[BioRuby-cvs] bioruby/lib/bio/appl/blast format0.rb,1.12,1.13

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/appl/blast
In directory pub.open-bio.org:/tmp/cvs-serv31454

Modified Files:
	format0.rb 
Log Message:
* RDoc are added.
* In Report class,
  * delegate_to_f0dbstat (private class method) is added, and 11 methods are
    changed to use it.
  * f0header, f0reference, f0query, f0database, f0dbstat methods are removed.
    (They were methods for debugging.)
  * in format0_split_stat_params, changed to use instance_eval (due to the
    removal of Iteration#f0stat and Iteration#f0dbstat methods).
* In F0dbstat class, 
  * method_after_parse_params and method_after_parse_dbstat
    (private class methods) are deleted and methods are changed not to
    use them.
* AlwaysNil class (include Singleton) are added for internal use.
  Users must not use the class directly.
* In Iteration class,
  * Default value of @f0dbstat is changed to AlwaysNil.instance.
  * f0message, f0hitlist, f0stat, f0dbstat methods are removed.
    (They were internal use only.)
  * method_delegate_f0dbstat (private class method) are changed to
    delegate_to_f0dbstat.
* In Hit class,
  * f0hitname method is removed. (It was only for debugging.)
* In HSP class,
  * f0score and f0alignment are removed. (They are methods for debugging.)


Index: format0.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/format0.rb,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** format0.rb	26 Sep 2005 13:00:04 -0000	1.12
--- format0.rb	26 Oct 2005 09:12:06 -0000	1.13
***************
*** 1,6 ****
  #
! # bio/appl/blast/format0.rb - BLAST default output (-m 0) parser
  # 
! #   Copyright (C) 2003 GOTO Naohisa <ng at bioruby.org>
  #
  #  This library is free software; you can redistribute it and/or
--- 1,8 ----
  #
! # = bio/appl/blast/format0.rb - BLAST default output (-m 0) parser
  # 
[...1016 lines suppressed...]
! 
!           # start position of the hit (the first position is 1)
!           attr_reader                  :hit_from if false #dummy
!           method_after_parse_alignment :hit_from
! 
!           # end position of the hit (including its position)
!           attr_reader                  :hit_to if false #dummy
!           method_after_parse_alignment :hit_to
! 
          end #class HSP
  
        end #class Report
  
+       # 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.
        class Report_TBlast < Report
+         # Delimter of each entry for TBLAST. Bio::FlatFile uses it.
          DELIMITER = RS = "\nTBLAST"
        end #class Report_TBlast