[BioRuby-cvs] bioruby/lib/bio/db/kegg glycan.rb,1.2,1.3
Katayama Toshiaki
k at dev.open-bio.org
Tue Sep 19 05:53:15 UTC 2006
Update of /home/repository/bioruby/bioruby/lib/bio/db/kegg
In directory dev.open-bio.org:/tmp/cvs-serv31854/lib/bio/db/kegg
Modified Files:
glycan.rb
Log Message:
* license is changed from LGPL to Ruby's
Index: glycan.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/glycan.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** glycan.rb 8 Sep 2005 01:22:11 -0000 1.2
--- glycan.rb 19 Sep 2006 05:53:13 -0000 1.3
***************
*** 1,22 ****
#
! # bio/db/kegg/glycan.rb - KEGG GLYCAN database class
! #
! # Copyright (C) 2004 KATAYAMA Toshiaki <k 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
! # License as published by the Free Software Foundation; either
! # version 2 of the License, or (at your option) any later version.
! #
! # This library is distributed in the hope that it will be useful,
! # but WITHOUT ANY WARRANTY; without even the implied warranty of
! # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
! # Lesser General Public License for more details.
#
! # You should have received a copy of the GNU Lesser General Public
! # License along with this library; if not, write to the Free Software
! # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
! # $Id$
#
--- 1,9 ----
#
! # = bio/db/kegg/glycan.rb - KEGG GLYCAN database class
#
! # Copyright:: Copyright (C) 2004 Toshiaki Katayama <k at bioruby.org>
! # License:: Ruby's
#
! # $Id$
#
***************
*** 24,193 ****
module Bio
! class KEGG
!
! class GLYCAN < KEGGDB
! DELIMITER = RS = "\n///\n"
! TAGSIZE = 12
! def initialize(entry)
! super(entry, TAGSIZE)
! end
! # ENTRY
! def entry_id
! unless @data['ENTRY']
! @data['ENTRY'] = fetch('ENTRY').split(/\s+/).first
! end
! @data['ENTRY']
! end
! # NAME
! def name
! field_fetch('NAME')
! end
! # COMPOSITION
! def composition
! unless @data['COMPOSITION']
! hash = Hash.new(0)
! fetch('COMPOSITION').scan(/\((\S+)\)(\d+)/).each do |key, val|
! hash[key] = val.to_i
! end
! @data['COMPOSITION'] = hash
! end
! @data['COMPOSITION']
end
! # MASS
! def mass
! unless @data['MASS']
! hash = Hash.new
! fetch('MASS').scan(/(\S+)\s+\((\S+)\)/).each do |val, key|
! hash[key] = val.to_f
! end
! @data['MASS'] = hash
! end
! @data['MASS']
end
! # CLASS
! def keggclass
! field_fetch('CLASS')
! end
! # BINDING
! def bindings
! unless @data['BINDING']
! ary = Array.new
! lines = lines_fetch('BINDING')
! lines.each do |line|
! if /^\S/.match(line)
! ary << line
! else
! ary.last << " #{line.strip}"
! end
! end
! @data['BINDING'] = ary
end
- @data['BINDING']
end
! # COMPOUND
! def compounds
! unless @data['COMPOUND']
! @data['COMPOUND'] = fetch('COMPOUND').split(/\s+/)
! end
! @data['COMPOUND']
! end
! # REACTION
! def reactions
! unless @data['REACTION']
! @data['REACTION'] = fetch('REACTION').split(/\s+/)
! end
! @data['REACTION']
! end
! # PATHWAY
! def pathways
! lines_fetch('PATHWAY')
! end
! # ENZYME
! def enzymes
! unless @data['ENZYME']
! field = fetch('ENZYME')
! if /\(/.match(field) # old version
! @data['ENZYME'] = field.scan(/\S+ \(\S+\)/)
! else
! @data['ENZYME'] = field.scan(/\S+/)
! end
! end
! @data['ENZYME']
end
! # ORTHOLOG
! def orthologs
! unless @data['ORTHOLOG']
! ary = Array.new
! lines = lines_fetch('ORTHOLOG')
! lines.each do |line|
! if /^\S/.match(line)
! ary << line
! else
! ary.last << " #{line.strip}"
! end
! end
! @data['ORTHOLOG'] = ary
end
- @data['ORTHOLOG']
end
! # REFERENCE
! def references
! unless @data['REFERENCE']
! ary = Array.new
! lines = lines_fetch('REFERENCE')
! lines.each do |line|
! if /^\d+\s+\[PMID/.match(line)
! ary << line
! else
! ary.last << " #{line.strip}"
! end
! end
! @data['REFERENCE'] = ary
end
- @data['REFERENCE']
end
! # DBLINKS
! def dblinks
! unless @data['DBLINKS']
! ary = Array.new
! lines = lines_fetch('DBLINKS')
! lines.each do |line|
! if /^\S/.match(line)
! ary << line
! else
! ary.last << " #{line.strip}"
! end
! end
! @data['DBLINKS'] = ary
end
- @data['DBLINKS']
end
!
! # ATOM, BOND
! def kcf
! return "#{get('NODE')}#{get('EDGE')}"
! end
!
end
end
! end
--- 11,178 ----
module Bio
+ class KEGG
! class GLYCAN < KEGGDB
! DELIMITER = RS = "\n///\n"
! TAGSIZE = 12
! def initialize(entry)
! super(entry, TAGSIZE)
! end
! # ENTRY
! def entry_id
! unless @data['ENTRY']
! @data['ENTRY'] = fetch('ENTRY').split(/\s+/).first
! end
! @data['ENTRY']
! end
! # NAME
! def name
! field_fetch('NAME')
! end
! # COMPOSITION
! def composition
! unless @data['COMPOSITION']
! hash = Hash.new(0)
! fetch('COMPOSITION').scan(/\((\S+)\)(\d+)/).each do |key, val|
! hash[key] = val.to_i
end
+ @data['COMPOSITION'] = hash
+ end
+ @data['COMPOSITION']
+ end
! # MASS
! def mass
! unless @data['MASS']
! hash = Hash.new
! fetch('MASS').scan(/(\S+)\s+\((\S+)\)/).each do |val, key|
! hash[key] = val.to_f
end
+ @data['MASS'] = hash
+ end
+ @data['MASS']
+ end
! # CLASS
! def keggclass
! field_fetch('CLASS')
! end
! # BINDING
! def bindings
! unless @data['BINDING']
! ary = Array.new
! lines = lines_fetch('BINDING')
! lines.each do |line|
! if /^\S/.match(line)
! ary << line
! else
! ary.last << " #{line.strip}"
end
end
+ @data['BINDING'] = ary
+ end
+ @data['BINDING']
+ end
! # COMPOUND
! def compounds
! unless @data['COMPOUND']
! @data['COMPOUND'] = fetch('COMPOUND').split(/\s+/)
! end
! @data['COMPOUND']
! end
! # REACTION
! def reactions
! unless @data['REACTION']
! @data['REACTION'] = fetch('REACTION').split(/\s+/)
! end
! @data['REACTION']
! end
! # PATHWAY
! def pathways
! lines_fetch('PATHWAY')
! end
! # ENZYME
! def enzymes
! unless @data['ENZYME']
! field = fetch('ENZYME')
! if /\(/.match(field) # old version
! @data['ENZYME'] = field.scan(/\S+ \(\S+\)/)
! else
! @data['ENZYME'] = field.scan(/\S+/)
end
+ end
+ @data['ENZYME']
+ end
! # ORTHOLOG
! def orthologs
! unless @data['ORTHOLOG']
! ary = Array.new
! lines = lines_fetch('ORTHOLOG')
! lines.each do |line|
! if /^\S/.match(line)
! ary << line
! else
! ary.last << " #{line.strip}"
end
end
+ @data['ORTHOLOG'] = ary
+ end
+ @data['ORTHOLOG']
+ end
! # REFERENCE
! def references
! unless @data['REFERENCE']
! ary = Array.new
! lines = lines_fetch('REFERENCE')
! lines.each do |line|
! if /^\d+\s+\[PMID/.match(line)
! ary << line
! else
! ary.last << " #{line.strip}"
end
end
+ @data['REFERENCE'] = ary
+ end
+ @data['REFERENCE']
+ end
! # DBLINKS
! def dblinks
! unless @data['DBLINKS']
! ary = Array.new
! lines = lines_fetch('DBLINKS')
! lines.each do |line|
! if /^\S/.match(line)
! ary << line
! else
! ary.last << " #{line.strip}"
end
end
! @data['DBLINKS'] = ary
end
+ @data['DBLINKS']
+ end
+ # ATOM, BOND
+ def kcf
+ return "#{get('NODE')}#{get('EDGE')}"
end
! end # GLYCAN
!
! end # KEGG
! end # Bio
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