[BioRuby-cvs] bioruby/lib/bio/db prosite.rb,0.11,0.12
Mitsuteru C. Nakao
nakao at pub.open-bio.org
Sun Dec 18 12:08:31 EST 2005
Update of /home/repository/bioruby/bioruby/lib/bio/db
In directory pub.open-bio.org:/tmp/cvs-serv29744/lib/bio/db
Modified Files:
prosite.rb
Log Message:
* Added some RDoc documents.
Index: prosite.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/prosite.rb,v
retrieving revision 0.11
retrieving revision 0.12
diff -C2 -d -r0.11 -r0.12
*** prosite.rb 26 Sep 2005 13:00:06 -0000 0.11
--- prosite.rb 18 Dec 2005 17:08:29 -0000 0.12
***************
*** 1,6 ****
#
! # bio/db/prosite.rb - PROSITE database class
#
! # Copyright (C) 2001 KATAYAMA Toshiaki <k at bioruby.org>
#
# This library is free software; you can redistribute it and/or
--- 1,16 ----
#
! # = bio/db/prosite.rb - PROSITE database class
! #
! # Copyright:: Copyright (C) 2001 KATAYAMA Toshiaki <k at bioruby.org>
! # Licence:: LGPL
! #
! # $Id$
! #
! # == Description
#
! #
! # == Example
! # == References
! #--
#
# This library is free software; you can redistribute it and/or
***************
*** 18,22 ****
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
! # $Id$
#
--- 28,32 ----
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
! #++
#
***************
*** 27,32 ****
class PROSITE < EMBLDB
! DELIMITER = RS = "\n//\n"
! TAGSIZE = 5
def initialize(entry)
--- 37,49 ----
class PROSITE < EMBLDB
! # Delimiter
! DELIMITER = "\n//\n"
!
! # Delimiter
! RS = DELIMITER
!
! # Bio::DB API
! TAGSIZE = 5
!
def initialize(entry)
***************
*** 39,42 ****
--- 56,60 ----
# ID ENTRY_NAME; ENTRY_TYPE. (ENTRY_TYPE : PATTERN, MATRIX, RULE)
#
+ # Returns
def name
unless @data['ID']
***************
*** 45,48 ****
--- 63,68 ----
@data['ID']
end
+
+ # Returns
def division
unless @data['TYPE']
***************
*** 57,60 ****
--- 77,81 ----
# AC PSnnnnn;
#
+ # Returns
def ac
unless @data['AC']
***************
*** 63,66 ****
--- 84,88 ----
@data['AC']
end
+
alias entry_id ac
***************
*** 70,76 ****
--- 92,100 ----
# DT MMM-YYYY (CREATED); MMM-YYYY (DATA UPDATE); MMM-YYYY (INFO UPDATE).
#
+ # Returns
def dt
field_fetch('DT')
end
+
alias date dt
***************
*** 80,86 ****
--- 104,112 ----
# DE Description.
#
+ # Returns
def de
field_fetch('DE')
end
+
alias definition de
***************
*** 90,93 ****
--- 116,120 ----
# see - pa2re method
#
+ # Returns
def pa
field_fetch('PA')
***************
*** 96,99 ****
--- 123,127 ----
@data['PA']
end
+
alias pattern pa
***************
*** 103,109 ****
--- 131,139 ----
# see - ma2re method
#
+ # Returns
def ma
field_fetch('MA')
end
+
alias profile ma
***************
*** 115,121 ****
--- 145,153 ----
# The rule is described in ordinary English and is free-format.
#
+ # Returns
def ru
field_fetch('RU')
end
+
alias rule ru
***************
*** 138,141 ****
--- 170,174 ----
# profile because they are partial (fragment) sequences.
#
+ # Returns
def nr
unless @data['NR']
***************
*** 159,224 ****
--- 192,274 ----
@data['NR']
end
+
alias statistics nr
+ # Returns
def release
statistics['RELEASE']
end
+ # Returns
def swissprot_release_number
release.first
end
+ # Returns
def swissprot_release_sequences
release.last
end
+ # Returns
def total
statistics['TOTAL']
end
+ # Returns
def total_hits
total.first
end
+ # Returns
def total_sequences
total.last
end
+ # Returns
def positive
statistics['POSITIVE']
end
+ # Returns
def positive_hits
positive.first
end
+ # Returns
def positive_sequences
positive.last
end
+ # Returns
def unknown
statistics['UNKNOWN']
end
+ # Returns
def unknown_hits
unknown.first
end
+ # Returns
def unknown_sequences
unknown.last
end
+ # Returns
def false_pos
statistics['FALSE_POS']
end
+ # Returns
def false_positive_hits
false_pos.first
end
+ # Returns
def false_positive_sequences
false_pos.last
end
+ # Returns
def false_neg
statistics['FALSE_NEG']
***************
*** 226,229 ****
--- 276,280 ----
alias false_negative_hits false_neg
+ # Returns
def partial
statistics['PARTIAL']
***************
*** 242,245 ****
--- 293,297 ----
# by a program (because it is too unspecific).
#
+ # Returns
def cc
unless @data['CC']
***************
*** 252,257 ****
--- 304,311 ----
@data['CC']
end
+
alias comment cc
+ # Returns
def taxon_range(expand = nil)
range = comment['TAXO-RANGE']
***************
*** 272,279 ****
--- 326,335 ----
end
+ # Returns
def max_repeat
comment['MAX-REPEAT'].to_i
end
+ # Returns
def site
if comment['SITE']
***************
*** 283,286 ****
--- 339,343 ----
end
+ # Returns
def skip_flag
if comment['SKIP-FLAG'] == 'TRUE'
***************
*** 312,315 ****
--- 369,373 ----
# consideration.
#
+ # Returns
def dr
unless @data['DR']
***************
*** 324,329 ****
--- 382,389 ----
@data['DR']
end
+
alias sp_xref dr
+ # Returns
def list_xref(flag, by_name = nil)
ary = []
***************
*** 341,360 ****
--- 401,425 ----
end
+ # Returns
def list_truepositive(by_name = nil)
list_xref('T', by_name)
end
+ # Returns
def list_falsenegative(by_name = nil)
list_xref('F', by_name)
end
+ # Returns
def list_falsepositive(by_name = nil)
list_xref('P', by_name)
end
+ # Returns
def list_potentialhit(by_name = nil)
list_xref('P', by_name)
end
+ # Returns
def list_unknown(by_name = nil)
list_xref('?', by_name)
***************
*** 366,369 ****
--- 431,435 ----
# 3D name; [name2;...]
#
+ # Returns
def pdb_xref
unless @data['3D']
***************
*** 378,381 ****
--- 444,448 ----
# DO PDOCnnnnn;
#
+ # Returns
def pdoc_xref
@data['DO'] = fetch('DO').chomp(';')
***************
*** 421,424 ****
--- 488,492 ----
# translated as: Ala-any-[Ser or Thr]-[Ser or Thr]-(any or none)-Val
#
+ # Returns
def pa2re(pattern)
pattern.gsub!(/\s/, '') # remove white spaces
***************
*** 442,445 ****
--- 510,514 ----
# prosite/profile.txt:
#
+ # Returns
def ma2re(matrix)
raise NotImplementedError
More information about the bioruby-cvs
mailing list