[BioRuby-cvs] bioruby/lib/bio/appl/bl2seq report.rb,1.3,1.4
Naohisa Goto
ngoto at pub.open-bio.org
Mon Oct 31 09:37:32 EST 2005
Update of /home/repository/bioruby/bioruby/lib/bio/appl/bl2seq
In directory pub.open-bio.org:/tmp/cvs-serv32761
Modified Files:
report.rb
Log Message:
Changes to follow modifications of Bio::Blast::Default::Report classes.
Added RDoc documents.
Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/bl2seq/report.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** report.rb 8 Sep 2005 01:22:08 -0000 1.3
--- report.rb 31 Oct 2005 14:37:30 -0000 1.4
***************
*** 1,7 ****
#
! # bio/appl/bl2seq/report.rb - bl2seq (BLAST 2 sequences) parser
#
! # Copyright (C) 2005 GOTO Naohisa <ng at bioruby.org>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
--- 1,9 ----
#
! # = bio/appl/bl2seq/report.rb - bl2seq (BLAST 2 sequences) parser
#
! # Copyright:: Copyright (C) 2005 GOTO Naohisa <ng at bioruby.org>
! # Licence:: LGPL
#
+ #--
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
***************
*** 17,36 ****
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# $Id$
#
! # Acknowledgements:
! # Thanks to Tomoaki NISHIYAMA <tomoakin at kenroku.kanazawa-u.ac.jp>
! # for providing bl2seq parser patches based on
! # lib/bio/appl/blast/format0.rb.
#
require 'bio/appl/blast/format0'
! module Bio
! class Blast
! class Bl2seq
class Report < Bio::Blast::Default::Report
DELIMITER = RS = nil
--- 19,50 ----
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ #++
#
# $Id$
#
! # Bio::Bl2seq::Report is a NCBI bl2seq (BLAST 2 sequences) output parser.
! #
! # = Acknowledgements
! #
! # Thanks to Tomoaki NISHIYAMA <tomoakin __at__ kenroku.kanazawa-u.ac.jp>
! # for providing bl2seq parser patches based on
! # lib/bio/appl/blast/format0.rb.
#
require 'bio/appl/blast/format0'
! module Bio #:nodoc:
! class Blast #:nodoc:
! class Bl2seq #:nodoc:
!
! # Bio::Bl2seq::Report is a NCBI bl2seq (BLAST 2 sequences) output parser.
! # It inherits Bio::Blast::Default::Report.
! # Most of its methods are the same as Bio::Blast::Default::Report,
! # but it lacks many methods.
class Report < Bio::Blast::Default::Report
+
+ # Delimiter of each entry. Bio::FlatFile uses it.
+ # In Bio::Bl2seq::Report, it it nil (1 entry 1 file).
DELIMITER = RS = nil
***************
*** 39,46 ****
--- 53,63 ----
message, converged?, reference, db
+ # Splits headers.
def format0_split_headers(data)
@f0query = data.shift
end
+ private :format0_split_headers
+ # Splits the search results.
def format0_split_search(data)
iterations = []
***************
*** 53,58 ****
iterations
end
! class F0dbstat < Bio::Blast::Default::Report::F0dbstat
def db_num
unless defined?(@db_num)
--- 70,79 ----
iterations
end
+ private :format0_split_search
! # Stores format0 database statistics.
! # Internal use only. Users must not use the class.
! class F0dbstat < Bio::Blast::Default::Report::F0dbstat #:nodoc:
! # Returns number of sequences in database.
def db_num
unless defined?(@db_num)
***************
*** 63,66 ****
--- 84,88 ----
end
+ # Returns number of letters in database.
def db_len
unless defined?(@db_len)
***************
*** 72,79 ****
end #class F0dbstat
class Iteration < Bio::Blast::Default::Report::Iteration
def initialize(data)
@f0stat = []
! @f0dbstat = nil
@hits = []
@num = 1
--- 94,111 ----
end #class F0dbstat
+ # Bio::Bl2seq::Report::Iteration stores information about
+ # a iteration.
+ # Normally, it may contain some Bio::Bl2seq::Report::Hit objects.
+ #
+ # Note that its main existance reason is to keep complatibility
+ # between Bio::Blast::Default::Report::* classes.
class Iteration < Bio::Blast::Default::Report::Iteration
+ # Creates a new Iteration object.
+ # It is designed to be called only internally from
+ # the Bio::Blast::Default::Report class.
+ # Users shall not use the method directly.
def initialize(data)
@f0stat = []
! @f0dbstat = Bio::Blast::Default::Report::AlwaysNil.instance
@hits = []
@num = 1
***************
*** 83,88 ****
end
def hits; @hits; end
! undef message, pattern_in_database, f0message, f0hitlist,
pattern, pattern_positions, hits_found_again,
hits_newly_found, hits_for_pattern, parse_hitlist,
--- 115,123 ----
end
+ # Returns the hits of the iteration.
+ # It returns an array of Bio::Bl2seq::Report::Hit objects.
def hits; @hits; end
!
! undef message, pattern_in_database,
pattern, pattern_positions, hits_found_again,
hits_newly_found, hits_for_pattern, parse_hitlist,
***************
*** 90,97 ****
end #class Iteration
class Hit < Bio::Blast::Default::Report::Hit
end #class Hit
! # NOTE: HSP class below is NOT used!!
class HSP < Bio::Blast::Default::Report::HSP
end #class HSP
--- 125,141 ----
end #class Iteration
+ # Bio::Bl2seq::Report::Hit contains information about a hit.
+ # It may contain some Bio::Blast::Default::Report::HSP objects.
+ # All methods are the same as Bio::Blast::Default::Report::Hit class.
+ # Please refer to Bio::Blast::Default::Report::Hit.
class Hit < Bio::Blast::Default::Report::Hit
end #class Hit
! # Bio::Bl2seq::Report::HSP holds information about the hsp
! # (high-scoring segment pair).
! # NOTE that the HSP class below is NOT used because
! # Ruby's constants namespace are normally statically determined
! # and HSP object is created in Bio::Blast::Default::Report::Hit class.
! # Please refer to Bio::Blast::Default::Report::HSP.
class HSP < Bio::Blast::Default::Report::HSP
end #class HSP
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