::Report parses NCBI BLAST default output
--- 41,52 ----
  require 'singleton'
  
+ #--
  #require 'bio/db'
+ #++
  require 'bio/io/flatfile'
  
! module Bio #:nodoc:
!   class Blast #:nodoc:
!     module Default #:nodoc:
  
        # Bio::Blast::Default::Report parses NCBI BLAST default output
***************
*** 1387,1402 ****
  
  ######################################################################
- 
- =begin
- 
- = Bio::Blast::Default::Report
- 
-     NCBI BLAST default (-m 0 option) output parser
- 
- = Bio::Blast::Default::Report_TBlast
- 
-     NCBI BLAST default (-m 0 option) output parser for TBLAST.
-     All methods are equal to Bio::Blast::Default::Report.
-     Only DELIMITER (and RS) is different.
- 
- =end
--- 1401,1402 ----