From aerts at dev.open-bio.org  Thu Apr 20 11:58:36 2006
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Thu, 20 Apr 2006 15:58:36 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio location.rb,0.22,0.23
Message-ID: <200604201558.k3KFwa79014586@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv14566

Modified Files:
	location.rb 
Log Message:
Added and reformatted documentation.


Index: location.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/location.rb,v
retrieving revision 0.22
retrieving revision 0.23
diff -C2 -d -r0.22 -r0.23
*** location.rb	18 Dec 2005 15:50:06 -0000	0.22
--- location.rb	20 Apr 2006 15:58:34 -0000	0.23
***************
*** 2,16 ****
  # = bio/location.rb - Locations/Location class (GenBank location format)
  #
! # Copyright::	Copyright (C) 2001, 2005
! #		KATAYAMA Toshiaki <k at bioruby.org>
  # License::	LGPL
  #
  # $Id$
  #
! # == Appendix : GenBank location descriptor classification
  # 
  # === Definition of the position notation of the GenBank location format
  # 
! # According to the GenBank manual 'gbrel.txt', I classified position notations
  # into 10 patterns - (A) to (J).
  # 
--- 2,167 ----
  # = bio/location.rb - Locations/Location class (GenBank location format)
  #
! # Copyright::	Copyright (C) 2001, 2005 KATAYAMA Toshiaki <k at bioruby.org>
! #                             2006 Jan Aerts <jan.aerts at bbsrc.ac.uk>
  # License::	LGPL
  #
  # $Id$
  #
! # 
! #--
! #
! #  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
! #
! #++
! #
! 
! module Bio
! 
! # = DESCRIPTION
! # The Bio::Location class describes the position of a genomic locus. Typically,
! # Bio::Location objects are created automatically when the user creates a
! # Bio::Locations object, instead of initialized directly.
! #
! # = USAGE
! #   location = Bio::Location.new('500..550')
! #   puts "start=" + location.from.to_s + ";end=" + location.to.to_s
! #
! #   #, or better: through Bio::Locations
! #   locations = Bio::Locations.new('500..550')
! #   locations.each do |location|
! #     puts "start=" + location.from.to_s + ";end=" + location.to.to_s
! #   end
! class Location
! 
!   # Parses a'location' segment, which can be 'ID:' + ('n' or 'n..m' or 'n^m'
!   # or "seq") with '<' or '>', and returns a Bio::Location object.
!   #   location = Bio::Location.new('500..550')
!   # 
!   # ---
!   # *Arguments*:
!   # * (required) _str_: GenBank style position string (see Bio::Locations documentation)
!   # *Returns*:: Bio::Location object
!   def initialize(location = nil)
! 
!     if location
!       if location =~ /:/				# (G) ID:location
!         xref_id, location = location.split(':')
!       end
!       if location =~ /</				# (I) <,>
!         lt = true
!       end
!       if location =~ />/
!         gt = true
!       end
!     end
! 
!     # s : start base, e : end base => from, to
!     case location
!     when /^[<>]?(\d+)$/				# (A, I) n
!       s = e = $1.to_i
!     when /^[<>]?(\d+)\.\.[<>]?(\d+)$/			# (B, I) n..m
!       s = $1.to_i
!       e = $2.to_i
!       if e - s < 0
! #       raise "Error: invalid range : #{location}"
!         $stderr.puts "[Warning] invalid range : #{location}" if $DEBUG
!       end
!     when /^[<>]?(\d+)\^[<>]?(\d+)$/			# (C, I) n^m
!       s = $1.to_i
!       e = $2.to_i
!       if e - s != 1
! #       raise "Error: invalid range : #{location}"
!         $stderr.puts "[Warning] invalid range : #{location}" if $DEBUG
!       end
!     when /^"?([ATGCatgc]+)"?$/                  # (H) literal sequence
!       sequence = $1.downcase
!       s = e = nil
!     when nil
!       ;
!     else
!       raise "Error: unknown location format : #{location}"
!     end
! 
!     @from       = s             # start position of the location
!     @to         = e             # end position of the location
!     @strand     = 1             # strand direction of the location
!                                 #   forward => 1 or complement => -1
!     @sequence   = sequence      # literal sequence of the location
!     @lt         = lt            # true if the position contains '<'
!     @gt         = gt            # true if the position contains '>'
!     @xref_id    = xref_id       # link to the external entry as GenBank ID
!   end
! 
!   attr_accessor :from, :to, :strand, :sequence, :lt, :gt, :xref_id
! 
!   # Complements the sequence (i.e. alternates the strand).
!   # ---
!   # *Returns*:: the Bio::Location object
!   def complement
!     @strand *= -1
!     self					# return Location object
!   end
! 
!   # Replaces the sequence of the location.
!   # ---
!   # *Arguments*:
!   # * (required) _sequence_: sequence to be used to replace the sequence at the location
!   # *Returns*:: the Bio::Location object
!   def replace(sequence)
!     @sequence = sequence.downcase
!     self					# return Location object
!   end
! 
!   # Returns the range (from..to) of the location as a Range object.
!   def range
!     @from.. at to
!   end
! 
! end # class location
! 
! # = DESCRIPTION
! # The Bio::Locations class is a container for Bio::Location objects: creating a 
! # Bio::Locations object (based on a GenBank style position string) will
! # spawn an array of Bio::Location objects.
! #
! # = USAGE
! #   locations = Bio::Locations.new('join(complement(500..550), 600..625)')
! #   locations.each do |location|
! #     puts "class=" + location.class.to_s
! #     puts "start=" + location.from.to_s + ";end=" + location.to.to_s \
! #          + ";strand=" + location.strand.to_s
! #   end
! #     # Output would be:
! #     # class=Bio::Location
! #     # start=500;end=550;strand=-1
! #     # class=Bio::Location
! #     # start=600;end=625;strand=1
! # 
! #  # For the following three location strings, print the span and range
! #  ['one-of(898,900)..983',
! #   'one-of(5971..6308,5971..6309)',
! #   '8050..one-of(10731,10758,10905,11242)'].each do |loc|
! #      location = Bio::Locations.new(loc)
! #      puts location.span
! #      puts location.range
! #  end
! #
! # = GENBANK LOCATION DESCRIPTOR CLASSIFICATION
  # 
  # === Definition of the position notation of the GenBank location format
  # 
! # According to the GenBank manual 'gbrel.txt', position notations were classified
  # into 10 patterns - (A) to (J).
  # 
***************
*** 84,115 ****
  # === Reduction strategy of the position notations
  # 
! #   (A) Location n
! #   
! #   (B) Location n..m
! #   
! #   (C) Location n^m
! #   
! #   (D) (n.m)		=> Location n
! #   
! #   (E) one-of(n,m,..)	=> Location n
! #       one-of(n..m,..)	=> Location n..m
! #   
! #   (F) order(loc,loc,..)	=> join(loc, loc,..)
! #       group(loc,loc,..)	=> join(loc, loc,..)
! #       join(loc,loc,..)	=> Sequence
! #   
! #   (G) ID:loc		=> Location with ID
! #   
! #   (H) "atgc"		=> Location only with Sequence
! #   
! #   (I) <n			=> Location n with lt flag
! #       >n			=> Location n with gt flag
! #       <n..m		=> Location n..m with lt flag
! #       n..>m		=> Location n..m with gt flag
! #       <n..>m		=> Location n..m with lt, gt flag
! #   
! #   (J) complement(loc)	=> Sequence
! #   
! #   (K) replace(loc, str)	=> Location with replacement Sequence
  # 
  # === GenBank location examples
--- 235,259 ----
  # === Reduction strategy of the position notations
  # 
! # * (A) Location n
! # * (B) Location n..m
! # * (C) Location n^m
! # * (D) (n.m)		=> Location n
! # * (E)
! #   * one-of(n,m,..)	=> Location n
! #   * one-of(n..m,..)	=> Location n..m
! # * (F)
! #   * order(loc,loc,..)	=> join(loc, loc,..)
! #   * group(loc,loc,..)	=> join(loc, loc,..)
! #   * join(loc,loc,..)	=> Sequence
! # * (G) ID:loc		=> Location with ID
! # * (H) "atgc"		=> Location only with Sequence
! # * (I)
! #   * <n			=> Location n with lt flag
! #   * >n			=> Location n with gt flag
! #   * <n..m		=> Location n..m with lt flag
! #   * n..>m		=> Location n..m with gt flag
! #   * <n..>m		=> Location n..m with lt, gt flag
! # * (J) complement(loc)	=> Sequence
! # * (K) replace(loc, str)	=> Location with replacement Sequence
  # 
  # === GenBank location examples
***************
*** 232,340 ****
  # * [ADR40FIB]	replace(510..520,	<= replace(510..520, "taatcctaccg")
  # * [RATDYIIAAB]	replace(1306..1443,"aagaacatccacggagtcagaactgggctcttcacgccggatttggcgttcgaggccattgtgaaaaagcaggcaatgcaccagcaagctcagttcctacccctgcgtggacctggttatccaggagctaatcagtacagttaggtggtcaagctgaaagagccctgtctgaaa")
- # 
- #--
- #
- #  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
- #
- #++
- #
- 
- module Bio
- 
- class Location
- 
-   # Pass a range of the 'location' segment.  The 'location' segment can be
-   # 'ID:' + ('n' or 'n..m' or 'n^m' or "seq") with '<' or '>'.
-   def initialize(location = nil)
- 
-     if location
-       if location =~ /:/				# (G) ID:location
-         xref_id, location = location.split(':')
-       end
-       if location =~ /</				# (I) <,>
-         lt = true
-       end
-       if location =~ />/
-         gt = true
-       end
-     end
- 
-     # s : start base, e : end base => from, to
-     case location
-     when /^[<>]?(\d+)$/				# (A, I) n
-       s = e = $1.to_i
-     when /^[<>]?(\d+)\.\.[<>]?(\d+)$/			# (B, I) n..m
-       s = $1.to_i
-       e = $2.to_i
-       if e - s < 0
- #       raise "Error: invalid range : #{location}"
-         $stderr.puts "[Warning] invalid range : #{location}" if $DEBUG
-       end
-     when /^[<>]?(\d+)\^[<>]?(\d+)$/			# (C, I) n^m
-       s = $1.to_i
-       e = $2.to_i
-       if e - s != 1
- #       raise "Error: invalid range : #{location}"
-         $stderr.puts "[Warning] invalid range : #{location}" if $DEBUG
-       end
-     when /^"?([ATGCatgc]+)"?$/                  # (H) literal sequence
-       sequence = $1.downcase
-       s = e = nil
-     when nil
-       ;
-     else
-       raise "Error: unknown location format : #{location}"
-     end
- 
-     @from       = s             # start position of the location
-     @to         = e             # end position of the location
-     @strand     = 1             # strand direction of the location
-                                 #   forward => 1 or complement => -1
-     @sequence   = sequence      # literal sequence of the location
-     @lt         = lt            # true if the position contains '<'
-     @gt         = gt            # true if the position contains '>'
-     @xref_id    = xref_id       # link to the external entry as GenBank ID
-   end
- 
-   attr_accessor :from, :to, :strand, :sequence, :lt, :gt, :xref_id
- 
-   # Complement the sequence from outside.
-   def complement
-     @strand *= -1
-     self					# return Location object
-   end
- 
-   # Replace the sequence from outside.
-   def replace(sequence)
-     @sequence	= sequence.downcase
-     self					# return Location object
-   end
- 
-   # Returns a range (from..to) of the segment as a Range object.
-   def range
-     @from.. at to
-   end
- 
- end # class location
- 
- 
  class Locations
- 
    include Enumerable
  
!   # Parse a GenBank style position string and returns a Locations object,
!   # which contains a list of Location objects.
    def initialize(position)
      if position.is_a? Array
--- 376,390 ----
  # * [ADR40FIB]	replace(510..520,	<= replace(510..520, "taatcctaccg")
  # * [RATDYIIAAB]	replace(1306..1443,"aagaacatccacggagtcagaactgggctcttcacgccggatttggcgttcgaggccattgtgaaaaagcaggcaatgcaccagcaagctcagttcctacccctgcgtggacctggttatccaggagctaatcagtacagttaggtggtcaagctgaaagagccctgtctgaaa")
  class Locations
    include Enumerable
  
!   # Parses a GenBank style position string and returns a Bio::Locations object,
!   # which contains a list of Bio::Location objects.
!   #   locations = Bio::Locations.new('join(complement(500..550), 600..625)')
!   #
!   # ---
!   # *Arguments*:
!   # * (required) _str_: GenBank style position string
!   # *Returns*:: Bio::Locations object
    def initialize(position)
      if position.is_a? Array
***************
*** 342,351 ****
      else
        position   = gbl_cleanup(position)	# preprocessing
!       @locations = gbl_pos2loc(position)	# create an Array of Location
      end
    end
    attr_accessor :locations
  
!   # Iterates on each Location object.
    def each
      @locations.each do |x|
--- 392,403 ----
      else
        position   = gbl_cleanup(position)	# preprocessing
!       @locations = gbl_pos2loc(position)	# create an Array of Bio::Location objects
      end
    end
+ 
+   # An Array of Bio::Location objects
    attr_accessor :locations
  
!   # Iterates on each Bio::Location object.
    def each
      @locations.each do |x|
***************
*** 354,368 ****
    end
  
!   # Returns nth Location object.
    def [](n)
      @locations[n]
    end
  
!   # Returns first Location object.
    def first
      @locations.first
    end
  
!   # Returns last Location object.
    def last
      @locations.last
--- 406,420 ----
    end
  
!   # Returns nth Bio::Location object.
    def [](n)
      @locations[n]
    end
  
!   # Returns first Bio::Location object.
    def first
      @locations.first
    end
  
!   # Returns last Bio::Location object.
    def last
      @locations.last
***************
*** 370,374 ****
  
    # Returns an Array containing overall min and max position [min, max]
!   # of this Locations object.
    def span
      span_min = @locations.min { |a,b| a.from <=> b.from }
--- 422,426 ----
  
    # Returns an Array containing overall min and max position [min, max]
!   # of this Bio::Locations object.
    def span
      span_min = @locations.min { |a,b| a.from <=> b.from }
***************
*** 397,403 ****
    alias size length
  
!   # Convert absolute position in DNA (na) to relative position in RNA (na).
!   # If type == :aa,
!   # convert absolute position in DNA (na) to relative position in Protein (aa).
    def relative(n, type = nil)
      case type
--- 449,466 ----
    alias size length
  
!   # Converts absolute position in the whole of the DNA sequence to relative 
!   # position in the locus.
!   # 
!   # This method can for example be used to relate positions in a DNA-sequence
!   # with those in RNA. In this use, the optional ':aa'-flag returns the position
!   # of the associated amino-acid rather than the nucleotide.
!   #   loc = Bio::Locations.new('complement(12838..13533)')
!   #   puts loc.relative(13524)        # => 10
!   #   puts loc.relative(13506, :aa)   # => 3
!   # ---
!   # *Arguments*:
!   # * (required) _position_: nucleotide position within whole of the sequence
!   # * _:aa_: flag that lets method return position in aminoacid coordinates
!   # *Returns*:: position within the location
    def relative(n, type = nil)
      case type
***************
*** 415,430 ****
    end
  
!   # Convert relative position in RNA (na) to absolute position in DNA (na).
!   # If type == :aa,
!   # convert relative position in Protein (aa) -> absolute position in DNA (na).
!   #
!   # * Examples
!   #
!   #     loc = Bio::Locations.new('complement(12838..13533)')
!   #     loc.absolute(10)          #=> 13524 (rel2abs)
!   #     loc.relative(13524)       #=> 10    (abs2rel)
!   #     loc.absolute(10, :aa)     #=> 13506 (rel2abs)
!   #     loc.relative(13506, :aa)  #=> 10    (abs2rel)
!   #
    def absolute(n, type = nil)
      case type
--- 478,495 ----
    end
  
!   # Converts relative position in the locus to position in the whole of the
!   # DNA sequence.
!   # 
!   # This method can for example be used to relate positions in a DNA-sequence
!   # with those in RNA. In this use, the optional ':aa'-flag returns the position
!   # of the associated amino-acid rather than the nucleotide.
!   #   loc = Bio::Locations.new('complement(12838..13533)')
!   #   puts loc.absolute(10)          # => 13524
!   #   puts loc.absolute(10, :aa)     # => 13506
!   # ---
!   # *Arguments*:
!   # * (required) _position_: nucleotide position within locus
!   # * _:aa_: flag to be used if _position_ is a aminoacid position rather than a nucleotide position
!   # *Returns*:: position within the whole of the sequence
    def absolute(n, type = nil)
      case type
***************
*** 591,594 ****
--- 656,664 ----
    puts "Test new & span methods"
    [
+     '450',
+     '500..600',
+     'join(500..550, 600..625)',
+     'complement(join(500..550, 600..625))',
+     'join(complement(500..550), 600..625)',
      '754^755',
      'complement(53^54)',
***************
*** 618,624 ****
    ].each do |pos|
      p pos
!     p Bio::Locations.new(pos).span
!     p Bio::Locations.new(pos).range
!     p Bio::Locations.new(pos)
    end
  
--- 688,699 ----
    ].each do |pos|
      p pos
! #    p Bio::Locations.new(pos)
! #    p Bio::Locations.new(pos).span
! #    p Bio::Locations.new(pos).range
!     Bio::Locations.new(pos).each do |location|
!       puts "class=" + location.class.to_s
!       puts "start=" + location.from.to_s + "\tend=" + location.to.to_s + "\tstrand=" + location.strand.to_s
!     end
! 
    end
  


From aerts at dev.open-bio.org  Wed Apr 26 07:05:52 2006
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Wed, 26 Apr 2006 11:05:52 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio feature.rb,1.10,1.11
Message-ID: <200604261105.k3QB5q61032048@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv32028

Modified Files:
	feature.rb 
Log Message:
Added and reformatted documentation.
Qualifiers are now automatically converted into Bio::Feature::Qualifier objects when initializing a new Bio::Feature object.


Index: feature.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/feature.rb,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** feature.rb	27 Feb 2006 09:13:46 -0000	1.10
--- feature.rb	26 Apr 2006 11:05:50 -0000	1.11
***************
*** 2,42 ****
  # = bio/feature.rb - Features/Feature class (GenBank Feature table)
  #
! # Copyright::	Copyright (c) 2002, 2005
! #		Toshiaki Katayama <k at bioruby.org>
  # License::	Ruby's
  #
  # $Id$
- #
- # == INSD Feature table definition
- #
- # See http://www.ddbj.nig.ac.jp/FT/full_index.html for the INSD
- # (GenBank/EMBL/DDBJ) Feature table definition.
- #
- # === Example
- #
- #  # suppose features is a Bio::Features object
- #  features.each do |feature|
- #    f_name = feature.feature
- #    f_pos  = feature.position
- #    puts "#{f_name}:\t#{f_pos}"
- #    feature.each do |qualifier|
- #      q_name = qualifier.qualifier
- #      q_val  = qualifier.value
- #      puts "- #{q_name}:\t#{q_val}"
- #    end
- #  end
- #
- #  # Iterates only on CDS features and extract translated amino acid sequences
- #  features.each("CDS") do |feature|
- #    hash = feature.assoc
- #    name = hash["gene"] || hash["product"] || hash["note"] 
- #    seq  = hash["translation"]
- #    pos  = feature.position
- #    if gene and seq
- #      puts ">#{gene} #{feature.position}"
- #      puts aaseq
- #    end
- #  end
- #
  
  require 'bio/location'
--- 2,10 ----
  # = bio/feature.rb - Features/Feature class (GenBank Feature table)
  #
! # Copyright::	Copyright (c) 2002, 2005  Toshiaki Katayama <k at bioruby.org>
! #                             2006        Jan Aerts <jan.aerts at bbsrc.ac.uk>
  # License::	Ruby's
  #
  # $Id$
  
  require 'bio/location'
***************
*** 44,52 ****
  module Bio
  
  # Container for the sequence annotation.
  class Feature
! 
    def initialize(feature = '', position = '', qualifiers = [])
!     @feature, @position, @qualifiers = feature, position, qualifiers
    end
  
--- 12,54 ----
  module Bio
  
+ # = DESCRIPTION
  # Container for the sequence annotation.
+ #
+ # = USAGE
+ #  # Create a Bio::Feature object.
+ #  # For example: the GenBank-formatted entry in genbank for accession M33388
+ #  # contains the following feature:
+ #  #    exon     1532..1799
+ #  #             /gene="CYP2D6"
+ #  #             /note="cytochrome P450 IID6; GOO-132-127"
+ #  #             /number="1"
+ #  feature = Bio::Feature.new('exon','1532..1799',['gene' => 'CYP2D6','note' => 'cytochrome P450 IID6; GOO-132-127','number' => '1'])
+ #
+ #  # Print the feature
+ #  puts feature.feature + "\t" + feature.position
+ #  feature.each do |qualifier|
+ #    puts "- " + qualifier.qualifier + ": " + qualifier.value
+ #  end
+ #
+ # = REFERENCES
+ # INSD feature table definition:: http://www.ddbj.nig.ac.jp/FT/full_index.html
  class Feature
!   # Create a new Bio::Feature object.
!   # *Arguments*:
!   # * (required) _feature_: type of feature (e.g. "exon")
!   # * (required) _position_: position of feature (e.g. "complement(1532..1799)")
!   # * (optional) _qualifiers_: list of qualifiers (e.g. "['gene' => 'CYP2D6','number' => '1']")
!   # *Returns*:: Bio::Feature object
    def initialize(feature = '', position = '', qualifiers = [])
!     @feature, @position = feature, position
!     @qualifiers = Array.new
!     if qualifiers.length.modulo(2) > 0
!       $stderr.puts "WARNING"
!     end
!     while qualifiers.length > 0
!       key = qualifiers.shift
!       value = qualifiers.shift || ''
!       self.append(Qualifier.new(key, value))
!     end
    end
  
***************
*** 66,73 ****
  
    # Appends a Qualifier object to the Feature.
!   #
!   # * Returns an Array of Qualifier objects.
!   # * If the argument is not a Qualifier object, returns nil.
!   #
    def append(a)
      @qualifiers.push(a) if a.is_a? Qualifier
--- 68,75 ----
  
    # Appends a Qualifier object to the Feature.
!   # 
!   # *Arguments*:
!   # * (required) _qualifier_: Bio::Feature::Qualifier object
!   # *Returns*:: Bio::Feature object
    def append(a)
      @qualifiers.push(a) if a.is_a? Qualifier
***************
*** 75,79 ****
    end
  
!   # Iterates on each qualifier.
    def each(arg = nil)
      @qualifiers.each do |x|
--- 77,84 ----
    end
  
!   # Iterates on each qualifier object.
!   #
!   # *Arguments*:
!   # * (optional) _key_: if specified, only iterates over qualifiers with this key
    def each(arg = nil)
      @qualifiers.each do |x|
***************
*** 108,114 ****
    end
  
!   # Container for the qualifier-value pair.
    class Qualifier
! 
      def initialize(key, value)
        @qualifier, @value = key, value
--- 113,124 ----
    end
  
!   # Container for qualifier-value pairs for sequence features.
    class Qualifier
!     # Creates a new Bio::Feature::Qualifier object
!     #
!     # *Arguments*:
!     # * (required) _key_: key of the qualifier (e.g. "gene")
!     # * (required) _value_: value of the qualifier (e.g. "CYP2D6")
!     # *Returns*:: Bio::Feature::Qualifier object
      def initialize(key, value)
        @qualifier, @value = key, value
***************
*** 126,132 ****
  
  
! # Container for the list of Feature objects.
  class Features
! 
    def initialize(ary = [])
      @features = ary
--- 136,177 ----
  
  
! # = DESCRIPTION
! # Container for a list of Feature objects.
! #
! # = USAGE
! #  # First, create some Bio::Feature objects
! #  feature1 = Bio::Feature.new('intron','3627..4059',['gene', 'CYP2D6', 'note', 'G00-132-127','number','4'])
! #  feature2 = Bio::Feature.new('exon','4060..4236',['gene', 'CYP2D6', 'note', 'G00-132-127','number','5'])
! #  feature3 = Bio::Feature.new('intron','4237..4426',['gene', 'CYP2D6', 'note', 'G00-132-127','number','5'])
! #  feature4 = Bio::Feature.new('CDS','join(2538..3626,4060..4236)',['gene', 'CYP2D6','translation','MGXXTVMHLL...'])
! #
! #  # And create a container for them
! #  feature_container = Bio::Features.new([ feature1, feature2, feature3, feature4 ])
! #
! #  # Iterate over all features and print
! #  feature_container.each do |feature|
! #    puts feature.feature + "\t" + feature.position
! #    feature.each do |qualifier|
! #      puts "- " + qualifier.qualifier + ": " + qualifier.value
! #    end
! #  end
! #
! #  # Iterate only over CDS features and extract translated amino acid sequences
! #  features.each("CDS") do |feature|
! #    hash = feature.to_hash
! #    name = hash["gene"] || hash["product"] || hash["note"] 
! #    aaseq  = hash["translation"]
! #    pos  = feature.position
! #    if name and seq
! #      puts ">#{gene} #{feature.position}"
! #      puts aaseq
! #    end
! #  end
  class Features
!   # Create a new Bio::Features object.
!   #
!   # *Arguments*:
!   # * (optional) _list of features_: list of Bio::Feature objects
!   # *Returns*:: Bio::Features object
    def initialize(ary = [])
      @features = ary
***************
*** 137,140 ****
--- 182,189 ----
  
    # Appends a Feature object to Features.
+   # 
+   # *Arguments*:
+   # * (required) _feature_: Bio::Feature object
+   # *Returns*:: Bio::Features object
    def append(a)
      @features.push(a) if a.is_a? Feature
***************
*** 142,147 ****
    end
  
!   # Iterates on each feature.  If a feature name is given as an argument,
!   # only iterates on each feature belongs to the name (e.g. 'CDS' etc.)
    def each(arg = nil)
      @features.each do |x|
--- 191,198 ----
    end
  
!   # Iterates on each feature object.
!   #
!   # *Arguments*:
!   # * (optional) _key_: if specified, only iterates over features with this key
    def each(arg = nil)
      @features.each do |x|
***************
*** 170,172 ****
--- 221,257 ----
  end # Bio
  
+ if __FILE__ == $0
+   puts "---TESTING Bio::Feature"
+   feature1 = Bio::Feature.new('exon','1532..1799',['gene','CYP2D6','note','cytochrome P450 IID6; GOO-132-127','number','1', 'note', 'a second note'])
+ 
+   # Print the feature out
+   puts feature1.feature + "\t" + feature1.position
+   feature1.each do |qualifier|
+     puts "- " + qualifier.qualifier + ": " + qualifier.value
+   end
+   
+   feature2 = Bio::Feature.new('CDS','join(2538..3626,4060..4236)',['gene', 'CYP2D6','translation','MGXXTVMHLL...'])
+ 
+   puts "---TESTING Bio::Features"
+   feature3 = Bio::Feature.new('intron','3627..4059',['gene', 'CYP2D6', 'note', 'G00-132-127','number','4'])
+   feature4 = Bio::Feature.new('exon','4060..4236',['gene', 'CYP2D6', 'note', 'G00-132-127','number','5'])
+   feature5 = Bio::Feature.new('intron','4237..4426',['gene', 'CYP2D6', 'note', 'G00-132-127','number','5'])
+   feature_container = Bio::Features.new([ feature1, feature2, feature3, feature4, feature5 ])
+   feature_container.each do |feature|
+     puts "-NEXT FEATURE"
+     puts feature.feature + "\t" + feature.position
+     feature.each do |qualifier|
+       puts "- " + qualifier.qualifier + ": " + qualifier.value
+     end
+   end
  
+   puts "---TESTING hash function"
+   feature_container.each('CDS') do |feature|
+     hash = feature.to_hash
+     name = hash["gene"] || hash["product"] || hash["note"] 
+     aaseq  = hash["translation"]
+     pos  = feature.position
+     puts ">#{name} #{feature.position}"
+     puts aaseq
+   end
+ end


From aerts at dev.open-bio.org  Thu Apr 27 05:29:37 2006
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Thu, 27 Apr 2006 09:29:37 +0000
Subject: [BioRuby-cvs] bioruby/lib bio.rb,1.66,1.67
Message-ID: <200604270929.k3R9Tbx2003641@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib
In directory dev.open-bio.org:/tmp/cvs-serv3621

Modified Files:
	bio.rb 
Log Message:
Added bio/io/ensembl.rb to be autoloaded.


Index: bio.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio.rb,v
retrieving revision 1.66
retrieving revision 1.67
diff -C2 -d -r1.66 -r1.67
*** bio.rb	27 Feb 2006 09:11:01 -0000	1.66
--- bio.rb	27 Apr 2006 09:29:35 -0000	1.67
***************
*** 132,135 ****
--- 132,137 ----
    autoload :DBGET,          'bio/io/dbget'
  
+   autoload :Ensembl,        'bio/io/ensembl'
+ 
    ## below are described in bio/appl/blast.rb
    #class Blast


From nakao at dev.open-bio.org  Fri Apr 14 00:49:46 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Fri, 14 Apr 2006 04:49:46 -0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db/embl embl.rb,1.26,1.27
Message-ID: <200604140549.k3E5nWFn009694@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db/embl
In directory dev.open-bio.org:/tmp/cvs-serv9674

Modified Files:
	embl.rb 
Log Message:
* Removed example codes (if __FILE__ == $0 ... end).
* Changed license (LGPL -> Ruby's).


Index: embl.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/embl.rb,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** embl.rb	28 Jan 2006 06:40:38 -0000	1.26
--- embl.rb	14 Apr 2006 05:49:30 -0000	1.27
***************
*** 3,8 ****
  #
  # 
! # Copyright::   Copyright (C) 2001-2005 Mitsuteru C. Nakao <n at bioruby.org>
! # License::     LGPL
  #
  # $Id$
--- 3,8 ----
  #
  # 
! # Copyright::   Copyright (C) 2001-2006 Mitsuteru C. Nakao <n at bioruby.org>
! # License::     Ruby's
  #
  # $Id$
***************
*** 29,50 ****
  #   http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html
  #
- #--
- #
- #  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
- #
- #++
- #
  
  require 'bio/db'
--- 29,32 ----
***************
*** 395,454 ****
    end
  
! end
! 
! end
! 
! 
! if __FILE__ == $0
!   while ent = $<.gets(Bio::EMBL::RS)
!     puts "\n ==> e = Bio::EMBL.new(ent) "
!     e = Bio::EMBL.new(ent)
! 
!     puts "\n ==> e.entry_id "
!     p e.entry_id
!     puts "\n ==> e.id_line "
!     p e.id_line
!     puts "\n ==> e.id_line('molecule') "
!     p e.id_line('molecule')
!     puts "\n ==> e.molecule "
!     p e.molecule
!     puts "\n ==> e.ac "
!     p e.ac
!     puts "\n ==> e.sv "
!     p e.sv
!     puts "\n ==> e.dt "
!     p e.dt
!     puts "\n ==> e.dt('created') "
!     p e.dt('created')
!     puts "\n ==> e.de "
!     p e.de
!     puts "\n ==> e.kw "
!     p e.kw
!     puts "\n ==> e.os "
!     p e.os
!     puts "\n ==> e.oc "
!     p e.oc
!     puts "\n ==> e.og "
!     p e.og
!     puts "\n ==> e.ref "
!     p e.ref
!     puts "\n ==> e.dr "
!     p e.dr
!     puts "\n ==> e.ft "
!     p e.ft
!     puts "\n ==> e.each_cds {|c| p c}"
!     p e.each_cds {|c| p c }
!     puts "\n ==> e.sq "
!     p e.sq
!     puts "\n ==> e.sq('a') "
!     p e.sq('a')
!     puts "\n ==> e.gc"    
!     p e.gc
!     puts "\n ==> e.seq "
!     p e.seq
!   end
! 
! end
! 
! 
  
--- 377,381 ----
    end
  
! end # class EMBL
  
+ end # module Bio


From nakao at dev.open-bio.org  Fri Apr 14 00:52:42 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Fri, 14 Apr 2006 04:52:42 -0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db/embl sptr.rb,1.30,1.31
Message-ID: <200604140552.k3E5qU1e009726@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db/embl
In directory dev.open-bio.org:/tmp/cvs-serv9706

Modified Files:
	sptr.rb 
Log Message:
* Removed example codes (if __FILE__ == $0 ... end).
* Changed license (LGPL -> Ruby's).


Index: sptr.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/sptr.rb,v
retrieving revision 1.30
retrieving revision 1.31
diff -C2 -d -r1.30 -r1.31
*** sptr.rb	28 Jan 2006 06:40:38 -0000	1.30
--- sptr.rb	14 Apr 2006 05:52:28 -0000	1.31
***************
*** 2,7 ****
  # = bio/db/embl/sptr.rb - UniProt/SwissProt and TrEMBL database class
  # 
! # Copyright::   Copyright (C) 2001-2005 Mitsuteru C. Nakao <n at bioruby.org>
! # License::     LGPL
  #
  # $Id$
--- 2,7 ----
  # = bio/db/embl/sptr.rb - UniProt/SwissProt and TrEMBL database class
  # 
! # Copyright::   Copyright (C) 2001-2006 Mitsuteru C. Nakao <n at bioruby.org>
! # License::     Ruby's
  #
  # $Id$
***************
*** 32,53 ****
  #   http://www.expasy.org/sprot/userman.html
  #
! #--
! #
! #  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
! #
! #++
! #
  
  require 'bio/db'
--- 32,36 ----
  #   http://www.expasy.org/sprot/userman.html
  #
! 
  
  require 'bio/db'
***************
*** 760,841 ****
  
  
- if __FILE__ == $0
-   # Usage: ruby __FILE__ uniprot_sprot.dat 
-   # Usage: ruby __FILE__ uniprot_sprot.dat | egrep '^RuntimeError'
- 
-   begin
-     require 'pp'
-     alias pp p
-   rescue LoadError
-   end
- 
-   def cmd(cmd, tag = nil, ent = $ent)
-     puts " ==> #{cmd} "
-     puts Bio::SPTR.new(ent).get(tag) if tag
-     begin
-       p eval(cmd)
-     rescue RuntimeError
-       puts "RuntimeError(#{Bio::SPTR.new($ent).entry_id})}: #{$!} "
-     end
-     puts
-   end
- 
- 
-   while $ent = $<.gets(Bio::SPTR::RS)
-     
-     cmd "Bio::SPTR.new($ent).entry_id"
- 
-     cmd "Bio::SPTR.new($ent).id_line", 'ID'
-     cmd "Bio::SPTR.new($ent).entry"
-     cmd "Bio::SPTR.new($ent).entry_name"
-     cmd "Bio::SPTR.new($ent).molecule"
-     cmd "Bio::SPTR.new($ent).sequence_length"
- 
-     cmd "Bio::SPTR.new($ent).ac", 'AC'
-     cmd "Bio::SPTR.new($ent).accession"
- 
- 
-     cmd "Bio::SPTR.new($ent).gn", 'GN'
-     cmd "Bio::SPTR.new($ent).gene_name"
-     cmd "Bio::SPTR.new($ent).gene_names"
- 
-     cmd "Bio::SPTR.new($ent).dt", "DT"
-     ['created','annotation','sequence'].each do |key|
-       cmd "Bio::SPTR.new($ent).dt('#{key}')"
-     end
- 
-     cmd "Bio::SPTR.new($ent).de", 'DE'
-     cmd "Bio::SPTR.new($ent).definition"
-     cmd "Bio::SPTR.new($ent).protein_name"
-     cmd "Bio::SPTR.new($ent).synonyms"
- 
-     cmd "Bio::SPTR.new($ent).kw", 'KW'
- 
-     cmd "Bio::SPTR.new($ent).os", 'OS'
- 
-     cmd "Bio::SPTR.new($ent).oc", 'OC'
- 
-     cmd "Bio::SPTR.new($ent).og", 'OG'
- 
-     cmd "Bio::SPTR.new($ent).ox", 'OX'
- 
-     cmd "Bio::SPTR.new($ent).ref", 'R'
- 
-     cmd "Bio::SPTR.new($ent).cc", 'CC'
-     cmd "Bio::SPTR.new($ent).cc('ALTERNATIVE PRODUCTS')"
-     cmd "Bio::SPTR.new($ent).cc('DATABASE')"
-     cmd "Bio::SPTR.new($ent).cc('MASS SPECTOMETRY')"
- 
-     cmd "Bio::SPTR.new($ent).dr", 'DR'
- 
-     cmd "Bio::SPTR.new($ent).ft", 'FT'
-     cmd "Bio::SPTR.new($ent).ft['DOMAIN']"
- 
-     cmd "Bio::SPTR.new($ent).sq", "SQ"
-     cmd "Bio::SPTR.new($ent).seq"
-   end
- 
- end
- 
  
  =begin
--- 743,746 ----


From nakao at dev.open-bio.org  Fri Apr 14 01:04:22 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Fri, 14 Apr 2006 05:04:22 -0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db/embl common.rb,1.9,1.10
Message-ID: <200604140604.k3E64BXK009760@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db/embl
In directory dev.open-bio.org:/tmp/cvs-serv9740

Modified Files:
	common.rb 
Log Message:
* Changed license (LGPL -> Ruby's).


Index: common.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/common.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** common.rb	28 Jan 2006 06:40:38 -0000	1.9
--- common.rb	14 Apr 2006 06:04:09 -0000	1.10
***************
*** 3,7 ****
  #
  # Copyright::   Copyright (C) 2001-2005 Mitsuteru C. Nakao <n at bioruby.org>
! # License::     LGPL
  #
  # $Id$
--- 3,7 ----
  #
  # Copyright::   Copyright (C) 2001-2005 Mitsuteru C. Nakao <n at bioruby.org>
! # License::     Ruby's
  #
  # $Id$
***************
*** 70,91 ****
  #   http://www.expasy.org/sprot/userman.html
  #
- #--
- #
- #  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
- #
- #++
- #
  
  require 'bio/db'
--- 70,73 ----


From nakao at dev.open-bio.org  Fri Apr 14 01:28:29 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Fri, 14 Apr 2006 05:28:29 -0000
Subject: [BioRuby-cvs] bioruby/lib/bio/io ensembl.rb,NONE,1.1
Message-ID: <200604140628.k3E6SBGn009942@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv9920/d/d/d

Added Files:
	ensembl.rb 
Log Message:
* ensembl.rb) newly added.
* test_ensembl.rb) newly added.


--- NEW FILE: ensembl.rb ---
#
# = bio/io/ensembl.rb - An Ensembl Genome Browser client.
#
# Copyright::   Copyright (C) 2006
#               Mitsuteru C. Nakao <n at bioruby.org>
# License::     Ruby's
#
# $Id: ensembl.rb,v 1.1 2006/04/14 06:28:09 nakao Exp $
#
# == Description
#
# Client classes for Ensembl Genome Browser.
#
# == Examples
#
#  seq = Bio::Ensembl::Human.exportview(1, 1000, 100000)
#  gff = Bio::Ensembl::Human.exportview(1, 1000, 100000, ['gene'])
#
#  seq = Bio::Ensembl::Mouse.exportview(1, 1000, 100000)
#  gff = Bio::Ensembl::Mouse.exportview(1, 1000, 100000, ['gene', 'variation', 'genscan'])
#
#  
# == References
#
# * Ensembl
#   http:/www.ensembl.org/
#

require 'bio'
require 'cgi'

module Bio

# == Description
#
# An Ensembl Genome Browser client class.
#
# == Examples
#
#  seq = Bio::Ensembl::Human.exportview(1, 1000, 100000)
#  gff = Bio::Ensembl::Human.exportview(1, 1000, 100000, ['gene'])
#
#  seq = Bio::Ensembl::Mouse.exportview(1, 1000, 100000)
#  gff = Bio::Ensembl::Mouse.exportview(1, 1000, 100000, ['gene', 'variation', 'genscan'])
#
# == References
#
# * Ensembl
#   http:/www.ensembl.org/
#
class Ensembl

  # Hostname of Ensembl Genome Browser.
  ServerName = 'www.ensembl.org'


  # Ensembl Genome Browser Client Super Class
  #
  # == Examples
  #   
  #   module Bio
  #     class Ensembl::Kumamushi < Base
  #       Organism = 'Milnesium_tardigradum'
  #     end
  #   end
  #   fna = Bio::Ensembl::Kumamushi.exportview(1, 1000, 20000)
  #
  class Base

    # Ensembl ExportView Client.
    #
    # Retrieve genomic sequence/features from Ensembl ExportView in plain text.
    # Ensembl ExportView exports genomic data (sequence and features) in 
    # several file formats including fasta, GFF and tab.
    #
    # * ExportViwe (http://www.ensembl.org/Homo_sapiens/exportview).
    #
    # == Examples
    #
    #   # Genomic sequence in Fasta format
    #   Bio::Ensembl::Human.exportview(:seq_region_name => 1, :anchor1 => 1149206, :anchor2 => 1149229)
    #   Bio::Ensembl::Human.exportview(1, 1149206, 1149229)
    #
    #   # Feature in GFF
    #   Bio::Ensembl::Human.exportview(:seq_region_name => 1, :anchor1 => 1149206, :anchor2 => 1150000, 
    #                                  :options => ['similarity', 'repeat', 'genscan', 'variation', 'gene'])
    #   Bio::Ensembl::Human.exportview(1, 1149206, 1150000, ['variation', 'gene'])
    #
    # == Arguments
    #
    # Bio::Ensembl::Base#exportview method allow both orderd arguments and 
    # named arguments. 
    # Note: mandatory arguments marked '*'.
    #
    # === Orderd Arguments
    #
    # 1. seq_region_name - Chromosome number (*)
    # 2. anchor1         - From coordination (*)
    # 3. anchor2         - To coordination (*)
    # 4. options         - Features to export (in :format => 'gff' or 'tab')
    #                      ['similarity', 'repeat', 'genscan', 'variation', 'gene']
    #
    # === Named Arguments
    # 
    # * :seq_region_name - Chromosome number (*)
    # * :anchor1         - From coordination (*)
    # * :anchor2         - To coordination (*)
    # * :type1           - From coordination type ['bp', ]
    # * :type2           - To coordination type ['bp', ]
    # * :upstream        - Bp upstream
    # * :downstream      - Bp downstream
    # * :format          - File format ['fasta', 'gff', 'tab']
    # * :options         - Features to export (for :format => 'gff' or 'tab')
    #                      ['similarity', 'repeat', 'genscan', 'variation', 'gene']
    # 
    def self.exportview(*args)
      cgi = Client.new('exportview', self::Organism)

      if args.first.class == Hash then opts = args.first
      else
        opts = {:seq_region_name => args[0], :anchor1 => args[1], :anchor2 => args[2]}
        case args.size
        when 3 then opts.update({:format => 'fasta'})
        when 4 then opts.update({:format => 'gff', :options => args[3]}) ;        end
      end
      @hash = {:type1 => 'bp', 
               :type2 => 'bp', 
               :downstream => '', 
               :upstream => '', 
               :format => 'fasta',
               :options => [],
               :action => 'export', :_format => 'Text', :output => 'txt', :submit => 'Continue >>'}

      cgi.exec(@hash.update(opts))
    end

    # An Ensembl CGI client class
    # 
    # === Examples
    #
    #  cgi = Client('martview', 'Homo_sapiens')
    #  cgi.exec(hash_data)
    #
    class Client < PSORT::CGIDriver
      def initialize(cgi_name, genome_name)
        super(Ensembl::ServerName, ['', genome_name, cgi_name].join('/'))
      end

      private

      def make_args(query)
        @args = {}
        query.each { |k, v| @args[k.to_s] = v }
        nested_args_join(query)
      end

      def nested_args_join(hash)
        tmp = []
        hash.each do |key, value|
          if value.class == Array then value.each { |val| tmp << [key, val] } else tmp << [key, value] end
        end
        tmp.map {|x| x.map {|x| CGI.escape(x.to_s) }.join("=") }.join('&')
      end

      def parse_report(result_body)
        result_body
      end
    end # class Client

  end # class Base


  # Ensembl Human Genome
  # 
  # See Bio::Ensembl::Base class.
  # 
  class Human < Base
    Organism = 'Homo_sapiens'
  end # class Human

  # Ensembl Mouse Genome
  #
  # See Bio::Ensembl::Base class.
  #
  class Mouse < Base
    Organism = 'Mus_musculus'
  end # class Mouse

end # class Ensembl

end # module Bio




From nakao at dev.open-bio.org  Fri Apr 14 01:28:42 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Fri, 14 Apr 2006 05:28:42 -0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/io test_ensembl.rb,NONE,1.1
Message-ID: <200604140628.k3E6SBo7009947@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv9920/test/unit/bio/io

Added Files:
	test_ensembl.rb 
Log Message:
* ensembl.rb) newly added.
* test_ensembl.rb) newly added.


--- NEW FILE: test_ensembl.rb ---
#
# = test/unit/bio/io/test_ensembl.rb - Unit test for Bio::Ensembl.
#
# Copyright::   Copyright (C) 2006
#               Mitsuteru C. Nakao <n at bioruby.org>
# License::     Ruby's
#
# $Id: test_ensembl.rb,v 1.1 2006/04/14 06:28:09 nakao Exp $
#

require 'pathname'
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
$:.unshift(libpath) unless $:.include?(libpath)

require 'test/unit'
require 'bio/io/ensembl'


class TestEnsembl < Test::Unit::TestCase
  def test_server_name
    assert_equal('www.ensembl.org', Bio::Ensembl::ServerName)
  end

end

class TestEnsemblBase < Test::Unit::TestCase
  def test_exportview
    
  end
end

class TestEnsemblBaseClient < Test::Unit::TestCase
  def test_class
    assert_equal(Bio::PSORT::CGIDriver, Bio::Ensembl::Base::Client.superclass)
  end
end


class TestEnsemblHuman < Test::Unit::TestCase
  def test_organism
    assert_equal("Homo_sapiens", Bio::Ensembl::Human::Organism)
  end
end

class TestEnsemblMouse < Test::Unit::TestCase
  def test_organism
    assert_equal("Mus_musculus", Bio::Ensembl::Mouse::Organism)
  end
end


From nakao at dev.open-bio.org  Fri Apr 14 01:33:32 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Fri, 14 Apr 2006 05:33:32 -0000
Subject: [BioRuby-cvs] bioruby ChangeLog,1.50,1.51
Message-ID: <200604140633.k3E6XL90010004@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv9984

Modified Files:
	ChangeLog 
Log Message:
* Bio::Ensembl first commit.


Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.50
retrieving revision 1.51
diff -C2 -d -r1.50 -r1.51
*** ChangeLog	27 Feb 2006 11:38:14 -0000	1.50
--- ChangeLog	14 Apr 2006 06:33:19 -0000	1.51
***************
*** 1,2 ****
--- 1,10 ----
+ 2006-04-14  Mitsuteru Nakao <n at bioruby.org>
+ 
+         * lib/bio/io/ensembl.rb
+ 
+           Bio::Ensembl first commit. It is a client class for Ensembl Genome
+           Browser.
+ 
+ 
  2006-02-27  Toshiaki Katayama <k at bioruby.org>
  


From ngoto at dev.open-bio.org  Wed Apr 26 08:04:15 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Wed, 26 Apr 2006 12:04:15 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio command.rb,1.5,1.6
Message-ID: <200604261204.k3QC4FZN032162@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv32140/lib/bio

Modified Files:
	command.rb 
Log Message:
Experimentally added Bio::Command::NetTools.net_http_start() method. Note that it would be removed or the method name would be changed.


Index: command.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/command.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** command.rb	28 Mar 2006 14:00:48 -0000	1.5
--- command.rb	26 Apr 2006 12:04:13 -0000	1.6
***************
*** 13,16 ****
--- 13,17 ----
  require 'uri'
  require 'open-uri'
+ require 'net/http'
  
  module Bio
***************
*** 162,165 ****
--- 163,190 ----
      OpenURI.open_uri(uri).read
    end
+ 
+   # Same as:
+   #  uri = URI.parse(uri); Net::HTTP.start(uri.host, uri.port)
+   # and 
+   # it uses proxy if an environment variable (same as OpenURI.open_uri)
+   # is set.
+   # uri must be a string or a URI object.
+   def self.net_http_start(uri, &block)
+     unless uri.kind_of?(URI::Generic)
+       uri = URI.parse(uri)
+     end
+     if uri.scheme != 'http' then
+       raise "only http is supported: #{uri.inspect}"
+     end
+     # Note: URI#find_proxy is an unofficial method defined in open-uri.rb.
+     # If the spec of open-uri.rb would be changed, we should change below.
+     if proxyuri = uri.find_proxy then
+       raise 'Non-HTTP proxy' if proxyuri.class != URI::HTTP
+       http = Net::HTTP.Proxy(proxyuri.host, proxyuri.port)
+     else
+       http = Net::HTTP
+     end
+     http.start(uri.host, uri.port, &block)
+   end
  end #module NetTools
  


From ngoto at dev.open-bio.org  Wed Apr 26 22:33:45 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Thu, 27 Apr 2006 02:33:45 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio command.rb,1.6,1.7
Message-ID: <200604270233.k3R2XjuZ002237@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv2217/lib/bio

Modified Files:
	command.rb 
Log Message:
changed spec of Bio::Command::NetTools.net_http_start()


Index: command.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/command.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** command.rb	26 Apr 2006 12:04:13 -0000	1.6
--- command.rb	27 Apr 2006 02:33:43 -0000	1.7
***************
*** 165,180 ****
  
    # Same as:
!   #  uri = URI.parse(uri); Net::HTTP.start(uri.host, uri.port)
    # and 
    # it uses proxy if an environment variable (same as OpenURI.open_uri)
    # is set.
!   # uri must be a string or a URI object.
!   def self.net_http_start(uri, &block)
!     unless uri.kind_of?(URI::Generic)
!       uri = URI.parse(uri)
!     end
!     if uri.scheme != 'http' then
!       raise "only http is supported: #{uri.inspect}"
!     end
      # Note: URI#find_proxy is an unofficial method defined in open-uri.rb.
      # If the spec of open-uri.rb would be changed, we should change below.
--- 165,175 ----
  
    # Same as:
!   #   Net::HTTP.start(address, port)
    # and 
    # it uses proxy if an environment variable (same as OpenURI.open_uri)
    # is set.
!   #
!   def self.net_http_start(address, port = 80, &block)
!     uri = URI.parse("http://#{address}:#{port}")
      # Note: URI#find_proxy is an unofficial method defined in open-uri.rb.
      # If the spec of open-uri.rb would be changed, we should change below.
***************
*** 185,189 ****
        http = Net::HTTP
      end
!     http.start(uri.host, uri.port, &block)
    end
  end #module NetTools
--- 180,184 ----
        http = Net::HTTP
      end
!     http.start(address, port, &block)
    end
  end #module NetTools


From ngoto at dev.open-bio.org  Wed Apr 26 23:15:29 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Thu, 27 Apr 2006 03:15:29 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio command.rb,1.7,1.8
Message-ID: <200604270315.k3R3FTmK002447@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv2392/lib/bio

Modified Files:
	command.rb 
Log Message:
Bio::Command::NetTools can be included in classes.


Index: command.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/command.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** command.rb	27 Apr 2006 02:33:43 -0000	1.7
--- command.rb	27 Apr 2006 03:15:27 -0000	1.8
***************
*** 160,166 ****
  
    # Same as OpenURI.open_uri(uri).read.
!   def self.read_uri(uri)
      OpenURI.open_uri(uri).read
    end
  
    # Same as:
--- 160,167 ----
  
    # Same as OpenURI.open_uri(uri).read.
!   def read_uri(uri)
      OpenURI.open_uri(uri).read
    end
+   module_function :read_uri
  
    # Same as:
***************
*** 170,174 ****
    # is set.
    #
!   def self.net_http_start(address, port = 80, &block)
      uri = URI.parse("http://#{address}:#{port}")
      # Note: URI#find_proxy is an unofficial method defined in open-uri.rb.
--- 171,175 ----
    # is set.
    #
!   def net_http_start(address, port = 80, &block)
      uri = URI.parse("http://#{address}:#{port}")
      # Note: URI#find_proxy is an unofficial method defined in open-uri.rb.
***************
*** 182,185 ****
--- 183,188 ----
      http.start(address, port, &block)
    end
+   module_function :net_http_start
+ 
  end #module NetTools
  


From nakao at dev.open-bio.org  Thu Apr 27 01:38:52 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Thu, 27 Apr 2006 05:38:52 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/io test_ensembl.rb,1.1,1.2
Message-ID: <200604270538.k3R5cqVL002709@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv2667/test/unit/bio/io

Modified Files:
	test_ensembl.rb 
Log Message:
* ensembl.rb: Use Bio::Command::NetTools.net_http_start for proxy server.
* ensembl.rb: Added Ensembl.server_uri method.



Index: test_ensembl.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/io/test_ensembl.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** test_ensembl.rb	14 Apr 2006 06:28:09 -0000	1.1
--- test_ensembl.rb	27 Apr 2006 05:38:50 -0000	1.2
***************
*** 19,25 ****
  class TestEnsembl < Test::Unit::TestCase
    def test_server_name
!     assert_equal('www.ensembl.org', Bio::Ensembl::ServerName)
    end
  
  end
  
--- 19,34 ----
  class TestEnsembl < Test::Unit::TestCase
    def test_server_name
!     assert_equal('http://www.ensembl.org', Bio::Ensembl::EBIServerURI)
    end
  
+   def test_server_uri
+     assert_equal('http://www.ensembl.org', Bio::Ensembl.server_uri)
+   end
+   
+   def test_set_server_uri
+     host = 'http://localhost'
+     Bio::Ensembl.server_uri(host)
+     assert_equal(host, Bio::Ensembl.server_uri)
+   end
  end
  
***************
*** 32,36 ****
  class TestEnsemblBaseClient < Test::Unit::TestCase
    def test_class
!     assert_equal(Bio::PSORT::CGIDriver, Bio::Ensembl::Base::Client.superclass)
    end
  end
--- 41,45 ----
  class TestEnsemblBaseClient < Test::Unit::TestCase
    def test_class
! 
    end
  end


From nakao at dev.open-bio.org  Thu Apr 27 01:38:52 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Thu, 27 Apr 2006 05:38:52 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/io ensembl.rb,1.1,1.2
Message-ID: <200604270538.k3R5cqbu002714@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv2667/lib/bio/io

Modified Files:
	ensembl.rb 
Log Message:
* ensembl.rb: Use Bio::Command::NetTools.net_http_start for proxy server.
* ensembl.rb: Added Ensembl.server_uri method.



Index: ensembl.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/ensembl.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** ensembl.rb	14 Apr 2006 06:28:09 -0000	1.1
--- ensembl.rb	27 Apr 2006 05:38:50 -0000	1.2
***************
*** 27,31 ****
  #
  
! require 'bio'
  require 'cgi'
  
--- 27,32 ----
  #
  
! require 'bio/command'
! require 'uri'
  require 'cgi'
  
***************
*** 44,47 ****
--- 45,54 ----
  #  gff = Bio::Ensembl::Mouse.exportview(1, 1000, 100000, ['gene', 'variation', 'genscan'])
  #
+ #  Bio::Enesmbl.server_uri("http://www.gramene.org")
+ #  class Rice < Base
+ #    Organism = 'Oryza_sativa'
+ #  end
+ #  seq = Bio::Ensembl::Rice.exportview(1, 1000, 100000)
+ #
  # == References
  #
***************
*** 49,56 ****
  #   http:/www.ensembl.org/
  #
  class Ensembl
  
!   # Hostname of Ensembl Genome Browser.
!   ServerName = 'www.ensembl.org'
  
  
--- 56,86 ----
  #   http:/www.ensembl.org/
  #
+ # * GRAMENE
+ #   http://www.gramene.org/
+ #
  class Ensembl
  
!   # Hostname of the Ensembl Genome Browser.
!   EBIServerURI = 'http://www.ensembl.org'
! 
!   # An Alternative Hostname for Ensembl Genome Browser.
!   @@server_uri = nil
! 
!   # Sets and uses an alternative hostname for ensembl genome browser.
!   #
!   # == Example
!   #
!   #   require 'bio'
!   #   p Bio::Enesmbl.server_uri #=> 'http://www.ensembl.org'
!   #   Bio::Enesmbl.server_uri("http://www.gramene.org")
!   #   p Bio::Enesmbl.server_uri #=> "http://www.gramene.org"
!   #
!   def self.server_uri(uri = nil)
!     if uri
!       @@server_uri = uri
!     else
!       @@server_uri || EBIServerURI
!     end
!   end
  
  
***************
*** 79,89 ****
      #
      #   # Genomic sequence in Fasta format
!     #   Bio::Ensembl::Human.exportview(:seq_region_name => 1, :anchor1 => 1149206, :anchor2 => 1149229)
      #   Bio::Ensembl::Human.exportview(1, 1149206, 1149229)
      #
      #   # Feature in GFF
!     #   Bio::Ensembl::Human.exportview(:seq_region_name => 1, :anchor1 => 1149206, :anchor2 => 1150000, 
!     #                                  :options => ['similarity', 'repeat', 'genscan', 'variation', 'gene'])
!     #   Bio::Ensembl::Human.exportview(1, 1149206, 1150000, ['variation', 'gene'])
      #
      # == Arguments
--- 109,124 ----
      #
      #   # Genomic sequence in Fasta format
!     #   Bio::Ensembl::Human.exportview(:seq_region_name => 1, 
!     #                                  :anchor1 => 1149206, :anchor2 => 1149229)
      #   Bio::Ensembl::Human.exportview(1, 1149206, 1149229)
      #
      #   # Feature in GFF
!     #   Bio::Ensembl::Human.exportview(:seq_region_name => 1, 
!     #                                  :anchor1 => 1149206, :anchor2 => 1150000, 
!     #                                  :options => ['similarity', 'repeat', 
!     #                                               'genscan', 'variation', 
!     #                                               'gene'])
!     #   Bio::Ensembl::Human.exportview(1, 1149206, 1150000, 
!     #                                  ['variation', 'gene'])
      #
      # == Arguments
***************
*** 99,103 ****
      # 3. anchor2         - To coordination (*)
      # 4. options         - Features to export (in :format => 'gff' or 'tab')
!     #                      ['similarity', 'repeat', 'genscan', 'variation', 'gene']
      #
      # === Named Arguments
--- 134,139 ----
      # 3. anchor2         - To coordination (*)
      # 4. options         - Features to export (in :format => 'gff' or 'tab')
!     #                      ['similarity', 'repeat', 'genscan', 'variation', 
!     #                       'gene']
      #
      # === Named Arguments
***************
*** 112,128 ****
      # * :format          - File format ['fasta', 'gff', 'tab']
      # * :options         - Features to export (for :format => 'gff' or 'tab')
!     #                      ['similarity', 'repeat', 'genscan', 'variation', 'gene']
      # 
      def self.exportview(*args)
-       cgi = Client.new('exportview', self::Organism)
- 
        if args.first.class == Hash then opts = args.first
        else
!         opts = {:seq_region_name => args[0], :anchor1 => args[1], :anchor2 => args[2]}
          case args.size
!         when 3 then opts.update({:format => 'fasta'})
!         when 4 then opts.update({:format => 'gff', :options => args[3]}) ;        end
        end
!       @hash = {:type1 => 'bp', 
                 :type2 => 'bp', 
                 :downstream => '', 
--- 148,169 ----
      # * :format          - File format ['fasta', 'gff', 'tab']
      # * :options         - Features to export (for :format => 'gff' or 'tab')
!     #                      ['similarity', 'repeat', 'genscan', 'variation', 
!     #                       'gene']
      # 
      def self.exportview(*args)
        if args.first.class == Hash then opts = args.first
        else
!         options = {:seq_region_name => args[0], 
!                    :anchor1 => args[1], 
!                    :anchor2 => args[2]}
          case args.size
!         when 3 then 
!           options.update({:format => 'fasta'})
!         when 4 then 
!           options.update({:format => 'gff', :options => args[3]})
!         end
        end
! 
!       @data = {:type1 => 'bp', 
                 :type2 => 'bp', 
                 :downstream => '', 
***************
*** 130,169 ****
                 :format => 'fasta',
                 :options => [],
!                :action => 'export', :_format => 'Text', :output => 'txt', :submit => 'Continue >>'}
  
!       cgi.exec(@hash.update(opts))
      end
  
      # An Ensembl CGI client class
      # 
      # === Examples
      #
!     #  cgi = Client('martview', 'Homo_sapiens')
!     #  cgi.exec(hash_data)
      #
!     class Client < PSORT::CGIDriver
        def initialize(cgi_name, genome_name)
!         super(Ensembl::ServerName, ['', genome_name, cgi_name].join('/'))
        end
  
!       private
  
!       def make_args(query)
!         @args = {}
!         query.each { |k, v| @args[k.to_s] = v }
!         nested_args_join(query)
        end
  
!       def nested_args_join(hash)
          tmp = []
          hash.each do |key, value|
!           if value.class == Array then value.each { |val| tmp << [key, val] } else tmp << [key, value] end
          end
!         tmp.map {|x| x.map {|x| CGI.escape(x.to_s) }.join("=") }.join('&')
        end
  
-       def parse_report(result_body)
-         result_body
-       end
      end # class Client
  
--- 171,238 ----
                 :format => 'fasta',
                 :options => [],
!                :action => 'export', 
!                :_format => 'Text', 
!                :output => 'txt', 
!                :submit => 'Continue >>'}
  
!       cgi = Client.new('exportview', self::Organism)
!       cgi.exec(@data.update(options))
      end
  
+ 
+ 
      # An Ensembl CGI client class
+     #
+     # Enable the use of HTTP access via a proxy by setting the proxy address up
+     # as the 'http_proxy' enviroment variable. 
      # 
      # === Examples
      #
!     #  cgi = Client.new('martview', 'Homo_sapiens')
!     #  result_body = cgi.exec(hash_data)
      #
!     class Client
! 
!       # Sets cgi_name and genome_name.
!       #
!       # === Example
!       #
!       #  cgi = Client.new('martview', 'Homo_sapiens')
!       #
        def initialize(cgi_name, genome_name)
!         @uri = URI.parse(Ensembl.server_uri)
!         @path = ['', genome_name, cgi_name].join('/')
        end
  
!       # Executes query with data.
!       #
!       # === Example
!       #
!       #  result_body = cgi.exec(hash_data)
!       #
!       def exec(data_hash)
!         data = make_args(data_hash)
  
!         result = nil      
!         Bio::Command::NetTools.net_http_start(@uri.host, @uri.port) {|http|
!           result, = http.post(@path, data)
!         }
!         result.body
        end
  
!       private
! 
!       def make_args(hash)
          tmp = []
          hash.each do |key, value|
!           if value.class == Array then 
!             value.each { |val| tmp << [key, val] } 
!           else 
!             tmp << [key, value] 
!           end
          end
!         tmp.map {|e| e.map {|x| CGI.escape(x.to_s) }.join("=") }.join('&')
        end
  
      end # class Client
  


From ngoto at dev.open-bio.org  Sun Apr 30 01:40:25 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Sun, 30 Apr 2006 05:40:25 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/bl2seq report.rb,1.6,1.7
Message-ID: <200604300540.k3U5ePMf018074@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/bl2seq
In directory dev.open-bio.org:/tmp/cvs-serv18054

Modified Files:
	report.rb 
Log Message:
changes license to Ruby's.


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/bl2seq/report.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** report.rb	18 Dec 2005 15:58:39 -0000	1.6
--- report.rb	30 Apr 2006 05:40:23 -0000	1.7
***************
*** 3,23 ****
  # 
  # Copyright:: Copyright (C) 2005 GOTO Naohisa <ng at bioruby.org>
! # License::   LGPL
! #
! #--
! #  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
! #++
  #
  #  $Id$
--- 3,7 ----
  # 
  # Copyright:: Copyright (C) 2005 GOTO Naohisa <ng at bioruby.org>
! # License::   Ruby's
  #
  #  $Id$


From ngoto at dev.open-bio.org  Sun Apr 30 01:47:27 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Sun, 30 Apr 2006 05:47:27 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/blast wublast.rb,1.6,1.7
Message-ID: <200604300547.k3U5lRRv018148@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/blast
In directory dev.open-bio.org:/tmp/cvs-serv18107/blast

Modified Files:
	wublast.rb 
Log Message:
parse error (missing hits) for some hits of which database sequence names
contain 'Score'.


Index: wublast.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/wublast.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** wublast.rb	22 Feb 2006 08:46:15 -0000	1.6
--- wublast.rb	30 Apr 2006 05:47:25 -0000	1.7
***************
*** 281,285 ****
                  r = data.first
                end
!               if /^\s+Score/ =~ r then
                  @hsps << HSP.new(data)
                else
--- 281,285 ----
                  r = data.first
                end
!               if /\A\s+Score/ =~ r then
                  @hsps << HSP.new(data)
                else


From ngoto at dev.open-bio.org  Sun Apr 30 01:48:01 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Sun, 30 Apr 2006 05:48:01 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/blast format0.rb,1.17,1.18
Message-ID: <200604300548.k3U5m18v018180@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/blast
In directory dev.open-bio.org:/tmp/cvs-serv18160/blast

Modified Files:
	format0.rb 
Log Message:
parse error (missing hits) for some hits of which database sequence names contain 'Score'.


Index: format0.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/format0.rb,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** format0.rb	22 Feb 2006 08:46:15 -0000	1.17
--- format0.rb	30 Apr 2006 05:47:59 -0000	1.18
***************
*** 781,785 ****
              @f0hitname = data.shift
              @hsps = []
!             while r = data[0] and /^\s+Score/ =~ r
                @hsps << HSP.new(data)
              end
--- 781,785 ----
              @f0hitname = data.shift
              @hsps = []
!             while r = data[0] and /\A\s+Score/ =~ r
                @hsps << HSP.new(data)
              end


From ngoto at dev.open-bio.org  Sun Apr 30 01:50:21 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Sun, 30 Apr 2006 05:50:21 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl clustalw.rb, 1.10, 1.11 mafft.rb,
	1.9, 1.10 sim4.rb, 1.5, 1.6
Message-ID: <200604300550.k3U5oLwo018302@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv18276

Modified Files:
	clustalw.rb mafft.rb sim4.rb 
Log Message:
changed license to Ruby's


Index: sim4.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/sim4.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** sim4.rb	18 Dec 2005 15:58:40 -0000	1.5
--- sim4.rb	30 Apr 2006 05:50:19 -0000	1.6
***************
*** 3,23 ****
  #
  # Copyright:: Copyright (C) 2004 GOTO Naohisa <ng at bioruby.org>
! # License::   LGPL
! #
! #--
! #  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
! #++
  #
  #  $Id$
--- 3,7 ----
  #
  # Copyright:: Copyright (C) 2004 GOTO Naohisa <ng at bioruby.org>
! # License::   Ruby's
  #
  #  $Id$

Index: clustalw.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/clustalw.rb,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** clustalw.rb	18 Dec 2005 15:58:40 -0000	1.10
--- clustalw.rb	30 Apr 2006 05:50:19 -0000	1.11
***************
*** 3,23 ****
  #
  # Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! # License::   LGPL
! #
! #--
! #  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
! #++
  #
  #  $Id$
--- 3,7 ----
  #
  # Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! # License::   Ruby's
  #
  #  $Id$

Index: mafft.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/mafft.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** mafft.rb	18 Dec 2005 15:58:40 -0000	1.9
--- mafft.rb	30 Apr 2006 05:50:19 -0000	1.10
***************
*** 3,23 ****
  #
  # Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! # License::   LGPL
! #
! #--
! #  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
! #++
  #
  #  $Id$
--- 3,7 ----
  #
  # Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! # License::   Ruby's
  #
  #  $Id$


From ngoto at dev.open-bio.org  Sun Apr 30 01:50:21 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Sun, 30 Apr 2006 05:50:21 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/clustalw report.rb,1.9,1.10
Message-ID: <200604300550.k3U5oLJO018309@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/clustalw
In directory dev.open-bio.org:/tmp/cvs-serv18276/clustalw

Modified Files:
	report.rb 
Log Message:
changed license to Ruby's


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/clustalw/report.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** report.rb	18 Dec 2005 15:58:40 -0000	1.9
--- report.rb	30 Apr 2006 05:50:19 -0000	1.10
***************
*** 3,23 ****
  #
  # Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! # License::   LGPL
! #
! #--
! #  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
! #++
  #
  #  $Id$
--- 3,7 ----
  #
  # Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! # License::   Ruby's
  #
  #  $Id$


From ngoto at dev.open-bio.org  Sun Apr 30 01:50:21 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Sun, 30 Apr 2006 05:50:21 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/mafft report.rb,1.8,1.9
Message-ID: <200604300550.k3U5oLpH018314@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/mafft
In directory dev.open-bio.org:/tmp/cvs-serv18276/mafft

Modified Files:
	report.rb 
Log Message:
changed license to Ruby's


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/mafft/report.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** report.rb	18 Dec 2005 15:58:40 -0000	1.8
--- report.rb	30 Apr 2006 05:50:19 -0000	1.9
***************
*** 3,23 ****
  #
  # Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! # License::   LGPL
! #
! #--
! #  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
! #++
  #
  #  $Id$
--- 3,7 ----
  #
  # Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! # License::   Ruby's
  #
  #  $Id$


From ngoto at dev.open-bio.org  Sun Apr 30 01:50:21 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Sun, 30 Apr 2006 05:50:21 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/sim4 report.rb,1.7,1.8
Message-ID: <200604300550.k3U5oLFj018319@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/sim4
In directory dev.open-bio.org:/tmp/cvs-serv18276/sim4

Modified Files:
	report.rb 
Log Message:
changed license to Ruby's


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/sim4/report.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** report.rb	18 Dec 2005 15:58:40 -0000	1.7
--- report.rb	30 Apr 2006 05:50:19 -0000	1.8
***************
*** 3,23 ****
  #
  # Copyright:: Copyright (C) 2004 GOTO Naohisa <ng at bioruby.org>
! # License::   LGPL
! #
! #--
! #  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
! #++
  #
  #  $Id$
--- 3,7 ----
  #
  # Copyright:: Copyright (C) 2004 GOTO Naohisa <ng at bioruby.org>
! # License::   Ruby's
  #
  #  $Id$


From ngoto at dev.open-bio.org  Sun Apr 30 01:56:42 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Sun, 30 Apr 2006 05:56:42 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio alignment.rb,1.15,1.16
Message-ID: <200604300556.k3U5ugBr018426@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv18406

Modified Files:
	alignment.rb 
Log Message:
changed license to Ruby's


Index: alignment.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/alignment.rb,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** alignment.rb	24 Jan 2006 14:16:59 -0000	1.15
--- alignment.rb	30 Apr 2006 05:56:40 -0000	1.16
***************
*** 5,28 ****
  #             GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
  #
! # License:: LGPL
  #
  #  $Id$
  #
- #--
- #  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
- #++
- #
  # = About Bio::Alignment
  #
--- 5,12 ----
  #             GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
  #
! # License:: Ruby's
  #
  #  $Id$
  #
  # = About Bio::Alignment
  #


From ngoto at dev.open-bio.org  Sun Apr 30 01:57:42 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Sun, 30 Apr 2006 05:57:42 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db fantom.rb,1.11,1.12
Message-ID: <200604300557.k3U5vgsw018500@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db
In directory dev.open-bio.org:/tmp/cvs-serv18480/db

Modified Files:
	fantom.rb 
Log Message:
changed license to Ruby's


Index: fantom.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/fantom.rb,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** fantom.rb	26 Sep 2005 13:00:06 -0000	1.11
--- fantom.rb	30 Apr 2006 05:57:40 -0000	1.12
***************
*** 2,20 ****
  # bio/db/fantom.rb - RIKEN FANTOM2 database classes
  #
! #   Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! #
! #  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
  #
  #  $Id$
--- 2,7 ----
  # bio/db/fantom.rb - RIKEN FANTOM2 database classes
  #
! # Copyright:: Copyright (C) 2003 GOTO Naohisa <ng at bioruby.org> 
! # License::   Ruby's
  #
  #  $Id$


From ngoto at dev.open-bio.org  Sun Apr 30 01:58:52 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Sun, 30 Apr 2006 05:58:52 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/io/flatfile bdb.rb,1.8,1.9
Message-ID: <200604300558.k3U5wqaF018532@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/io/flatfile
In directory dev.open-bio.org:/tmp/cvs-serv18512/io/flatfile

Modified Files:
	bdb.rb 
Log Message:
changed license to Ruby's


Index: bdb.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/flatfile/bdb.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** bdb.rb	26 Sep 2005 13:00:08 -0000	1.8
--- bdb.rb	30 Apr 2006 05:58:50 -0000	1.9
***************
*** 2,20 ****
  # bio/io/flatfile/bdb.rb - OBDA flatfile index by Berkley DB 
  # 
! #   Copyright (C) 2002 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp> 
! # 
! #  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 
  # 
  #  $Id$ 
--- 2,7 ----
  # bio/io/flatfile/bdb.rb - OBDA flatfile index by Berkley DB 
  # 
! # Copyright:: Copyright (C) 2002 GOTO Naohisa <ng at bioruby.org> 
! # License::   Ruby's
  # 
  #  $Id$ 


From nakao at dev.open-bio.org  Sun Apr 30 03:11:30 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Sun, 30 Apr 2006 07:11:30 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/blast xmlparser.rb,1.13,1.14
Message-ID: <200604300711.k3U7BUm3018668@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/blast
In directory dev.open-bio.org:/tmp/cvs-serv18631/lib/bio/appl/blast

Modified Files:
	xmlparser.rb 
Log Message:
* changed license to Ruby's 


Index: xmlparser.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/xmlparser.rb,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** xmlparser.rb	8 Sep 2005 01:22:08 -0000	1.13
--- xmlparser.rb	30 Apr 2006 07:11:28 -0000	1.14
***************
*** 1,23 ****
  #
! # bio/appl/blast/xmlparser.rb - BLAST XML output (-m 7) parser by XMLParser
  # 
! #   Copyright (C) 2001 Mitsuteru C. Nakao <n at bioruby.org>
! #   Copyright (C) 2003 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
  #
! #  $Id$
  #
  
--- 1,31 ----
  #
! # = bio/appl/blast/xmlparser.rb - BLAST XML output (-m 7) parser by XMLParser
  # 
! # Copyright::    Copyright (C) 2001 
! #                Mitsuteru C. Nakao <n at bioruby.org>
! # Copyright::    Copyright (C) 2003 
! #                KATAYAMA Toshiaki <k at bioruby.org>
! # Lisence::      Ruby's
  #
! # $Id$
  #
! # == Description
! # 
! # A parser for blast XML report (format 7) based on the XMLParser.
! # This file is automatically loaded by bio/appl/blast/report.rb if
! # the XMLParser installed.
  #
! # BioRuby provides two implements of the paser for the blast XML format report
! # (format 7) based on the XMLParser and the REXML.
  #
! # == Examples
! #
! # == References
! #
! # * Blast
! #   http://
! #
! # * XMLParser
! #   http://
  #
  
***************
*** 28,217 ****
  
  module Bio
!   class Blast
!     class Report
  
!       private
  
!       def xmlparser_parse(xml)
!         parser = XMLParser.new
!         def parser.default; end
!         
!         begin
!           tag_stack = Array.new
!           hash = Hash.new
  
!           parser.parse(xml) do |type, name, data|
!             #print "type=#{type.inspect} name=#{name.inspect} data=#{data.inspect}\n" # for DEBUG
!             case type
!             when XMLParser::START_ELEM
!               tag_stack.push(name)
!               hash.update(data)
!               case name
!               when 'Iteration'
!                 iteration = Iteration.new
!                 @iterations.push(iteration)
!               when 'Hit'
!                 hit = Hit.new
!                 hit.query_id = @query_id
!                 hit.query_def = @query_def
!                 hit.query_len = @query_len
!                 @iterations.last.hits.push(hit)
!               when 'Hsp'
!                 hsp = Hsp.new
!                 @iterations.last.hits.last.hsps.push(hsp)
!               end
!             when XMLParser::END_ELEM
!               case name
!               when /^BlastOutput/
!                 xmlparser_parse_program(name,hash)
!                 hash = Hash.new
!               when /^Parameters$/
!                 xmlparser_parse_parameters(hash)
!                 hash = Hash.new
!               when /^Iteration/
!                 xmlparser_parse_iteration(name, hash)
!                 hash = Hash.new
!               when /^Hit/
!                 xmlparser_parse_hit(name, hash)
!                 hash = Hash.new
!               when /^Hsp$/
!                 xmlparser_parse_hsp(hash)
!                 hash = Hash.new
!               when /^Statistics$/
!                 xmlparser_parse_statistics(hash)
!                 hash = Hash.new
!               end
!               tag_stack.pop
!             when XMLParser::CDATA
!               if hash[tag_stack.last].nil?
!                 hash[tag_stack.last] = data unless data.strip.empty?
!               else
!                 hash[tag_stack.last].concat(data) if data
!               end
!             when XMLParser::PI
              end
            end
-         rescue XMLParserError
-           line = parser.line
-           column = parser.column
-           print "Parse error at #{line}(#{column}) : #{$!}\n"
          end
        end
  
  
!       def xmlparser_parse_program(tag, hash)
!         case tag
!         when 'BlastOutput_program'
!           @program = hash[tag]
!         when 'BlastOutput_version'
!           @version = hash[tag]
!         when 'BlastOutput_reference'
!           @reference = hash[tag]
!         when 'BlastOutput_db'
!           @db = hash[tag].strip
!         when 'BlastOutput_query-ID'
!           @query_id = hash[tag]
!         when 'BlastOutput_query-def'
!           @query_def = hash[tag]
!         when 'BlastOutput_query-len'
!           @query_len = hash[tag].to_i
!         end
        end
  
!       def xmlparser_parse_parameters(hash)
!         labels = { 
!           'matrix'	=> 'Parameters_matrix',
!           'expect'	=> 'Parameters_expect',
!           'include'	=> 'Parameters_include',
!           'sc-match'	=> 'Parameters_sc-match',
!           'sc-mismatch'	=> 'Parameters_sc-mismatch',
!           'gap-open'	=> 'Parameters_gap-open',
!           'gap-extend'	=> 'Parameters_gap-extend',
!           'filter'	=> 'Parameters_filter',
!           'pattern'	=> 'Parameters_pattern',
!           'entrez-query'=> 'Parameters_entrez-query',
!         }
!         labels.each do |k,v|
!           case k
!           when 'filter', 'matrix'
!             @parameters[k] = hash[v].to_s
!           else
!             @parameters[k] = hash[v].to_i
!           end
          end
        end
  
!       def xmlparser_parse_iteration(tag, hash)
!         case tag
!         when 'Iteration_iter-num'
!           @iterations.last.num = hash[tag].to_i
!         when 'Iteration_message'
!           @iterations.last.message = hash[tag].to_s
!         end
        end
  
!       def xmlparser_parse_hit(tag, hash)
!         hit = @iterations.last.hits.last
!         case tag
!         when 'Hit_num'
!           hit.num = hash[tag].to_i
!         when 'Hit_id'
!           hit.hit_id = hash[tag].clone
!         when 'Hit_def'
!           hit.definition = hash[tag].clone
!         when 'Hit_accession'
!           hit.accession = hash[tag].clone
!         when 'Hit_len'
!           hit.len = hash[tag].clone.to_i
!         end
        end
  
!       def xmlparser_parse_hsp(hash)
!         hsp = @iterations.last.hits.last.hsps.last
!         hsp.num			= hash['Hsp_num'].to_i
!         hsp.bit_score		= hash['Hsp_bit-score'].to_f
!         hsp.score		= hash['Hsp_score'].to_i
!         hsp.evalue		= hash['Hsp_evalue'].to_f
!         hsp.query_from		= hash['Hsp_query-from'].to_i
!         hsp.query_to		= hash['Hsp_query-to'].to_i
!         hsp.hit_from		= hash['Hsp_hit-from'].to_i
!         hsp.hit_to		= hash['Hsp_hit-to'].to_i
!         hsp.pattern_from	= hash['Hsp_pattern-from'].to_i
!         hsp.pattern_to		= hash['Hsp_pattern-to'].to_i
!    	hsp.query_frame		= hash['Hsp_query-frame'].to_i
!         hsp.hit_frame		= hash['Hsp_hit-frame'].to_i
!         hsp.identity		= hash['Hsp_identity'].to_i
!         hsp.positive		= hash['Hsp_positive'].to_i
!         hsp.gaps		= hash['Hsp_gaps'].to_i
!         hsp.align_len		= hash['Hsp_align-len'].to_i
!         hsp.density		= hash['Hsp_density'].to_i
!         hsp.qseq		= hash['Hsp_qseq']
!         hsp.hseq		= hash['Hsp_hseq']
!         hsp.midline		= hash['Hsp_midline']
!       end
  
!       def xmlparser_parse_statistics(hash)
!         labels = {
!           'db-num'	=> 'Statistics_db-num',
!           'db-len'	=> 'Statistics_db-len',
!           'hsp-len'	=> 'Statistics_hsp-len',
!           'eff-space'	=> 'Statistics_eff-space',
!           'kappa'	=> 'Statistics_kappa',
!           'lambda'	=> 'Statistics_lambda',
!           'entropy'	=> 'Statistics_entropy'
!         }
!         labels.each do |k,v|
!           case k
!           when 'db-num', 'db-len', 'hsp-len'
!             @iterations.last.statistics[k] = hash[v].to_i
!           else
!             @iterations.last.statistics[k] = hash[v].to_f
!           end
          end
        end
-         
      end
!   end
! end
  
  
--- 36,224 ----
  
  module Bio
! class Blast
!   class Report
  
!     private
  
!     def xmlparser_parse(xml)
!       parser = XMLParser.new
!       def parser.default; end
!        
!       begin
!         tag_stack = Array.new
!         hash = Hash.new
  
!         parser.parse(xml) do |type, name, data|
!           case type
!           when XMLParser::START_ELEM
!             tag_stack.push(name)
!             hash.update(data)
!             case name
!             when 'Iteration'
!               iteration = Iteration.new
!               @iterations.push(iteration)
!             when 'Hit'
!               hit = Hit.new
!               hit.query_id = @query_id
!               hit.query_def = @query_def
!               hit.query_len = @query_len
!               @iterations.last.hits.push(hit)
!             when 'Hsp'
!               hsp = Hsp.new
!               @iterations.last.hits.last.hsps.push(hsp)
              end
+           when XMLParser::END_ELEM
+             case name
+             when /^BlastOutput/
+               xmlparser_parse_program(name,hash)
+               hash = Hash.new
+             when /^Parameters$/
+               xmlparser_parse_parameters(hash)
+               hash = Hash.new
+             when /^Iteration/
+               xmlparser_parse_iteration(name, hash)
+               hash = Hash.new
+             when /^Hit/
+               xmlparser_parse_hit(name, hash)
+               hash = Hash.new
+             when /^Hsp$/
+               xmlparser_parse_hsp(hash)
+               hash = Hash.new
+             when /^Statistics$/
+               xmlparser_parse_statistics(hash)
+               hash = Hash.new
+             end
+             tag_stack.pop
+           when XMLParser::CDATA
+             if hash[tag_stack.last].nil?
+               hash[tag_stack.last] = data unless data.strip.empty?
+             else
+               hash[tag_stack.last].concat(data) if data
+             end
+           when XMLParser::PI
            end
          end
+       rescue XMLParserError
+         line = parser.line
+         column = parser.column
+         print "Parse error at #{line}(#{column}) : #{$!}\n"
        end
+     end
  
  
!     def xmlparser_parse_program(tag, hash)
!       case tag
!       when 'BlastOutput_program'
!         @program = hash[tag]
!       when 'BlastOutput_version'
!         @version = hash[tag]
!       when 'BlastOutput_reference'
!         @reference = hash[tag]
!       when 'BlastOutput_db'
!         @db = hash[tag].strip
!       when 'BlastOutput_query-ID'
!         @query_id = hash[tag]
!       when 'BlastOutput_query-def'
!         @query_def = hash[tag]
!       when 'BlastOutput_query-len'
!         @query_len = hash[tag].to_i
        end
+     end
  
!     def xmlparser_parse_parameters(hash)
!       labels = { 
!         'matrix'       => 'Parameters_matrix',
!         'expect'       => 'Parameters_expect',
!         'include'      => 'Parameters_include',
!         'sc-match'     => 'Parameters_sc-match',
!         'sc-mismatch'  => 'Parameters_sc-mismatch',
!         'gap-open'     => 'Parameters_gap-open',
!         'gap-extend'   => 'Parameters_gap-extend',
!         'filter'       => 'Parameters_filter',
!         'pattern'      => 'Parameters_pattern',
!         'entrez-query' => 'Parameters_entrez-query',
!       }
!       labels.each do |k,v|
!         case k
!         when 'filter', 'matrix'
!           @parameters[k] = hash[v].to_s
!         else
!           @parameters[k] = hash[v].to_i
          end
        end
+     end
  
!     def xmlparser_parse_iteration(tag, hash)
!       case tag
!       when 'Iteration_iter-num'
!         @iterations.last.num = hash[tag].to_i
!       when 'Iteration_message'
!         @iterations.last.message = hash[tag].to_s
        end
+     end
  
!     def xmlparser_parse_hit(tag, hash)
!       hit = @iterations.last.hits.last
!       case tag
!       when 'Hit_num'
!         hit.num = hash[tag].to_i
!       when 'Hit_id'
!         hit.hit_id = hash[tag].clone
!       when 'Hit_def'
!         hit.definition = hash[tag].clone
!       when 'Hit_accession'
!         hit.accession = hash[tag].clone
!       when 'Hit_len'
!         hit.len = hash[tag].clone.to_i
        end
+     end
  
!     def xmlparser_parse_hsp(hash)
!       hsp = @iterations.last.hits.last.hsps.last
!       hsp.num          = hash['Hsp_num'].to_i
!       hsp.bit_score    = hash['Hsp_bit-score'].to_f
!       hsp.score        = hash['Hsp_score'].to_i
!       hsp.evalue       = hash['Hsp_evalue'].to_f
!       hsp.query_from   = hash['Hsp_query-from'].to_i
!       hsp.query_to     = hash['Hsp_query-to'].to_i
!       hsp.hit_from     = hash['Hsp_hit-from'].to_i
!       hsp.hit_to       = hash['Hsp_hit-to'].to_i
!       hsp.pattern_from = hash['Hsp_pattern-from'].to_i
!       hsp.pattern_to   = hash['Hsp_pattern-to'].to_i
!       hsp.query_frame  = hash['Hsp_query-frame'].to_i
!       hsp.hit_frame    = hash['Hsp_hit-frame'].to_i
!       hsp.identity     = hash['Hsp_identity'].to_i
!       hsp.positive     = hash['Hsp_positive'].to_i
!       hsp.gaps         = hash['Hsp_gaps'].to_i
!       hsp.align_len    = hash['Hsp_align-len'].to_i
!       hsp.density      = hash['Hsp_density'].to_i
!       hsp.qseq         = hash['Hsp_qseq']
!       hsp.hseq         = hash['Hsp_hseq']
!       hsp.midline      = hash['Hsp_midline']
!     end
  
!     def xmlparser_parse_statistics(hash)
!       labels = {
!         'db-num'	=> 'Statistics_db-num',
!         'db-len'	=> 'Statistics_db-len',
!         'hsp-len'	=> 'Statistics_hsp-len',
!         'eff-space'	=> 'Statistics_eff-space',
!         'kappa'	=> 'Statistics_kappa',
!         'lambda'	=> 'Statistics_lambda',
!         'entropy'	=> 'Statistics_entropy'
!       }
!       labels.each do |k,v|
!         case k
!         when 'db-num', 'db-len', 'hsp-len'
!           @iterations.last.statistics[k] = hash[v].to_i
!         else
!           @iterations.last.statistics[k] = hash[v].to_f
          end
        end
      end
!         
!   end # class Report
! end # class Blast
! end # module Bio
  
  


From nakao at dev.open-bio.org  Sun Apr 30 03:11:30 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Sun, 30 Apr 2006 07:11:30 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/psort report.rb,1.12,1.13
Message-ID: <200604300711.k3U7BUtC018673@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/psort
In directory dev.open-bio.org:/tmp/cvs-serv18631/lib/bio/appl/psort

Modified Files:
	report.rb 
Log Message:
* changed license to Ruby's 


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/psort/report.rb,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** report.rb	3 Nov 2005 10:50:58 -0000	1.12
--- report.rb	30 Apr 2006 07:11:28 -0000	1.13
***************
*** 2,7 ****
  # = bio/appl/psort/report.rb - PSORT systems report classes
  #
! # Copyright::   Copyright (C) 2003 Mitsuteru C. Nakao <n at bioruby.org>
! # License::     LGPL
  #
  #  $Id$
--- 2,8 ----
  # = bio/appl/psort/report.rb - PSORT systems report classes
  #
! # Copyright::   Copyright (C) 2003 
! #               Mitsuteru C. Nakao <n at bioruby.org>
! # License::     Ruby's
  #
  #  $Id$
***************
*** 9,30 ****
  # == A Report classes for PSORT Systems
  # 
- #--
- #
- #  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
- #
- # ++
- #
  
  require 'bio/sequence'
--- 10,13 ----


From nakao at dev.open-bio.org  Sun Apr 30 03:11:31 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Sun, 30 Apr 2006 07:11:31 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/targetp report.rb,1.7,1.8
Message-ID: <200604300711.k3U7BVlq018678@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/targetp
In directory dev.open-bio.org:/tmp/cvs-serv18631/lib/bio/appl/targetp

Modified Files:
	report.rb 
Log Message:
* changed license to Ruby's 


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/targetp/report.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** report.rb	18 Dec 2005 15:58:41 -0000	1.7
--- report.rb	30 Apr 2006 07:11:28 -0000	1.8
***************
*** 2,7 ****
  # = bio/appl/targetp/report.rb - TargetP report class
  # 
! # Copyright::  Copyright (C) 2003 Mitsuteru C. Nakao <n at bioruby.org>
! # License::    LGPL
  #
  #  $Id$
--- 2,8 ----
  # = bio/appl/targetp/report.rb - TargetP report class
  # 
! # Copyright::  Copyright (C) 2003 
! #              Mitsuteru C. Nakao <n at bioruby.org>
! # License::    Ruby's
  #
  #  $Id$
***************
*** 13,33 ****
  # == Example
  # == References
- #--
- #
- #  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
- #
- #++
  #
  
--- 14,17 ----


From nakao at dev.open-bio.org  Sun Apr 30 03:11:31 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Sun, 30 Apr 2006 07:11:31 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/genscan report.rb,1.8,1.9
Message-ID: <200604300711.k3U7BVhB018688@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/genscan
In directory dev.open-bio.org:/tmp/cvs-serv18631/lib/bio/appl/genscan

Modified Files:
	report.rb 
Log Message:
* changed license to Ruby's 


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/genscan/report.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** report.rb	18 Dec 2005 15:58:40 -0000	1.8
--- report.rb	30 Apr 2006 07:11:29 -0000	1.9
***************
*** 2,7 ****
  # = bio/appl/genscan/report.rb - Genscan report classes
  #
! # Copyright::  Copyright (C) 2003 Mitsuteru C. Nakao <n at bioruby.org>
! # License::    LGPL
  #
  #  $Id$
--- 2,8 ----
  # = bio/appl/genscan/report.rb - Genscan report classes
  #
! # Copyright::  Copyright (C) 2003 
! #              Mitsuteru C. Nakao <n at bioruby.org>
! # License::    Ruby's
  #
  #  $Id$
***************
*** 11,35 ****
  #
  # == Example
- # == References
- #
- #--
- #
- #  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
! #
! #  $Id$
! #
! #++
  #
  
--- 12,17 ----
  #
  # == Example
  #
! # == References
  #
  


From nakao at dev.open-bio.org  Sun Apr 30 03:11:31 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Sun, 30 Apr 2006 07:11:31 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/tmhmm report.rb,1.6,1.7
Message-ID: <200604300711.k3U7BVdR018683@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/tmhmm
In directory dev.open-bio.org:/tmp/cvs-serv18631/lib/bio/appl/tmhmm

Modified Files:
	report.rb 
Log Message:
* changed license to Ruby's 


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/tmhmm/report.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** report.rb	18 Dec 2005 15:58:41 -0000	1.6
--- report.rb	30 Apr 2006 07:11:29 -0000	1.7
***************
*** 2,7 ****
  # = bio/appl/tmhmm/report.rb - TMHMM report class
  # 
! # Copyright::  Copyright (C) 2003 Mitsuteru C. Nakao <n at bioruby.org>
! # License::    LGPL
  #
  #  $Id$
--- 2,8 ----
  # = bio/appl/tmhmm/report.rb - TMHMM report class
  # 
! # Copyright::  Copyright (C) 2003 
! #              Mitsuteru C. Nakao <n at bioruby.org>
! # License::    Ruby's
  #
  #  $Id$
***************
*** 12,32 ****
  # == Example
  # == References
- #--
- #
- #  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
- #
- #++
  #
  
--- 13,16 ----


From nakao at dev.open-bio.org  Sun Apr 30 03:11:31 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Sun, 30 Apr 2006 07:11:31 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db/embl common.rb,1.10,1.11
Message-ID: <200604300711.k3U7BV2X018693@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db/embl
In directory dev.open-bio.org:/tmp/cvs-serv18631/lib/bio/db/embl

Modified Files:
	common.rb 
Log Message:
* changed license to Ruby's 


Index: common.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/common.rb,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** common.rb	14 Apr 2006 06:04:09 -0000	1.10
--- common.rb	30 Apr 2006 07:11:29 -0000	1.11
***************
*** 2,6 ****
  # = bio/db/embl.rb - Common methods for EMBL style database classes
  #
! # Copyright::   Copyright (C) 2001-2005 Mitsuteru C. Nakao <n at bioruby.org>
  # License::     Ruby's
  #
--- 2,7 ----
  # = bio/db/embl.rb - Common methods for EMBL style database classes
  #
! # Copyright::   Copyright (C) 2001-2006
! #               Mitsuteru C. Nakao <n at bioruby.org>
  # License::     Ruby's
  #


From nakao at dev.open-bio.org  Sun Apr 30 03:11:30 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Sun, 30 Apr 2006 07:11:30 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db go.rb,1.9,1.10
Message-ID: <200604300711.k3U7BU1g018663@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db
In directory dev.open-bio.org:/tmp/cvs-serv18631/lib/bio/db

Modified Files:
	go.rb 
Log Message:
* changed license to Ruby's 


Index: go.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/go.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** go.rb	31 Oct 2005 18:32:36 -0000	1.9
--- go.rb	30 Apr 2006 07:11:28 -0000	1.10
***************
*** 2,7 ****
  # = bio/db/go.rb - Classes for Gene Ontology
  #
! # Copyright::   Copyright (C) 2003 Mitsuteru C. Nakao <n at bioruby.org>
! # License::
  #
  #  $Id$
--- 2,8 ----
  # = bio/db/go.rb - Classes for Gene Ontology
  #
! # Copyright::   Copyright (C) 2003 
! #               Mitsuteru C. Nakao <n at bioruby.org>
! # License::     Ruby's
  #
  #  $Id$
***************
*** 12,32 ****
  #
  # == References
- #--
- #
- #  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
- #
- #++
  #
  
--- 13,16 ----


From nakao at dev.open-bio.org  Sun Apr 30 03:13:41 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Sun, 30 Apr 2006 07:13:41 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/sosui report.rb,1.9,1.10
Message-ID: <200604300713.k3U7DfjR018777@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/sosui
In directory dev.open-bio.org:/tmp/cvs-serv18750/lib/bio/appl/sosui

Modified Files:
	report.rb 
Log Message:
* changed license to Ruby's 


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/sosui/report.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** report.rb	18 Dec 2005 15:58:41 -0000	1.9
--- report.rb	30 Apr 2006 07:13:39 -0000	1.10
***************
*** 2,7 ****
  # = bio/appl/sosui/report.rb - SOSUI report class
  # 
! # Copyright::   Copyright (C) 2003 Mitsuteru C. Nakao <n at bioruby.org>
! # License::     LGPL
  #
  #  $Id$
--- 2,8 ----
  # = bio/appl/sosui/report.rb - SOSUI report class
  # 
! # Copyright::   Copyright (C) 2003 
! #               Mitsuteru C. Nakao <n at bioruby.org>
! # License::     Ruby's
  #
  #  $Id$
***************
*** 10,31 ****
  #
  # == References
- # * http://sosui.proteome.bio.tuat.ac.jp/sosui_submit.html
- #--
- #
- #  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
! #
! #++
  #
  
--- 11,16 ----
  #
  # == References
  #
! # * http://sosui.proteome.bio.tuat.ac.jp/sosui_submit.html
  #
  


From nakao at dev.open-bio.org  Sun Apr 30 03:13:41 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Sun, 30 Apr 2006 07:13:41 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl psort.rb,1.8,1.9
Message-ID: <200604300713.k3U7Dfpp018772@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv18750/lib/bio/appl

Modified Files:
	psort.rb 
Log Message:
* changed license to Ruby's 


Index: psort.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/psort.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** psort.rb	1 Nov 2005 05:15:15 -0000	1.8
--- psort.rb	30 Apr 2006 07:13:39 -0000	1.9
***************
*** 1,8 ****
  #
  # = bio/appl/psort.rb - PSORT, protein sorting site prediction systems
  #
! # Copyright::   Copyright (C) 2003 Mitsuteru C. Nakao <n at bioruby.org>
! # License::     LGPL
! #
  #
  # $Id$
--- 1,10 ----
+ module Bio
+ 
  #
  # = bio/appl/psort.rb - PSORT, protein sorting site prediction systems
  #
! # Copyright::   Copyright (C) 2003-2006
! #               Mitsuteru C. Nakao <n at bioruby.org>
! # License::     Ruby's
  #
  # $Id$
***************
*** 25,59 ****
  #
  #
- #--
- #
- #  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
- #
- #++
- #
  
  require 'bio/sequence'
  require 'bio/db/fasta'
- require 'net/http'
  require 'cgi'
  
  
! module Bio
! 
!   
! 
! 
    class PSORT
      # a Hash for PSORT official hosts:
      #   Key      value (host)
--- 27,40 ----
  #
  #
  
  require 'bio/sequence'
+ require 'bio/command'
  require 'bio/db/fasta'
  require 'cgi'
  
  
!   #
    class PSORT
+ 
      # a Hash for PSORT official hosts:
      #   Key      value (host)
***************
*** 62,78 ****
      #   Okazaki  psort.nibb.ac.jp        
      #   Peking   srs.pku.edu.cn:8088     
!     WWWServer = {
!       'IMSUT'   => {'host' => 'psort.hgc.jp', #'psort.ims.u-tokyo.ac.jp', 
!                     'PSORT1' => '/cgi-bin/okumura.pl',
!                     'PSORT2' => '/cgi-bin/runpsort.pl'},
!       'Okazaki' => {'host' => 'psort.nibb.ac.jp', 
!                     'PSORT1' => '/cgi-bin/okumura.pl',
!                     'PSORT2' => '/cgi-bin/runpsort.pl'},
!       'Peking'  => {'host' => 'srs.pku.edu.en:8088', 
!                     'PSORT1' => '/cgi-bin/okumura.pl',
!                     'PSORT2' => '/cgi-bin/runpsort.pl'}
      }
  
- 
      # = Generic CGI client class
      # A generic CGI client class for Bio::PSORT::* classes.
--- 43,58 ----
      #   Okazaki  psort.nibb.ac.jp        
      #   Peking   srs.pku.edu.cn:8088     
!     ServerURI = {
!       :IMSUT   => {
!         :PSORT1 => URI.parse("http://psort.hgc.jp/cgi-bin/okumura.pl"),
!         :PSORT2 => URI.parse("http://psort.hgc.jp/cgi-bin/runpsort.pl") },
!       :Okazaki => {
!         :PSORT1 => URI.parse("http://psort.nibb.ac.jp/cgi-bin/okumura.pl"),
!         :PSORT2 => URI.parse("http://psort.nibb.ac.jp/cgi-bin/runpsort.pl") },
!       :Peking  => {
!         :PSORT1 => URI.parse("http:///src.pku.edu.cn:8088/cgi-bin/okumura.pl"),
!         :PSORT2 => URI.parse("http://src.pku.edu.cn:8088/cgi-bin/runpsort.pl") },
      }
  
      # = Generic CGI client class
      # A generic CGI client class for Bio::PSORT::* classes.
***************
*** 104,113 ****
  
  
!       # Sets remote ``host'' and cgi ``path''.
!       def initialize(host = '', path = '') 
!         @host = host
!         @path = path
          @args = {}
!         @report
        end
  
--- 84,107 ----
  
  
!       # Sets remote host name and cgi path or uri.
!       #
!       # == Examples
!       #
!       #   CGIDriver.new("localhost", "/cgi-bin/psort_www.pl")
!       #
!       #   CGIDriver.new("http://localhost/cgi-bin/psort_www.pl")
!       #
!       #   CGIDriver.new(URI.parse("http://localhost/cgi-bin/psort_www.pl"))
!       #
!       def initialize(host = '', path = '')
!         case host.to_s
!         when /^http:/
!           uri = host.to_s
!         else
!           uri = 'http://' + host + '/' + path
!         end
!         @uri = URI.parse(uri)
          @args = {}
!         @report = ''
        end
  
***************
*** 118,122 ****
  
          begin
!           result, = Net::HTTP.new(@host).post(@path, data)
            @report = result.body
            output = parse_report(@report)
--- 112,119 ----
  
          begin
!           result = nil
!           Bio::Command::NetTools.net_http_start(@uri.host) {|http|
!             result, = http.post(@uri.path, data)
!           }
            @report = result.body
            output = parse_report(@report)
***************
*** 140,144 ****
        # Erases HTML tags
        def erase_html_tags(str)
!         return str.gsub(/<\S.*?>/,'')
        end
  
--- 137,141 ----
        # Erases HTML tags
        def erase_html_tags(str)
!         return str.gsub(/<\S.*?>/, '')
        end
  
***************
*** 149,153 ****
            tmp << CGI.escape(key.to_s) + '=' + CGI.escape(val.to_s)
          end
!         return tmp.join(delim)  # not ';' but '&' in psort's cgi
        end
  
--- 146,150 ----
            tmp << CGI.escape(key.to_s) + '=' + CGI.escape(val.to_s)
          end
!         return tmp.join(delim)  # not ';' but '&' in the psort cgi script.
        end
  
***************
*** 157,160 ****
--- 154,158 ----
  
      # = Bio::PSORT::PSORT1
+     #
      # Bio::PSORT::PSORT1 is a wapper class for the original PSORT program.
      #
***************
*** 169,175 ****
--- 167,175 ----
      # 
      # == References
+     #
      # 1. Nakai, K. and Kanehisa, M., A knowledge base for predicting protein 
      #    localization sites in eukaryotic cells, Genomics 14, 897-911 (1992).
      #    [PMID:1478671]
+     #
      class PSORT1
  
***************
*** 179,184 ****
        # connecting to the IMSUT server.
        def self.imsut
!         self.new(Remote.new(WWWServer['IMSUT']['host'],
!                             WWWServer['IMSUT']['PSORT1']))
        end
  
--- 179,183 ----
        # connecting to the IMSUT server.
        def self.imsut
!         self.new(Remote.new(ServerURI[:IMSUT][:PSORT1]))
        end
  
***************
*** 187,192 ****
        # connecting to the NIBB server.
        def self.okazaki
!         self.new(Remote.new(WWWServer['Okazaki']['host'],
!                             WWWServer['Okazaki']['PSORT1']))
        end
        
--- 186,190 ----
        # connecting to the NIBB server.
        def self.okazaki
!         self.new(Remote.new(ServerURI[:Okazaki][:PSORT1]))
        end
        
***************
*** 195,209 ****
        # connecting to the Peking server.
        def self.peking
!         self.new(Remote.new(WWWServer['Peking']['host'],
!                             WWWServer['Peking']['PSORT1']))
        end
  
  
!       # Sets a server CGI Driver (Bio::PSORT::PSORT1::Remote).
!       def initialize(driver, origin = 'yeast')
!         @serv     = driver
!         @origin   = origin  # Gram-positive bacterium, Gram-negative bacterium,
!                             # yeast, aminal, plant
!         @title    = 'MYSEQ'
          @sequence = ''
        end
--- 193,207 ----
        # connecting to the Peking server.
        def self.peking
!         self.new(Remote.new(ServerURI[:Peking][:PSORT1]))
        end
  
  
!       # Sets a cgi client (Bio::PSORT::PSORT1::Remote).
!       #
!       def initialize(driver, origin = 'yeast', title = 'MYSEQ')
!         @serv = driver
!         @origin = origin  # Gram-positive bacterium, Gram-negative bacterium,
!                           # yeast, aminal, plant
!         @title = title
          @sequence = ''
        end
***************
*** 237,243 ****
        def exec(faa, parsing = true)
          if faa.class == Bio::FastaFormat
!           @title        = faa.entry_id if @title == 'MYSEQ'
!           @sequence     = faa.seq
!           @serv.args    = {'title' => @title, 'origin' => @origin}
            @serv.parsing = parsing
            return @serv.exec(sequence)
--- 235,241 ----
        def exec(faa, parsing = true)
          if faa.class == Bio::FastaFormat
!           @title = faa.entry_id if @title == 'MYSEQ'
!           @sequence = faa.seq
!           @serv.args = {'title' => @title, 'origin' => @origin}
            @serv.parsing = parsing
            return @serv.exec(sequence)
***************
*** 268,274 ****
          
          # Sets remote ``host'' and cgi ``path''.
!         def initialize(host, path)
!           @origin  = 'yeast'
!           @title   = 'MYSEQ'
            @parsing = true
            super(host, path)
--- 266,272 ----
          
          # Sets remote ``host'' and cgi ``path''.
!         def initialize(host, path = nil, title = 'MYSEQ', origin = 'yeast')
!           @title   = title
!           @origin  = origin
            @parsing = true
            super(host, path)
***************
*** 327,331 ****
        #  Okazaki  psort.nibb.ac.jp         /cgi-bin/runpsort.pl
        #  Peking   srs.pku.edu.cn:8088      /cgi-bin/runpsort.pl
!       def self.remote(host, path)
          self.new(Remote.new(host, path))
        end
--- 325,329 ----
        #  Okazaki  psort.nibb.ac.jp         /cgi-bin/runpsort.pl
        #  Peking   srs.pku.edu.cn:8088      /cgi-bin/runpsort.pl
!       def self.remote(host, path = nil)
          self.new(Remote.new(host, path))
        end
***************
*** 334,339 ****
        # connecting to the IMSUT server.
        def self.imsut
!         self.remote(WWWServer['IMSUT']['host'],
!                     WWWServer['IMSUT']['PSORT2'])
        end
  
--- 332,336 ----
        # connecting to the IMSUT server.
        def self.imsut
!         self.remote(ServerURI[:IMSUT][:PSORT2])
        end
  
***************
*** 341,346 ****
        # connecting to the NIBB server.
        def self.okazaki
!         self.remote(WWWServer['Okazaki']['host'],
!                     WWWServer['Okazaki']['PSORT2'])
        end
  
--- 338,342 ----
        # connecting to the NIBB server.
        def self.okazaki
!         self.remote(ServerURI[:Okazaki][:PSORT2])
        end
  
***************
*** 348,353 ****
        # connecting to the Peking server.
        def self.peking
!         self.remote(WWWServer['Peking']['host'],
!                     WWWServer['Peking']['PSORT2'])
        end
  
--- 344,348 ----
        # connecting to the Peking server.
        def self.peking
!         self.remote(ServerURI[:Peking][:PSORT2])
        end
  
***************
*** 374,380 ****
        def exec(faa, parsing = true)
          if faa.class == Bio::FastaFormat
!           @title        = faa.entry_id if @title == nil
!           @sequence     = faa.seq
!           @serv.args    = {'origin' => @origin, 'title' => @title}
            @serv.parsing = parsing
            return @serv.exec(@sequence)
--- 369,375 ----
        def exec(faa, parsing = true)
          if faa.class == Bio::FastaFormat
!           @title = faa.entry_id if @title == nil
!           @sequence = faa.seq
!           @serv.args = {'origin' => @origin, 'title' => @title}
            @serv.parsing = parsing
            return @serv.exec(@sequence)


From aerts at dev.open-bio.org  Thu Apr 20 15:58:36 2006
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Thu, 20 Apr 2006 15:58:36 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio location.rb,0.22,0.23
Message-ID: <200604201558.k3KFwa79014586@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv14566

Modified Files:
	location.rb 
Log Message:
Added and reformatted documentation.


Index: location.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/location.rb,v
retrieving revision 0.22
retrieving revision 0.23
diff -C2 -d -r0.22 -r0.23
*** location.rb	18 Dec 2005 15:50:06 -0000	0.22
--- location.rb	20 Apr 2006 15:58:34 -0000	0.23
***************
*** 2,16 ****
  # = bio/location.rb - Locations/Location class (GenBank location format)
  #
! # Copyright::	Copyright (C) 2001, 2005
! #		KATAYAMA Toshiaki <k at bioruby.org>
  # License::	LGPL
  #
  # $Id$
  #
! # == Appendix : GenBank location descriptor classification
  # 
  # === Definition of the position notation of the GenBank location format
  # 
! # According to the GenBank manual 'gbrel.txt', I classified position notations
  # into 10 patterns - (A) to (J).
  # 
--- 2,167 ----
  # = bio/location.rb - Locations/Location class (GenBank location format)
  #
! # Copyright::	Copyright (C) 2001, 2005 KATAYAMA Toshiaki <k at bioruby.org>
! #                             2006 Jan Aerts <jan.aerts at bbsrc.ac.uk>
  # License::	LGPL
  #
  # $Id$
  #
! # 
! #--
! #
! #  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
! #
! #++
! #
! 
! module Bio
! 
! # = DESCRIPTION
! # The Bio::Location class describes the position of a genomic locus. Typically,
! # Bio::Location objects are created automatically when the user creates a
! # Bio::Locations object, instead of initialized directly.
! #
! # = USAGE
! #   location = Bio::Location.new('500..550')
! #   puts "start=" + location.from.to_s + ";end=" + location.to.to_s
! #
! #   #, or better: through Bio::Locations
! #   locations = Bio::Locations.new('500..550')
! #   locations.each do |location|
! #     puts "start=" + location.from.to_s + ";end=" + location.to.to_s
! #   end
! class Location
! 
!   # Parses a'location' segment, which can be 'ID:' + ('n' or 'n..m' or 'n^m'
!   # or "seq") with '<' or '>', and returns a Bio::Location object.
!   #   location = Bio::Location.new('500..550')
!   # 
!   # ---
!   # *Arguments*:
!   # * (required) _str_: GenBank style position string (see Bio::Locations documentation)
!   # *Returns*:: Bio::Location object
!   def initialize(location = nil)
! 
!     if location
!       if location =~ /:/				# (G) ID:location
!         xref_id, location = location.split(':')
!       end
!       if location =~ /</				# (I) <,>
!         lt = true
!       end
!       if location =~ />/
!         gt = true
!       end
!     end
! 
!     # s : start base, e : end base => from, to
!     case location
!     when /^[<>]?(\d+)$/				# (A, I) n
!       s = e = $1.to_i
!     when /^[<>]?(\d+)\.\.[<>]?(\d+)$/			# (B, I) n..m
!       s = $1.to_i
!       e = $2.to_i
!       if e - s < 0
! #       raise "Error: invalid range : #{location}"
!         $stderr.puts "[Warning] invalid range : #{location}" if $DEBUG
!       end
!     when /^[<>]?(\d+)\^[<>]?(\d+)$/			# (C, I) n^m
!       s = $1.to_i
!       e = $2.to_i
!       if e - s != 1
! #       raise "Error: invalid range : #{location}"
!         $stderr.puts "[Warning] invalid range : #{location}" if $DEBUG
!       end
!     when /^"?([ATGCatgc]+)"?$/                  # (H) literal sequence
!       sequence = $1.downcase
!       s = e = nil
!     when nil
!       ;
!     else
!       raise "Error: unknown location format : #{location}"
!     end
! 
!     @from       = s             # start position of the location
!     @to         = e             # end position of the location
!     @strand     = 1             # strand direction of the location
!                                 #   forward => 1 or complement => -1
!     @sequence   = sequence      # literal sequence of the location
!     @lt         = lt            # true if the position contains '<'
!     @gt         = gt            # true if the position contains '>'
!     @xref_id    = xref_id       # link to the external entry as GenBank ID
!   end
! 
!   attr_accessor :from, :to, :strand, :sequence, :lt, :gt, :xref_id
! 
!   # Complements the sequence (i.e. alternates the strand).
!   # ---
!   # *Returns*:: the Bio::Location object
!   def complement
!     @strand *= -1
!     self					# return Location object
!   end
! 
!   # Replaces the sequence of the location.
!   # ---
!   # *Arguments*:
!   # * (required) _sequence_: sequence to be used to replace the sequence at the location
!   # *Returns*:: the Bio::Location object
!   def replace(sequence)
!     @sequence = sequence.downcase
!     self					# return Location object
!   end
! 
!   # Returns the range (from..to) of the location as a Range object.
!   def range
!     @from.. at to
!   end
! 
! end # class location
! 
! # = DESCRIPTION
! # The Bio::Locations class is a container for Bio::Location objects: creating a 
! # Bio::Locations object (based on a GenBank style position string) will
! # spawn an array of Bio::Location objects.
! #
! # = USAGE
! #   locations = Bio::Locations.new('join(complement(500..550), 600..625)')
! #   locations.each do |location|
! #     puts "class=" + location.class.to_s
! #     puts "start=" + location.from.to_s + ";end=" + location.to.to_s \
! #          + ";strand=" + location.strand.to_s
! #   end
! #     # Output would be:
! #     # class=Bio::Location
! #     # start=500;end=550;strand=-1
! #     # class=Bio::Location
! #     # start=600;end=625;strand=1
! # 
! #  # For the following three location strings, print the span and range
! #  ['one-of(898,900)..983',
! #   'one-of(5971..6308,5971..6309)',
! #   '8050..one-of(10731,10758,10905,11242)'].each do |loc|
! #      location = Bio::Locations.new(loc)
! #      puts location.span
! #      puts location.range
! #  end
! #
! # = GENBANK LOCATION DESCRIPTOR CLASSIFICATION
  # 
  # === Definition of the position notation of the GenBank location format
  # 
! # According to the GenBank manual 'gbrel.txt', position notations were classified
  # into 10 patterns - (A) to (J).
  # 
***************
*** 84,115 ****
  # === Reduction strategy of the position notations
  # 
! #   (A) Location n
! #   
! #   (B) Location n..m
! #   
! #   (C) Location n^m
! #   
! #   (D) (n.m)		=> Location n
! #   
! #   (E) one-of(n,m,..)	=> Location n
! #       one-of(n..m,..)	=> Location n..m
! #   
! #   (F) order(loc,loc,..)	=> join(loc, loc,..)
! #       group(loc,loc,..)	=> join(loc, loc,..)
! #       join(loc,loc,..)	=> Sequence
! #   
! #   (G) ID:loc		=> Location with ID
! #   
! #   (H) "atgc"		=> Location only with Sequence
! #   
! #   (I) <n			=> Location n with lt flag
! #       >n			=> Location n with gt flag
! #       <n..m		=> Location n..m with lt flag
! #       n..>m		=> Location n..m with gt flag
! #       <n..>m		=> Location n..m with lt, gt flag
! #   
! #   (J) complement(loc)	=> Sequence
! #   
! #   (K) replace(loc, str)	=> Location with replacement Sequence
  # 
  # === GenBank location examples
--- 235,259 ----
  # === Reduction strategy of the position notations
  # 
! # * (A) Location n
! # * (B) Location n..m
! # * (C) Location n^m
! # * (D) (n.m)		=> Location n
! # * (E)
! #   * one-of(n,m,..)	=> Location n
! #   * one-of(n..m,..)	=> Location n..m
! # * (F)
! #   * order(loc,loc,..)	=> join(loc, loc,..)
! #   * group(loc,loc,..)	=> join(loc, loc,..)
! #   * join(loc,loc,..)	=> Sequence
! # * (G) ID:loc		=> Location with ID
! # * (H) "atgc"		=> Location only with Sequence
! # * (I)
! #   * <n			=> Location n with lt flag
! #   * >n			=> Location n with gt flag
! #   * <n..m		=> Location n..m with lt flag
! #   * n..>m		=> Location n..m with gt flag
! #   * <n..>m		=> Location n..m with lt, gt flag
! # * (J) complement(loc)	=> Sequence
! # * (K) replace(loc, str)	=> Location with replacement Sequence
  # 
  # === GenBank location examples
***************
*** 232,340 ****
  # * [ADR40FIB]	replace(510..520,	<= replace(510..520, "taatcctaccg")
  # * [RATDYIIAAB]	replace(1306..1443,"aagaacatccacggagtcagaactgggctcttcacgccggatttggcgttcgaggccattgtgaaaaagcaggcaatgcaccagcaagctcagttcctacccctgcgtggacctggttatccaggagctaatcagtacagttaggtggtcaagctgaaagagccctgtctgaaa")
- # 
- #--
- #
- #  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
- #
- #++
- #
- 
- module Bio
- 
- class Location
- 
-   # Pass a range of the 'location' segment.  The 'location' segment can be
-   # 'ID:' + ('n' or 'n..m' or 'n^m' or "seq") with '<' or '>'.
-   def initialize(location = nil)
- 
-     if location
-       if location =~ /:/				# (G) ID:location
-         xref_id, location = location.split(':')
-       end
-       if location =~ /</				# (I) <,>
-         lt = true
-       end
-       if location =~ />/
-         gt = true
-       end
-     end
- 
-     # s : start base, e : end base => from, to
-     case location
-     when /^[<>]?(\d+)$/				# (A, I) n
-       s = e = $1.to_i
-     when /^[<>]?(\d+)\.\.[<>]?(\d+)$/			# (B, I) n..m
-       s = $1.to_i
-       e = $2.to_i
-       if e - s < 0
- #       raise "Error: invalid range : #{location}"
-         $stderr.puts "[Warning] invalid range : #{location}" if $DEBUG
-       end
-     when /^[<>]?(\d+)\^[<>]?(\d+)$/			# (C, I) n^m
-       s = $1.to_i
-       e = $2.to_i
-       if e - s != 1
- #       raise "Error: invalid range : #{location}"
-         $stderr.puts "[Warning] invalid range : #{location}" if $DEBUG
-       end
-     when /^"?([ATGCatgc]+)"?$/                  # (H) literal sequence
-       sequence = $1.downcase
-       s = e = nil
-     when nil
-       ;
-     else
-       raise "Error: unknown location format : #{location}"
-     end
- 
-     @from       = s             # start position of the location
-     @to         = e             # end position of the location
-     @strand     = 1             # strand direction of the location
-                                 #   forward => 1 or complement => -1
-     @sequence   = sequence      # literal sequence of the location
-     @lt         = lt            # true if the position contains '<'
-     @gt         = gt            # true if the position contains '>'
-     @xref_id    = xref_id       # link to the external entry as GenBank ID
-   end
- 
-   attr_accessor :from, :to, :strand, :sequence, :lt, :gt, :xref_id
- 
-   # Complement the sequence from outside.
-   def complement
-     @strand *= -1
-     self					# return Location object
-   end
- 
-   # Replace the sequence from outside.
-   def replace(sequence)
-     @sequence	= sequence.downcase
-     self					# return Location object
-   end
- 
-   # Returns a range (from..to) of the segment as a Range object.
-   def range
-     @from.. at to
-   end
- 
- end # class location
- 
- 
  class Locations
- 
    include Enumerable
  
!   # Parse a GenBank style position string and returns a Locations object,
!   # which contains a list of Location objects.
    def initialize(position)
      if position.is_a? Array
--- 376,390 ----
  # * [ADR40FIB]	replace(510..520,	<= replace(510..520, "taatcctaccg")
  # * [RATDYIIAAB]	replace(1306..1443,"aagaacatccacggagtcagaactgggctcttcacgccggatttggcgttcgaggccattgtgaaaaagcaggcaatgcaccagcaagctcagttcctacccctgcgtggacctggttatccaggagctaatcagtacagttaggtggtcaagctgaaagagccctgtctgaaa")
  class Locations
    include Enumerable
  
!   # Parses a GenBank style position string and returns a Bio::Locations object,
!   # which contains a list of Bio::Location objects.
!   #   locations = Bio::Locations.new('join(complement(500..550), 600..625)')
!   #
!   # ---
!   # *Arguments*:
!   # * (required) _str_: GenBank style position string
!   # *Returns*:: Bio::Locations object
    def initialize(position)
      if position.is_a? Array
***************
*** 342,351 ****
      else
        position   = gbl_cleanup(position)	# preprocessing
!       @locations = gbl_pos2loc(position)	# create an Array of Location
      end
    end
    attr_accessor :locations
  
!   # Iterates on each Location object.
    def each
      @locations.each do |x|
--- 392,403 ----
      else
        position   = gbl_cleanup(position)	# preprocessing
!       @locations = gbl_pos2loc(position)	# create an Array of Bio::Location objects
      end
    end
+ 
+   # An Array of Bio::Location objects
    attr_accessor :locations
  
!   # Iterates on each Bio::Location object.
    def each
      @locations.each do |x|
***************
*** 354,368 ****
    end
  
!   # Returns nth Location object.
    def [](n)
      @locations[n]
    end
  
!   # Returns first Location object.
    def first
      @locations.first
    end
  
!   # Returns last Location object.
    def last
      @locations.last
--- 406,420 ----
    end
  
!   # Returns nth Bio::Location object.
    def [](n)
      @locations[n]
    end
  
!   # Returns first Bio::Location object.
    def first
      @locations.first
    end
  
!   # Returns last Bio::Location object.
    def last
      @locations.last
***************
*** 370,374 ****
  
    # Returns an Array containing overall min and max position [min, max]
!   # of this Locations object.
    def span
      span_min = @locations.min { |a,b| a.from <=> b.from }
--- 422,426 ----
  
    # Returns an Array containing overall min and max position [min, max]
!   # of this Bio::Locations object.
    def span
      span_min = @locations.min { |a,b| a.from <=> b.from }
***************
*** 397,403 ****
    alias size length
  
!   # Convert absolute position in DNA (na) to relative position in RNA (na).
!   # If type == :aa,
!   # convert absolute position in DNA (na) to relative position in Protein (aa).
    def relative(n, type = nil)
      case type
--- 449,466 ----
    alias size length
  
!   # Converts absolute position in the whole of the DNA sequence to relative 
!   # position in the locus.
!   # 
!   # This method can for example be used to relate positions in a DNA-sequence
!   # with those in RNA. In this use, the optional ':aa'-flag returns the position
!   # of the associated amino-acid rather than the nucleotide.
!   #   loc = Bio::Locations.new('complement(12838..13533)')
!   #   puts loc.relative(13524)        # => 10
!   #   puts loc.relative(13506, :aa)   # => 3
!   # ---
!   # *Arguments*:
!   # * (required) _position_: nucleotide position within whole of the sequence
!   # * _:aa_: flag that lets method return position in aminoacid coordinates
!   # *Returns*:: position within the location
    def relative(n, type = nil)
      case type
***************
*** 415,430 ****
    end
  
!   # Convert relative position in RNA (na) to absolute position in DNA (na).
!   # If type == :aa,
!   # convert relative position in Protein (aa) -> absolute position in DNA (na).
!   #
!   # * Examples
!   #
!   #     loc = Bio::Locations.new('complement(12838..13533)')
!   #     loc.absolute(10)          #=> 13524 (rel2abs)
!   #     loc.relative(13524)       #=> 10    (abs2rel)
!   #     loc.absolute(10, :aa)     #=> 13506 (rel2abs)
!   #     loc.relative(13506, :aa)  #=> 10    (abs2rel)
!   #
    def absolute(n, type = nil)
      case type
--- 478,495 ----
    end
  
!   # Converts relative position in the locus to position in the whole of the
!   # DNA sequence.
!   # 
!   # This method can for example be used to relate positions in a DNA-sequence
!   # with those in RNA. In this use, the optional ':aa'-flag returns the position
!   # of the associated amino-acid rather than the nucleotide.
!   #   loc = Bio::Locations.new('complement(12838..13533)')
!   #   puts loc.absolute(10)          # => 13524
!   #   puts loc.absolute(10, :aa)     # => 13506
!   # ---
!   # *Arguments*:
!   # * (required) _position_: nucleotide position within locus
!   # * _:aa_: flag to be used if _position_ is a aminoacid position rather than a nucleotide position
!   # *Returns*:: position within the whole of the sequence
    def absolute(n, type = nil)
      case type
***************
*** 591,594 ****
--- 656,664 ----
    puts "Test new & span methods"
    [
+     '450',
+     '500..600',
+     'join(500..550, 600..625)',
+     'complement(join(500..550, 600..625))',
+     'join(complement(500..550), 600..625)',
      '754^755',
      'complement(53^54)',
***************
*** 618,624 ****
    ].each do |pos|
      p pos
!     p Bio::Locations.new(pos).span
!     p Bio::Locations.new(pos).range
!     p Bio::Locations.new(pos)
    end
  
--- 688,699 ----
    ].each do |pos|
      p pos
! #    p Bio::Locations.new(pos)
! #    p Bio::Locations.new(pos).span
! #    p Bio::Locations.new(pos).range
!     Bio::Locations.new(pos).each do |location|
!       puts "class=" + location.class.to_s
!       puts "start=" + location.from.to_s + "\tend=" + location.to.to_s + "\tstrand=" + location.strand.to_s
!     end
! 
    end
  



From aerts at dev.open-bio.org  Wed Apr 26 11:05:52 2006
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Wed, 26 Apr 2006 11:05:52 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio feature.rb,1.10,1.11
Message-ID: <200604261105.k3QB5q61032048@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv32028

Modified Files:
	feature.rb 
Log Message:
Added and reformatted documentation.
Qualifiers are now automatically converted into Bio::Feature::Qualifier objects when initializing a new Bio::Feature object.


Index: feature.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/feature.rb,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** feature.rb	27 Feb 2006 09:13:46 -0000	1.10
--- feature.rb	26 Apr 2006 11:05:50 -0000	1.11
***************
*** 2,42 ****
  # = bio/feature.rb - Features/Feature class (GenBank Feature table)
  #
! # Copyright::	Copyright (c) 2002, 2005
! #		Toshiaki Katayama <k at bioruby.org>
  # License::	Ruby's
  #
  # $Id$
- #
- # == INSD Feature table definition
- #
- # See http://www.ddbj.nig.ac.jp/FT/full_index.html for the INSD
- # (GenBank/EMBL/DDBJ) Feature table definition.
- #
- # === Example
- #
- #  # suppose features is a Bio::Features object
- #  features.each do |feature|
- #    f_name = feature.feature
- #    f_pos  = feature.position
- #    puts "#{f_name}:\t#{f_pos}"
- #    feature.each do |qualifier|
- #      q_name = qualifier.qualifier
- #      q_val  = qualifier.value
- #      puts "- #{q_name}:\t#{q_val}"
- #    end
- #  end
- #
- #  # Iterates only on CDS features and extract translated amino acid sequences
- #  features.each("CDS") do |feature|
- #    hash = feature.assoc
- #    name = hash["gene"] || hash["product"] || hash["note"] 
- #    seq  = hash["translation"]
- #    pos  = feature.position
- #    if gene and seq
- #      puts ">#{gene} #{feature.position}"
- #      puts aaseq
- #    end
- #  end
- #
  
  require 'bio/location'
--- 2,10 ----
  # = bio/feature.rb - Features/Feature class (GenBank Feature table)
  #
! # Copyright::	Copyright (c) 2002, 2005  Toshiaki Katayama <k at bioruby.org>
! #                             2006        Jan Aerts <jan.aerts at bbsrc.ac.uk>
  # License::	Ruby's
  #
  # $Id$
  
  require 'bio/location'
***************
*** 44,52 ****
  module Bio
  
  # Container for the sequence annotation.
  class Feature
! 
    def initialize(feature = '', position = '', qualifiers = [])
!     @feature, @position, @qualifiers = feature, position, qualifiers
    end
  
--- 12,54 ----
  module Bio
  
+ # = DESCRIPTION
  # Container for the sequence annotation.
+ #
+ # = USAGE
+ #  # Create a Bio::Feature object.
+ #  # For example: the GenBank-formatted entry in genbank for accession M33388
+ #  # contains the following feature:
+ #  #    exon     1532..1799
+ #  #             /gene="CYP2D6"
+ #  #             /note="cytochrome P450 IID6; GOO-132-127"
+ #  #             /number="1"
+ #  feature = Bio::Feature.new('exon','1532..1799',['gene' => 'CYP2D6','note' => 'cytochrome P450 IID6; GOO-132-127','number' => '1'])
+ #
+ #  # Print the feature
+ #  puts feature.feature + "\t" + feature.position
+ #  feature.each do |qualifier|
+ #    puts "- " + qualifier.qualifier + ": " + qualifier.value
+ #  end
+ #
+ # = REFERENCES
+ # INSD feature table definition:: http://www.ddbj.nig.ac.jp/FT/full_index.html
  class Feature
!   # Create a new Bio::Feature object.
!   # *Arguments*:
!   # * (required) _feature_: type of feature (e.g. "exon")
!   # * (required) _position_: position of feature (e.g. "complement(1532..1799)")
!   # * (optional) _qualifiers_: list of qualifiers (e.g. "['gene' => 'CYP2D6','number' => '1']")
!   # *Returns*:: Bio::Feature object
    def initialize(feature = '', position = '', qualifiers = [])
!     @feature, @position = feature, position
!     @qualifiers = Array.new
!     if qualifiers.length.modulo(2) > 0
!       $stderr.puts "WARNING"
!     end
!     while qualifiers.length > 0
!       key = qualifiers.shift
!       value = qualifiers.shift || ''
!       self.append(Qualifier.new(key, value))
!     end
    end
  
***************
*** 66,73 ****
  
    # Appends a Qualifier object to the Feature.
!   #
!   # * Returns an Array of Qualifier objects.
!   # * If the argument is not a Qualifier object, returns nil.
!   #
    def append(a)
      @qualifiers.push(a) if a.is_a? Qualifier
--- 68,75 ----
  
    # Appends a Qualifier object to the Feature.
!   # 
!   # *Arguments*:
!   # * (required) _qualifier_: Bio::Feature::Qualifier object
!   # *Returns*:: Bio::Feature object
    def append(a)
      @qualifiers.push(a) if a.is_a? Qualifier
***************
*** 75,79 ****
    end
  
!   # Iterates on each qualifier.
    def each(arg = nil)
      @qualifiers.each do |x|
--- 77,84 ----
    end
  
!   # Iterates on each qualifier object.
!   #
!   # *Arguments*:
!   # * (optional) _key_: if specified, only iterates over qualifiers with this key
    def each(arg = nil)
      @qualifiers.each do |x|
***************
*** 108,114 ****
    end
  
!   # Container for the qualifier-value pair.
    class Qualifier
! 
      def initialize(key, value)
        @qualifier, @value = key, value
--- 113,124 ----
    end
  
!   # Container for qualifier-value pairs for sequence features.
    class Qualifier
!     # Creates a new Bio::Feature::Qualifier object
!     #
!     # *Arguments*:
!     # * (required) _key_: key of the qualifier (e.g. "gene")
!     # * (required) _value_: value of the qualifier (e.g. "CYP2D6")
!     # *Returns*:: Bio::Feature::Qualifier object
      def initialize(key, value)
        @qualifier, @value = key, value
***************
*** 126,132 ****
  
  
! # Container for the list of Feature objects.
  class Features
! 
    def initialize(ary = [])
      @features = ary
--- 136,177 ----
  
  
! # = DESCRIPTION
! # Container for a list of Feature objects.
! #
! # = USAGE
! #  # First, create some Bio::Feature objects
! #  feature1 = Bio::Feature.new('intron','3627..4059',['gene', 'CYP2D6', 'note', 'G00-132-127','number','4'])
! #  feature2 = Bio::Feature.new('exon','4060..4236',['gene', 'CYP2D6', 'note', 'G00-132-127','number','5'])
! #  feature3 = Bio::Feature.new('intron','4237..4426',['gene', 'CYP2D6', 'note', 'G00-132-127','number','5'])
! #  feature4 = Bio::Feature.new('CDS','join(2538..3626,4060..4236)',['gene', 'CYP2D6','translation','MGXXTVMHLL...'])
! #
! #  # And create a container for them
! #  feature_container = Bio::Features.new([ feature1, feature2, feature3, feature4 ])
! #
! #  # Iterate over all features and print
! #  feature_container.each do |feature|
! #    puts feature.feature + "\t" + feature.position
! #    feature.each do |qualifier|
! #      puts "- " + qualifier.qualifier + ": " + qualifier.value
! #    end
! #  end
! #
! #  # Iterate only over CDS features and extract translated amino acid sequences
! #  features.each("CDS") do |feature|
! #    hash = feature.to_hash
! #    name = hash["gene"] || hash["product"] || hash["note"] 
! #    aaseq  = hash["translation"]
! #    pos  = feature.position
! #    if name and seq
! #      puts ">#{gene} #{feature.position}"
! #      puts aaseq
! #    end
! #  end
  class Features
!   # Create a new Bio::Features object.
!   #
!   # *Arguments*:
!   # * (optional) _list of features_: list of Bio::Feature objects
!   # *Returns*:: Bio::Features object
    def initialize(ary = [])
      @features = ary
***************
*** 137,140 ****
--- 182,189 ----
  
    # Appends a Feature object to Features.
+   # 
+   # *Arguments*:
+   # * (required) _feature_: Bio::Feature object
+   # *Returns*:: Bio::Features object
    def append(a)
      @features.push(a) if a.is_a? Feature
***************
*** 142,147 ****
    end
  
!   # Iterates on each feature.  If a feature name is given as an argument,
!   # only iterates on each feature belongs to the name (e.g. 'CDS' etc.)
    def each(arg = nil)
      @features.each do |x|
--- 191,198 ----
    end
  
!   # Iterates on each feature object.
!   #
!   # *Arguments*:
!   # * (optional) _key_: if specified, only iterates over features with this key
    def each(arg = nil)
      @features.each do |x|
***************
*** 170,172 ****
--- 221,257 ----
  end # Bio
  
+ if __FILE__ == $0
+   puts "---TESTING Bio::Feature"
+   feature1 = Bio::Feature.new('exon','1532..1799',['gene','CYP2D6','note','cytochrome P450 IID6; GOO-132-127','number','1', 'note', 'a second note'])
+ 
+   # Print the feature out
+   puts feature1.feature + "\t" + feature1.position
+   feature1.each do |qualifier|
+     puts "- " + qualifier.qualifier + ": " + qualifier.value
+   end
+   
+   feature2 = Bio::Feature.new('CDS','join(2538..3626,4060..4236)',['gene', 'CYP2D6','translation','MGXXTVMHLL...'])
+ 
+   puts "---TESTING Bio::Features"
+   feature3 = Bio::Feature.new('intron','3627..4059',['gene', 'CYP2D6', 'note', 'G00-132-127','number','4'])
+   feature4 = Bio::Feature.new('exon','4060..4236',['gene', 'CYP2D6', 'note', 'G00-132-127','number','5'])
+   feature5 = Bio::Feature.new('intron','4237..4426',['gene', 'CYP2D6', 'note', 'G00-132-127','number','5'])
+   feature_container = Bio::Features.new([ feature1, feature2, feature3, feature4, feature5 ])
+   feature_container.each do |feature|
+     puts "-NEXT FEATURE"
+     puts feature.feature + "\t" + feature.position
+     feature.each do |qualifier|
+       puts "- " + qualifier.qualifier + ": " + qualifier.value
+     end
+   end
  
+   puts "---TESTING hash function"
+   feature_container.each('CDS') do |feature|
+     hash = feature.to_hash
+     name = hash["gene"] || hash["product"] || hash["note"] 
+     aaseq  = hash["translation"]
+     pos  = feature.position
+     puts ">#{name} #{feature.position}"
+     puts aaseq
+   end
+ end



From aerts at dev.open-bio.org  Thu Apr 27 09:29:37 2006
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Thu, 27 Apr 2006 09:29:37 +0000
Subject: [BioRuby-cvs] bioruby/lib bio.rb,1.66,1.67
Message-ID: <200604270929.k3R9Tbx2003641@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib
In directory dev.open-bio.org:/tmp/cvs-serv3621

Modified Files:
	bio.rb 
Log Message:
Added bio/io/ensembl.rb to be autoloaded.


Index: bio.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio.rb,v
retrieving revision 1.66
retrieving revision 1.67
diff -C2 -d -r1.66 -r1.67
*** bio.rb	27 Feb 2006 09:11:01 -0000	1.66
--- bio.rb	27 Apr 2006 09:29:35 -0000	1.67
***************
*** 132,135 ****
--- 132,137 ----
    autoload :DBGET,          'bio/io/dbget'
  
+   autoload :Ensembl,        'bio/io/ensembl'
+ 
    ## below are described in bio/appl/blast.rb
    #class Blast



From nakao at dev.open-bio.org  Fri Apr 14 04:49:46 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Fri, 14 Apr 2006 04:49:46 -0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db/embl embl.rb,1.26,1.27
Message-ID: <200604140549.k3E5nWFn009694@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db/embl
In directory dev.open-bio.org:/tmp/cvs-serv9674

Modified Files:
	embl.rb 
Log Message:
* Removed example codes (if __FILE__ == $0 ... end).
* Changed license (LGPL -> Ruby's).


Index: embl.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/embl.rb,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** embl.rb	28 Jan 2006 06:40:38 -0000	1.26
--- embl.rb	14 Apr 2006 05:49:30 -0000	1.27
***************
*** 3,8 ****
  #
  # 
! # Copyright::   Copyright (C) 2001-2005 Mitsuteru C. Nakao <n at bioruby.org>
! # License::     LGPL
  #
  # $Id$
--- 3,8 ----
  #
  # 
! # Copyright::   Copyright (C) 2001-2006 Mitsuteru C. Nakao <n at bioruby.org>
! # License::     Ruby's
  #
  # $Id$
***************
*** 29,50 ****
  #   http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html
  #
- #--
- #
- #  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
- #
- #++
- #
  
  require 'bio/db'
--- 29,32 ----
***************
*** 395,454 ****
    end
  
! end
! 
! end
! 
! 
! if __FILE__ == $0
!   while ent = $<.gets(Bio::EMBL::RS)
!     puts "\n ==> e = Bio::EMBL.new(ent) "
!     e = Bio::EMBL.new(ent)
! 
!     puts "\n ==> e.entry_id "
!     p e.entry_id
!     puts "\n ==> e.id_line "
!     p e.id_line
!     puts "\n ==> e.id_line('molecule') "
!     p e.id_line('molecule')
!     puts "\n ==> e.molecule "
!     p e.molecule
!     puts "\n ==> e.ac "
!     p e.ac
!     puts "\n ==> e.sv "
!     p e.sv
!     puts "\n ==> e.dt "
!     p e.dt
!     puts "\n ==> e.dt('created') "
!     p e.dt('created')
!     puts "\n ==> e.de "
!     p e.de
!     puts "\n ==> e.kw "
!     p e.kw
!     puts "\n ==> e.os "
!     p e.os
!     puts "\n ==> e.oc "
!     p e.oc
!     puts "\n ==> e.og "
!     p e.og
!     puts "\n ==> e.ref "
!     p e.ref
!     puts "\n ==> e.dr "
!     p e.dr
!     puts "\n ==> e.ft "
!     p e.ft
!     puts "\n ==> e.each_cds {|c| p c}"
!     p e.each_cds {|c| p c }
!     puts "\n ==> e.sq "
!     p e.sq
!     puts "\n ==> e.sq('a') "
!     p e.sq('a')
!     puts "\n ==> e.gc"    
!     p e.gc
!     puts "\n ==> e.seq "
!     p e.seq
!   end
! 
! end
! 
! 
  
--- 377,381 ----
    end
  
! end # class EMBL
  
+ end # module Bio



From nakao at dev.open-bio.org  Fri Apr 14 04:52:42 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Fri, 14 Apr 2006 04:52:42 -0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db/embl sptr.rb,1.30,1.31
Message-ID: <200604140552.k3E5qU1e009726@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db/embl
In directory dev.open-bio.org:/tmp/cvs-serv9706

Modified Files:
	sptr.rb 
Log Message:
* Removed example codes (if __FILE__ == $0 ... end).
* Changed license (LGPL -> Ruby's).


Index: sptr.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/sptr.rb,v
retrieving revision 1.30
retrieving revision 1.31
diff -C2 -d -r1.30 -r1.31
*** sptr.rb	28 Jan 2006 06:40:38 -0000	1.30
--- sptr.rb	14 Apr 2006 05:52:28 -0000	1.31
***************
*** 2,7 ****
  # = bio/db/embl/sptr.rb - UniProt/SwissProt and TrEMBL database class
  # 
! # Copyright::   Copyright (C) 2001-2005 Mitsuteru C. Nakao <n at bioruby.org>
! # License::     LGPL
  #
  # $Id$
--- 2,7 ----
  # = bio/db/embl/sptr.rb - UniProt/SwissProt and TrEMBL database class
  # 
! # Copyright::   Copyright (C) 2001-2006 Mitsuteru C. Nakao <n at bioruby.org>
! # License::     Ruby's
  #
  # $Id$
***************
*** 32,53 ****
  #   http://www.expasy.org/sprot/userman.html
  #
! #--
! #
! #  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
! #
! #++
! #
  
  require 'bio/db'
--- 32,36 ----
  #   http://www.expasy.org/sprot/userman.html
  #
! 
  
  require 'bio/db'
***************
*** 760,841 ****
  
  
- if __FILE__ == $0
-   # Usage: ruby __FILE__ uniprot_sprot.dat 
-   # Usage: ruby __FILE__ uniprot_sprot.dat | egrep '^RuntimeError'
- 
-   begin
-     require 'pp'
-     alias pp p
-   rescue LoadError
-   end
- 
-   def cmd(cmd, tag = nil, ent = $ent)
-     puts " ==> #{cmd} "
-     puts Bio::SPTR.new(ent).get(tag) if tag
-     begin
-       p eval(cmd)
-     rescue RuntimeError
-       puts "RuntimeError(#{Bio::SPTR.new($ent).entry_id})}: #{$!} "
-     end
-     puts
-   end
- 
- 
-   while $ent = $<.gets(Bio::SPTR::RS)
-     
-     cmd "Bio::SPTR.new($ent).entry_id"
- 
-     cmd "Bio::SPTR.new($ent).id_line", 'ID'
-     cmd "Bio::SPTR.new($ent).entry"
-     cmd "Bio::SPTR.new($ent).entry_name"
-     cmd "Bio::SPTR.new($ent).molecule"
-     cmd "Bio::SPTR.new($ent).sequence_length"
- 
-     cmd "Bio::SPTR.new($ent).ac", 'AC'
-     cmd "Bio::SPTR.new($ent).accession"
- 
- 
-     cmd "Bio::SPTR.new($ent).gn", 'GN'
-     cmd "Bio::SPTR.new($ent).gene_name"
-     cmd "Bio::SPTR.new($ent).gene_names"
- 
-     cmd "Bio::SPTR.new($ent).dt", "DT"
-     ['created','annotation','sequence'].each do |key|
-       cmd "Bio::SPTR.new($ent).dt('#{key}')"
-     end
- 
-     cmd "Bio::SPTR.new($ent).de", 'DE'
-     cmd "Bio::SPTR.new($ent).definition"
-     cmd "Bio::SPTR.new($ent).protein_name"
-     cmd "Bio::SPTR.new($ent).synonyms"
- 
-     cmd "Bio::SPTR.new($ent).kw", 'KW'
- 
-     cmd "Bio::SPTR.new($ent).os", 'OS'
- 
-     cmd "Bio::SPTR.new($ent).oc", 'OC'
- 
-     cmd "Bio::SPTR.new($ent).og", 'OG'
- 
-     cmd "Bio::SPTR.new($ent).ox", 'OX'
- 
-     cmd "Bio::SPTR.new($ent).ref", 'R'
- 
-     cmd "Bio::SPTR.new($ent).cc", 'CC'
-     cmd "Bio::SPTR.new($ent).cc('ALTERNATIVE PRODUCTS')"
-     cmd "Bio::SPTR.new($ent).cc('DATABASE')"
-     cmd "Bio::SPTR.new($ent).cc('MASS SPECTOMETRY')"
- 
-     cmd "Bio::SPTR.new($ent).dr", 'DR'
- 
-     cmd "Bio::SPTR.new($ent).ft", 'FT'
-     cmd "Bio::SPTR.new($ent).ft['DOMAIN']"
- 
-     cmd "Bio::SPTR.new($ent).sq", "SQ"
-     cmd "Bio::SPTR.new($ent).seq"
-   end
- 
- end
- 
  
  =begin
--- 743,746 ----



From nakao at dev.open-bio.org  Fri Apr 14 05:04:22 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Fri, 14 Apr 2006 05:04:22 -0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db/embl common.rb,1.9,1.10
Message-ID: <200604140604.k3E64BXK009760@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db/embl
In directory dev.open-bio.org:/tmp/cvs-serv9740

Modified Files:
	common.rb 
Log Message:
* Changed license (LGPL -> Ruby's).


Index: common.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/common.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** common.rb	28 Jan 2006 06:40:38 -0000	1.9
--- common.rb	14 Apr 2006 06:04:09 -0000	1.10
***************
*** 3,7 ****
  #
  # Copyright::   Copyright (C) 2001-2005 Mitsuteru C. Nakao <n at bioruby.org>
! # License::     LGPL
  #
  # $Id$
--- 3,7 ----
  #
  # Copyright::   Copyright (C) 2001-2005 Mitsuteru C. Nakao <n at bioruby.org>
! # License::     Ruby's
  #
  # $Id$
***************
*** 70,91 ****
  #   http://www.expasy.org/sprot/userman.html
  #
- #--
- #
- #  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
- #
- #++
- #
  
  require 'bio/db'
--- 70,73 ----



From nakao at dev.open-bio.org  Fri Apr 14 05:28:29 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Fri, 14 Apr 2006 05:28:29 -0000
Subject: [BioRuby-cvs] bioruby/lib/bio/io ensembl.rb,NONE,1.1
Message-ID: <200604140628.k3E6SBGn009942@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv9920/d/d/d

Added Files:
	ensembl.rb 
Log Message:
* ensembl.rb) newly added.
* test_ensembl.rb) newly added.


--- NEW FILE: ensembl.rb ---
#
# = bio/io/ensembl.rb - An Ensembl Genome Browser client.
#
# Copyright::   Copyright (C) 2006
#               Mitsuteru C. Nakao <n at bioruby.org>
# License::     Ruby's
#
# $Id: ensembl.rb,v 1.1 2006/04/14 06:28:09 nakao Exp $
#
# == Description
#
# Client classes for Ensembl Genome Browser.
#
# == Examples
#
#  seq = Bio::Ensembl::Human.exportview(1, 1000, 100000)
#  gff = Bio::Ensembl::Human.exportview(1, 1000, 100000, ['gene'])
#
#  seq = Bio::Ensembl::Mouse.exportview(1, 1000, 100000)
#  gff = Bio::Ensembl::Mouse.exportview(1, 1000, 100000, ['gene', 'variation', 'genscan'])
#
#  
# == References
#
# * Ensembl
#   http:/www.ensembl.org/
#

require 'bio'
require 'cgi'

module Bio

# == Description
#
# An Ensembl Genome Browser client class.
#
# == Examples
#
#  seq = Bio::Ensembl::Human.exportview(1, 1000, 100000)
#  gff = Bio::Ensembl::Human.exportview(1, 1000, 100000, ['gene'])
#
#  seq = Bio::Ensembl::Mouse.exportview(1, 1000, 100000)
#  gff = Bio::Ensembl::Mouse.exportview(1, 1000, 100000, ['gene', 'variation', 'genscan'])
#
# == References
#
# * Ensembl
#   http:/www.ensembl.org/
#
class Ensembl

  # Hostname of Ensembl Genome Browser.
  ServerName = 'www.ensembl.org'


  # Ensembl Genome Browser Client Super Class
  #
  # == Examples
  #   
  #   module Bio
  #     class Ensembl::Kumamushi < Base
  #       Organism = 'Milnesium_tardigradum'
  #     end
  #   end
  #   fna = Bio::Ensembl::Kumamushi.exportview(1, 1000, 20000)
  #
  class Base

    # Ensembl ExportView Client.
    #
    # Retrieve genomic sequence/features from Ensembl ExportView in plain text.
    # Ensembl ExportView exports genomic data (sequence and features) in 
    # several file formats including fasta, GFF and tab.
    #
    # * ExportViwe (http://www.ensembl.org/Homo_sapiens/exportview).
    #
    # == Examples
    #
    #   # Genomic sequence in Fasta format
    #   Bio::Ensembl::Human.exportview(:seq_region_name => 1, :anchor1 => 1149206, :anchor2 => 1149229)
    #   Bio::Ensembl::Human.exportview(1, 1149206, 1149229)
    #
    #   # Feature in GFF
    #   Bio::Ensembl::Human.exportview(:seq_region_name => 1, :anchor1 => 1149206, :anchor2 => 1150000, 
    #                                  :options => ['similarity', 'repeat', 'genscan', 'variation', 'gene'])
    #   Bio::Ensembl::Human.exportview(1, 1149206, 1150000, ['variation', 'gene'])
    #
    # == Arguments
    #
    # Bio::Ensembl::Base#exportview method allow both orderd arguments and 
    # named arguments. 
    # Note: mandatory arguments marked '*'.
    #
    # === Orderd Arguments
    #
    # 1. seq_region_name - Chromosome number (*)
    # 2. anchor1         - From coordination (*)
    # 3. anchor2         - To coordination (*)
    # 4. options         - Features to export (in :format => 'gff' or 'tab')
    #                      ['similarity', 'repeat', 'genscan', 'variation', 'gene']
    #
    # === Named Arguments
    # 
    # * :seq_region_name - Chromosome number (*)
    # * :anchor1         - From coordination (*)
    # * :anchor2         - To coordination (*)
    # * :type1           - From coordination type ['bp', ]
    # * :type2           - To coordination type ['bp', ]
    # * :upstream        - Bp upstream
    # * :downstream      - Bp downstream
    # * :format          - File format ['fasta', 'gff', 'tab']
    # * :options         - Features to export (for :format => 'gff' or 'tab')
    #                      ['similarity', 'repeat', 'genscan', 'variation', 'gene']
    # 
    def self.exportview(*args)
      cgi = Client.new('exportview', self::Organism)

      if args.first.class == Hash then opts = args.first
      else
        opts = {:seq_region_name => args[0], :anchor1 => args[1], :anchor2 => args[2]}
        case args.size
        when 3 then opts.update({:format => 'fasta'})
        when 4 then opts.update({:format => 'gff', :options => args[3]}) ;        end
      end
      @hash = {:type1 => 'bp', 
               :type2 => 'bp', 
               :downstream => '', 
               :upstream => '', 
               :format => 'fasta',
               :options => [],
               :action => 'export', :_format => 'Text', :output => 'txt', :submit => 'Continue >>'}

      cgi.exec(@hash.update(opts))
    end

    # An Ensembl CGI client class
    # 
    # === Examples
    #
    #  cgi = Client('martview', 'Homo_sapiens')
    #  cgi.exec(hash_data)
    #
    class Client < PSORT::CGIDriver
      def initialize(cgi_name, genome_name)
        super(Ensembl::ServerName, ['', genome_name, cgi_name].join('/'))
      end

      private

      def make_args(query)
        @args = {}
        query.each { |k, v| @args[k.to_s] = v }
        nested_args_join(query)
      end

      def nested_args_join(hash)
        tmp = []
        hash.each do |key, value|
          if value.class == Array then value.each { |val| tmp << [key, val] } else tmp << [key, value] end
        end
        tmp.map {|x| x.map {|x| CGI.escape(x.to_s) }.join("=") }.join('&')
      end

      def parse_report(result_body)
        result_body
      end
    end # class Client

  end # class Base


  # Ensembl Human Genome
  # 
  # See Bio::Ensembl::Base class.
  # 
  class Human < Base
    Organism = 'Homo_sapiens'
  end # class Human

  # Ensembl Mouse Genome
  #
  # See Bio::Ensembl::Base class.
  #
  class Mouse < Base
    Organism = 'Mus_musculus'
  end # class Mouse

end # class Ensembl

end # module Bio





From nakao at dev.open-bio.org  Fri Apr 14 05:28:42 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Fri, 14 Apr 2006 05:28:42 -0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/io test_ensembl.rb,NONE,1.1
Message-ID: <200604140628.k3E6SBo7009947@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv9920/test/unit/bio/io

Added Files:
	test_ensembl.rb 
Log Message:
* ensembl.rb) newly added.
* test_ensembl.rb) newly added.


--- NEW FILE: test_ensembl.rb ---
#
# = test/unit/bio/io/test_ensembl.rb - Unit test for Bio::Ensembl.
#
# Copyright::   Copyright (C) 2006
#               Mitsuteru C. Nakao <n at bioruby.org>
# License::     Ruby's
#
# $Id: test_ensembl.rb,v 1.1 2006/04/14 06:28:09 nakao Exp $
#

require 'pathname'
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
$:.unshift(libpath) unless $:.include?(libpath)

require 'test/unit'
require 'bio/io/ensembl'


class TestEnsembl < Test::Unit::TestCase
  def test_server_name
    assert_equal('www.ensembl.org', Bio::Ensembl::ServerName)
  end

end

class TestEnsemblBase < Test::Unit::TestCase
  def test_exportview
    
  end
end

class TestEnsemblBaseClient < Test::Unit::TestCase
  def test_class
    assert_equal(Bio::PSORT::CGIDriver, Bio::Ensembl::Base::Client.superclass)
  end
end


class TestEnsemblHuman < Test::Unit::TestCase
  def test_organism
    assert_equal("Homo_sapiens", Bio::Ensembl::Human::Organism)
  end
end

class TestEnsemblMouse < Test::Unit::TestCase
  def test_organism
    assert_equal("Mus_musculus", Bio::Ensembl::Mouse::Organism)
  end
end



From nakao at dev.open-bio.org  Fri Apr 14 05:33:32 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Fri, 14 Apr 2006 05:33:32 -0000
Subject: [BioRuby-cvs] bioruby ChangeLog,1.50,1.51
Message-ID: <200604140633.k3E6XL90010004@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv9984

Modified Files:
	ChangeLog 
Log Message:
* Bio::Ensembl first commit.


Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.50
retrieving revision 1.51
diff -C2 -d -r1.50 -r1.51
*** ChangeLog	27 Feb 2006 11:38:14 -0000	1.50
--- ChangeLog	14 Apr 2006 06:33:19 -0000	1.51
***************
*** 1,2 ****
--- 1,10 ----
+ 2006-04-14  Mitsuteru Nakao <n at bioruby.org>
+ 
+         * lib/bio/io/ensembl.rb
+ 
+           Bio::Ensembl first commit. It is a client class for Ensembl Genome
+           Browser.
+ 
+ 
  2006-02-27  Toshiaki Katayama <k at bioruby.org>
  



From ngoto at dev.open-bio.org  Wed Apr 26 12:04:15 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Wed, 26 Apr 2006 12:04:15 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio command.rb,1.5,1.6
Message-ID: <200604261204.k3QC4FZN032162@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv32140/lib/bio

Modified Files:
	command.rb 
Log Message:
Experimentally added Bio::Command::NetTools.net_http_start() method. Note that it would be removed or the method name would be changed.


Index: command.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/command.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** command.rb	28 Mar 2006 14:00:48 -0000	1.5
--- command.rb	26 Apr 2006 12:04:13 -0000	1.6
***************
*** 13,16 ****
--- 13,17 ----
  require 'uri'
  require 'open-uri'
+ require 'net/http'
  
  module Bio
***************
*** 162,165 ****
--- 163,190 ----
      OpenURI.open_uri(uri).read
    end
+ 
+   # Same as:
+   #  uri = URI.parse(uri); Net::HTTP.start(uri.host, uri.port)
+   # and 
+   # it uses proxy if an environment variable (same as OpenURI.open_uri)
+   # is set.
+   # uri must be a string or a URI object.
+   def self.net_http_start(uri, &block)
+     unless uri.kind_of?(URI::Generic)
+       uri = URI.parse(uri)
+     end
+     if uri.scheme != 'http' then
+       raise "only http is supported: #{uri.inspect}"
+     end
+     # Note: URI#find_proxy is an unofficial method defined in open-uri.rb.
+     # If the spec of open-uri.rb would be changed, we should change below.
+     if proxyuri = uri.find_proxy then
+       raise 'Non-HTTP proxy' if proxyuri.class != URI::HTTP
+       http = Net::HTTP.Proxy(proxyuri.host, proxyuri.port)
+     else
+       http = Net::HTTP
+     end
+     http.start(uri.host, uri.port, &block)
+   end
  end #module NetTools
  



From ngoto at dev.open-bio.org  Thu Apr 27 02:33:45 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Thu, 27 Apr 2006 02:33:45 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio command.rb,1.6,1.7
Message-ID: <200604270233.k3R2XjuZ002237@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv2217/lib/bio

Modified Files:
	command.rb 
Log Message:
changed spec of Bio::Command::NetTools.net_http_start()


Index: command.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/command.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** command.rb	26 Apr 2006 12:04:13 -0000	1.6
--- command.rb	27 Apr 2006 02:33:43 -0000	1.7
***************
*** 165,180 ****
  
    # Same as:
!   #  uri = URI.parse(uri); Net::HTTP.start(uri.host, uri.port)
    # and 
    # it uses proxy if an environment variable (same as OpenURI.open_uri)
    # is set.
!   # uri must be a string or a URI object.
!   def self.net_http_start(uri, &block)
!     unless uri.kind_of?(URI::Generic)
!       uri = URI.parse(uri)
!     end
!     if uri.scheme != 'http' then
!       raise "only http is supported: #{uri.inspect}"
!     end
      # Note: URI#find_proxy is an unofficial method defined in open-uri.rb.
      # If the spec of open-uri.rb would be changed, we should change below.
--- 165,175 ----
  
    # Same as:
!   #   Net::HTTP.start(address, port)
    # and 
    # it uses proxy if an environment variable (same as OpenURI.open_uri)
    # is set.
!   #
!   def self.net_http_start(address, port = 80, &block)
!     uri = URI.parse("http://#{address}:#{port}")
      # Note: URI#find_proxy is an unofficial method defined in open-uri.rb.
      # If the spec of open-uri.rb would be changed, we should change below.
***************
*** 185,189 ****
        http = Net::HTTP
      end
!     http.start(uri.host, uri.port, &block)
    end
  end #module NetTools
--- 180,184 ----
        http = Net::HTTP
      end
!     http.start(address, port, &block)
    end
  end #module NetTools



From ngoto at dev.open-bio.org  Thu Apr 27 03:15:29 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Thu, 27 Apr 2006 03:15:29 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio command.rb,1.7,1.8
Message-ID: <200604270315.k3R3FTmK002447@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv2392/lib/bio

Modified Files:
	command.rb 
Log Message:
Bio::Command::NetTools can be included in classes.


Index: command.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/command.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** command.rb	27 Apr 2006 02:33:43 -0000	1.7
--- command.rb	27 Apr 2006 03:15:27 -0000	1.8
***************
*** 160,166 ****
  
    # Same as OpenURI.open_uri(uri).read.
!   def self.read_uri(uri)
      OpenURI.open_uri(uri).read
    end
  
    # Same as:
--- 160,167 ----
  
    # Same as OpenURI.open_uri(uri).read.
!   def read_uri(uri)
      OpenURI.open_uri(uri).read
    end
+   module_function :read_uri
  
    # Same as:
***************
*** 170,174 ****
    # is set.
    #
!   def self.net_http_start(address, port = 80, &block)
      uri = URI.parse("http://#{address}:#{port}")
      # Note: URI#find_proxy is an unofficial method defined in open-uri.rb.
--- 171,175 ----
    # is set.
    #
!   def net_http_start(address, port = 80, &block)
      uri = URI.parse("http://#{address}:#{port}")
      # Note: URI#find_proxy is an unofficial method defined in open-uri.rb.
***************
*** 182,185 ****
--- 183,188 ----
      http.start(address, port, &block)
    end
+   module_function :net_http_start
+ 
  end #module NetTools
  



From nakao at dev.open-bio.org  Thu Apr 27 05:38:52 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Thu, 27 Apr 2006 05:38:52 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/io test_ensembl.rb,1.1,1.2
Message-ID: <200604270538.k3R5cqVL002709@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv2667/test/unit/bio/io

Modified Files:
	test_ensembl.rb 
Log Message:
* ensembl.rb: Use Bio::Command::NetTools.net_http_start for proxy server.
* ensembl.rb: Added Ensembl.server_uri method.



Index: test_ensembl.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/io/test_ensembl.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** test_ensembl.rb	14 Apr 2006 06:28:09 -0000	1.1
--- test_ensembl.rb	27 Apr 2006 05:38:50 -0000	1.2
***************
*** 19,25 ****
  class TestEnsembl < Test::Unit::TestCase
    def test_server_name
!     assert_equal('www.ensembl.org', Bio::Ensembl::ServerName)
    end
  
  end
  
--- 19,34 ----
  class TestEnsembl < Test::Unit::TestCase
    def test_server_name
!     assert_equal('http://www.ensembl.org', Bio::Ensembl::EBIServerURI)
    end
  
+   def test_server_uri
+     assert_equal('http://www.ensembl.org', Bio::Ensembl.server_uri)
+   end
+   
+   def test_set_server_uri
+     host = 'http://localhost'
+     Bio::Ensembl.server_uri(host)
+     assert_equal(host, Bio::Ensembl.server_uri)
+   end
  end
  
***************
*** 32,36 ****
  class TestEnsemblBaseClient < Test::Unit::TestCase
    def test_class
!     assert_equal(Bio::PSORT::CGIDriver, Bio::Ensembl::Base::Client.superclass)
    end
  end
--- 41,45 ----
  class TestEnsemblBaseClient < Test::Unit::TestCase
    def test_class
! 
    end
  end



From nakao at dev.open-bio.org  Thu Apr 27 05:38:52 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Thu, 27 Apr 2006 05:38:52 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/io ensembl.rb,1.1,1.2
Message-ID: <200604270538.k3R5cqbu002714@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv2667/lib/bio/io

Modified Files:
	ensembl.rb 
Log Message:
* ensembl.rb: Use Bio::Command::NetTools.net_http_start for proxy server.
* ensembl.rb: Added Ensembl.server_uri method.



Index: ensembl.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/ensembl.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** ensembl.rb	14 Apr 2006 06:28:09 -0000	1.1
--- ensembl.rb	27 Apr 2006 05:38:50 -0000	1.2
***************
*** 27,31 ****
  #
  
! require 'bio'
  require 'cgi'
  
--- 27,32 ----
  #
  
! require 'bio/command'
! require 'uri'
  require 'cgi'
  
***************
*** 44,47 ****
--- 45,54 ----
  #  gff = Bio::Ensembl::Mouse.exportview(1, 1000, 100000, ['gene', 'variation', 'genscan'])
  #
+ #  Bio::Enesmbl.server_uri("http://www.gramene.org")
+ #  class Rice < Base
+ #    Organism = 'Oryza_sativa'
+ #  end
+ #  seq = Bio::Ensembl::Rice.exportview(1, 1000, 100000)
+ #
  # == References
  #
***************
*** 49,56 ****
  #   http:/www.ensembl.org/
  #
  class Ensembl
  
!   # Hostname of Ensembl Genome Browser.
!   ServerName = 'www.ensembl.org'
  
  
--- 56,86 ----
  #   http:/www.ensembl.org/
  #
+ # * GRAMENE
+ #   http://www.gramene.org/
+ #
  class Ensembl
  
!   # Hostname of the Ensembl Genome Browser.
!   EBIServerURI = 'http://www.ensembl.org'
! 
!   # An Alternative Hostname for Ensembl Genome Browser.
!   @@server_uri = nil
! 
!   # Sets and uses an alternative hostname for ensembl genome browser.
!   #
!   # == Example
!   #
!   #   require 'bio'
!   #   p Bio::Enesmbl.server_uri #=> 'http://www.ensembl.org'
!   #   Bio::Enesmbl.server_uri("http://www.gramene.org")
!   #   p Bio::Enesmbl.server_uri #=> "http://www.gramene.org"
!   #
!   def self.server_uri(uri = nil)
!     if uri
!       @@server_uri = uri
!     else
!       @@server_uri || EBIServerURI
!     end
!   end
  
  
***************
*** 79,89 ****
      #
      #   # Genomic sequence in Fasta format
!     #   Bio::Ensembl::Human.exportview(:seq_region_name => 1, :anchor1 => 1149206, :anchor2 => 1149229)
      #   Bio::Ensembl::Human.exportview(1, 1149206, 1149229)
      #
      #   # Feature in GFF
!     #   Bio::Ensembl::Human.exportview(:seq_region_name => 1, :anchor1 => 1149206, :anchor2 => 1150000, 
!     #                                  :options => ['similarity', 'repeat', 'genscan', 'variation', 'gene'])
!     #   Bio::Ensembl::Human.exportview(1, 1149206, 1150000, ['variation', 'gene'])
      #
      # == Arguments
--- 109,124 ----
      #
      #   # Genomic sequence in Fasta format
!     #   Bio::Ensembl::Human.exportview(:seq_region_name => 1, 
!     #                                  :anchor1 => 1149206, :anchor2 => 1149229)
      #   Bio::Ensembl::Human.exportview(1, 1149206, 1149229)
      #
      #   # Feature in GFF
!     #   Bio::Ensembl::Human.exportview(:seq_region_name => 1, 
!     #                                  :anchor1 => 1149206, :anchor2 => 1150000, 
!     #                                  :options => ['similarity', 'repeat', 
!     #                                               'genscan', 'variation', 
!     #                                               'gene'])
!     #   Bio::Ensembl::Human.exportview(1, 1149206, 1150000, 
!     #                                  ['variation', 'gene'])
      #
      # == Arguments
***************
*** 99,103 ****
      # 3. anchor2         - To coordination (*)
      # 4. options         - Features to export (in :format => 'gff' or 'tab')
!     #                      ['similarity', 'repeat', 'genscan', 'variation', 'gene']
      #
      # === Named Arguments
--- 134,139 ----
      # 3. anchor2         - To coordination (*)
      # 4. options         - Features to export (in :format => 'gff' or 'tab')
!     #                      ['similarity', 'repeat', 'genscan', 'variation', 
!     #                       'gene']
      #
      # === Named Arguments
***************
*** 112,128 ****
      # * :format          - File format ['fasta', 'gff', 'tab']
      # * :options         - Features to export (for :format => 'gff' or 'tab')
!     #                      ['similarity', 'repeat', 'genscan', 'variation', 'gene']
      # 
      def self.exportview(*args)
-       cgi = Client.new('exportview', self::Organism)
- 
        if args.first.class == Hash then opts = args.first
        else
!         opts = {:seq_region_name => args[0], :anchor1 => args[1], :anchor2 => args[2]}
          case args.size
!         when 3 then opts.update({:format => 'fasta'})
!         when 4 then opts.update({:format => 'gff', :options => args[3]}) ;        end
        end
!       @hash = {:type1 => 'bp', 
                 :type2 => 'bp', 
                 :downstream => '', 
--- 148,169 ----
      # * :format          - File format ['fasta', 'gff', 'tab']
      # * :options         - Features to export (for :format => 'gff' or 'tab')
!     #                      ['similarity', 'repeat', 'genscan', 'variation', 
!     #                       'gene']
      # 
      def self.exportview(*args)
        if args.first.class == Hash then opts = args.first
        else
!         options = {:seq_region_name => args[0], 
!                    :anchor1 => args[1], 
!                    :anchor2 => args[2]}
          case args.size
!         when 3 then 
!           options.update({:format => 'fasta'})
!         when 4 then 
!           options.update({:format => 'gff', :options => args[3]})
!         end
        end
! 
!       @data = {:type1 => 'bp', 
                 :type2 => 'bp', 
                 :downstream => '', 
***************
*** 130,169 ****
                 :format => 'fasta',
                 :options => [],
!                :action => 'export', :_format => 'Text', :output => 'txt', :submit => 'Continue >>'}
  
!       cgi.exec(@hash.update(opts))
      end
  
      # An Ensembl CGI client class
      # 
      # === Examples
      #
!     #  cgi = Client('martview', 'Homo_sapiens')
!     #  cgi.exec(hash_data)
      #
!     class Client < PSORT::CGIDriver
        def initialize(cgi_name, genome_name)
!         super(Ensembl::ServerName, ['', genome_name, cgi_name].join('/'))
        end
  
!       private
  
!       def make_args(query)
!         @args = {}
!         query.each { |k, v| @args[k.to_s] = v }
!         nested_args_join(query)
        end
  
!       def nested_args_join(hash)
          tmp = []
          hash.each do |key, value|
!           if value.class == Array then value.each { |val| tmp << [key, val] } else tmp << [key, value] end
          end
!         tmp.map {|x| x.map {|x| CGI.escape(x.to_s) }.join("=") }.join('&')
        end
  
-       def parse_report(result_body)
-         result_body
-       end
      end # class Client
  
--- 171,238 ----
                 :format => 'fasta',
                 :options => [],
!                :action => 'export', 
!                :_format => 'Text', 
!                :output => 'txt', 
!                :submit => 'Continue >>'}
  
!       cgi = Client.new('exportview', self::Organism)
!       cgi.exec(@data.update(options))
      end
  
+ 
+ 
      # An Ensembl CGI client class
+     #
+     # Enable the use of HTTP access via a proxy by setting the proxy address up
+     # as the 'http_proxy' enviroment variable. 
      # 
      # === Examples
      #
!     #  cgi = Client.new('martview', 'Homo_sapiens')
!     #  result_body = cgi.exec(hash_data)
      #
!     class Client
! 
!       # Sets cgi_name and genome_name.
!       #
!       # === Example
!       #
!       #  cgi = Client.new('martview', 'Homo_sapiens')
!       #
        def initialize(cgi_name, genome_name)
!         @uri = URI.parse(Ensembl.server_uri)
!         @path = ['', genome_name, cgi_name].join('/')
        end
  
!       # Executes query with data.
!       #
!       # === Example
!       #
!       #  result_body = cgi.exec(hash_data)
!       #
!       def exec(data_hash)
!         data = make_args(data_hash)
  
!         result = nil      
!         Bio::Command::NetTools.net_http_start(@uri.host, @uri.port) {|http|
!           result, = http.post(@path, data)
!         }
!         result.body
        end
  
!       private
! 
!       def make_args(hash)
          tmp = []
          hash.each do |key, value|
!           if value.class == Array then 
!             value.each { |val| tmp << [key, val] } 
!           else 
!             tmp << [key, value] 
!           end
          end
!         tmp.map {|e| e.map {|x| CGI.escape(x.to_s) }.join("=") }.join('&')
        end
  
      end # class Client
  



From ngoto at dev.open-bio.org  Sun Apr 30 05:40:25 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Sun, 30 Apr 2006 05:40:25 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/bl2seq report.rb,1.6,1.7
Message-ID: <200604300540.k3U5ePMf018074@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/bl2seq
In directory dev.open-bio.org:/tmp/cvs-serv18054

Modified Files:
	report.rb 
Log Message:
changes license to Ruby's.


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/bl2seq/report.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** report.rb	18 Dec 2005 15:58:39 -0000	1.6
--- report.rb	30 Apr 2006 05:40:23 -0000	1.7
***************
*** 3,23 ****
  # 
  # Copyright:: Copyright (C) 2005 GOTO Naohisa <ng at bioruby.org>
! # License::   LGPL
! #
! #--
! #  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
! #++
  #
  #  $Id$
--- 3,7 ----
  # 
  # Copyright:: Copyright (C) 2005 GOTO Naohisa <ng at bioruby.org>
! # License::   Ruby's
  #
  #  $Id$



From ngoto at dev.open-bio.org  Sun Apr 30 05:47:27 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Sun, 30 Apr 2006 05:47:27 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/blast wublast.rb,1.6,1.7
Message-ID: <200604300547.k3U5lRRv018148@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/blast
In directory dev.open-bio.org:/tmp/cvs-serv18107/blast

Modified Files:
	wublast.rb 
Log Message:
parse error (missing hits) for some hits of which database sequence names
contain 'Score'.


Index: wublast.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/wublast.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** wublast.rb	22 Feb 2006 08:46:15 -0000	1.6
--- wublast.rb	30 Apr 2006 05:47:25 -0000	1.7
***************
*** 281,285 ****
                  r = data.first
                end
!               if /^\s+Score/ =~ r then
                  @hsps << HSP.new(data)
                else
--- 281,285 ----
                  r = data.first
                end
!               if /\A\s+Score/ =~ r then
                  @hsps << HSP.new(data)
                else



From ngoto at dev.open-bio.org  Sun Apr 30 05:48:01 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Sun, 30 Apr 2006 05:48:01 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/blast format0.rb,1.17,1.18
Message-ID: <200604300548.k3U5m18v018180@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/blast
In directory dev.open-bio.org:/tmp/cvs-serv18160/blast

Modified Files:
	format0.rb 
Log Message:
parse error (missing hits) for some hits of which database sequence names contain 'Score'.


Index: format0.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/format0.rb,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** format0.rb	22 Feb 2006 08:46:15 -0000	1.17
--- format0.rb	30 Apr 2006 05:47:59 -0000	1.18
***************
*** 781,785 ****
              @f0hitname = data.shift
              @hsps = []
!             while r = data[0] and /^\s+Score/ =~ r
                @hsps << HSP.new(data)
              end
--- 781,785 ----
              @f0hitname = data.shift
              @hsps = []
!             while r = data[0] and /\A\s+Score/ =~ r
                @hsps << HSP.new(data)
              end



From ngoto at dev.open-bio.org  Sun Apr 30 05:50:21 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Sun, 30 Apr 2006 05:50:21 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl clustalw.rb, 1.10, 1.11 mafft.rb,
	1.9, 1.10 sim4.rb, 1.5, 1.6
Message-ID: <200604300550.k3U5oLwo018302@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv18276

Modified Files:
	clustalw.rb mafft.rb sim4.rb 
Log Message:
changed license to Ruby's


Index: sim4.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/sim4.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** sim4.rb	18 Dec 2005 15:58:40 -0000	1.5
--- sim4.rb	30 Apr 2006 05:50:19 -0000	1.6
***************
*** 3,23 ****
  #
  # Copyright:: Copyright (C) 2004 GOTO Naohisa <ng at bioruby.org>
! # License::   LGPL
! #
! #--
! #  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
! #++
  #
  #  $Id$
--- 3,7 ----
  #
  # Copyright:: Copyright (C) 2004 GOTO Naohisa <ng at bioruby.org>
! # License::   Ruby's
  #
  #  $Id$

Index: clustalw.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/clustalw.rb,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** clustalw.rb	18 Dec 2005 15:58:40 -0000	1.10
--- clustalw.rb	30 Apr 2006 05:50:19 -0000	1.11
***************
*** 3,23 ****
  #
  # Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! # License::   LGPL
! #
! #--
! #  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
! #++
  #
  #  $Id$
--- 3,7 ----
  #
  # Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! # License::   Ruby's
  #
  #  $Id$

Index: mafft.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/mafft.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** mafft.rb	18 Dec 2005 15:58:40 -0000	1.9
--- mafft.rb	30 Apr 2006 05:50:19 -0000	1.10
***************
*** 3,23 ****
  #
  # Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! # License::   LGPL
! #
! #--
! #  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
! #++
  #
  #  $Id$
--- 3,7 ----
  #
  # Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! # License::   Ruby's
  #
  #  $Id$



From ngoto at dev.open-bio.org  Sun Apr 30 05:50:21 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Sun, 30 Apr 2006 05:50:21 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/clustalw report.rb,1.9,1.10
Message-ID: <200604300550.k3U5oLJO018309@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/clustalw
In directory dev.open-bio.org:/tmp/cvs-serv18276/clustalw

Modified Files:
	report.rb 
Log Message:
changed license to Ruby's


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/clustalw/report.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** report.rb	18 Dec 2005 15:58:40 -0000	1.9
--- report.rb	30 Apr 2006 05:50:19 -0000	1.10
***************
*** 3,23 ****
  #
  # Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! # License::   LGPL
! #
! #--
! #  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
! #++
  #
  #  $Id$
--- 3,7 ----
  #
  # Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! # License::   Ruby's
  #
  #  $Id$



From ngoto at dev.open-bio.org  Sun Apr 30 05:50:21 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Sun, 30 Apr 2006 05:50:21 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/mafft report.rb,1.8,1.9
Message-ID: <200604300550.k3U5oLpH018314@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/mafft
In directory dev.open-bio.org:/tmp/cvs-serv18276/mafft

Modified Files:
	report.rb 
Log Message:
changed license to Ruby's


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/mafft/report.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** report.rb	18 Dec 2005 15:58:40 -0000	1.8
--- report.rb	30 Apr 2006 05:50:19 -0000	1.9
***************
*** 3,23 ****
  #
  # Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! # License::   LGPL
! #
! #--
! #  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
! #++
  #
  #  $Id$
--- 3,7 ----
  #
  # Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! # License::   Ruby's
  #
  #  $Id$



From ngoto at dev.open-bio.org  Sun Apr 30 05:50:21 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Sun, 30 Apr 2006 05:50:21 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/sim4 report.rb,1.7,1.8
Message-ID: <200604300550.k3U5oLFj018319@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/sim4
In directory dev.open-bio.org:/tmp/cvs-serv18276/sim4

Modified Files:
	report.rb 
Log Message:
changed license to Ruby's


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/sim4/report.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** report.rb	18 Dec 2005 15:58:40 -0000	1.7
--- report.rb	30 Apr 2006 05:50:19 -0000	1.8
***************
*** 3,23 ****
  #
  # Copyright:: Copyright (C) 2004 GOTO Naohisa <ng at bioruby.org>
! # License::   LGPL
! #
! #--
! #  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
! #++
  #
  #  $Id$
--- 3,7 ----
  #
  # Copyright:: Copyright (C) 2004 GOTO Naohisa <ng at bioruby.org>
! # License::   Ruby's
  #
  #  $Id$



From ngoto at dev.open-bio.org  Sun Apr 30 05:56:42 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Sun, 30 Apr 2006 05:56:42 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio alignment.rb,1.15,1.16
Message-ID: <200604300556.k3U5ugBr018426@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv18406

Modified Files:
	alignment.rb 
Log Message:
changed license to Ruby's


Index: alignment.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/alignment.rb,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** alignment.rb	24 Jan 2006 14:16:59 -0000	1.15
--- alignment.rb	30 Apr 2006 05:56:40 -0000	1.16
***************
*** 5,28 ****
  #             GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
  #
! # License:: LGPL
  #
  #  $Id$
  #
- #--
- #  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
- #++
- #
  # = About Bio::Alignment
  #
--- 5,12 ----
  #             GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
  #
! # License:: Ruby's
  #
  #  $Id$
  #
  # = About Bio::Alignment
  #



From ngoto at dev.open-bio.org  Sun Apr 30 05:57:42 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Sun, 30 Apr 2006 05:57:42 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db fantom.rb,1.11,1.12
Message-ID: <200604300557.k3U5vgsw018500@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db
In directory dev.open-bio.org:/tmp/cvs-serv18480/db

Modified Files:
	fantom.rb 
Log Message:
changed license to Ruby's


Index: fantom.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/fantom.rb,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** fantom.rb	26 Sep 2005 13:00:06 -0000	1.11
--- fantom.rb	30 Apr 2006 05:57:40 -0000	1.12
***************
*** 2,20 ****
  # bio/db/fantom.rb - RIKEN FANTOM2 database classes
  #
! #   Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! #
! #  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
  #
  #  $Id$
--- 2,7 ----
  # bio/db/fantom.rb - RIKEN FANTOM2 database classes
  #
! # Copyright:: Copyright (C) 2003 GOTO Naohisa <ng at bioruby.org> 
! # License::   Ruby's
  #
  #  $Id$



From ngoto at dev.open-bio.org  Sun Apr 30 05:58:52 2006
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Sun, 30 Apr 2006 05:58:52 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/io/flatfile bdb.rb,1.8,1.9
Message-ID: <200604300558.k3U5wqaF018532@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/io/flatfile
In directory dev.open-bio.org:/tmp/cvs-serv18512/io/flatfile

Modified Files:
	bdb.rb 
Log Message:
changed license to Ruby's


Index: bdb.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/flatfile/bdb.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** bdb.rb	26 Sep 2005 13:00:08 -0000	1.8
--- bdb.rb	30 Apr 2006 05:58:50 -0000	1.9
***************
*** 2,20 ****
  # bio/io/flatfile/bdb.rb - OBDA flatfile index by Berkley DB 
  # 
! #   Copyright (C) 2002 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp> 
! # 
! #  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 
  # 
  #  $Id$ 
--- 2,7 ----
  # bio/io/flatfile/bdb.rb - OBDA flatfile index by Berkley DB 
  # 
! # Copyright:: Copyright (C) 2002 GOTO Naohisa <ng at bioruby.org> 
! # License::   Ruby's
  # 
  #  $Id$ 



From nakao at dev.open-bio.org  Sun Apr 30 07:11:30 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Sun, 30 Apr 2006 07:11:30 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/blast xmlparser.rb,1.13,1.14
Message-ID: <200604300711.k3U7BUm3018668@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/blast
In directory dev.open-bio.org:/tmp/cvs-serv18631/lib/bio/appl/blast

Modified Files:
	xmlparser.rb 
Log Message:
* changed license to Ruby's 


Index: xmlparser.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/xmlparser.rb,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** xmlparser.rb	8 Sep 2005 01:22:08 -0000	1.13
--- xmlparser.rb	30 Apr 2006 07:11:28 -0000	1.14
***************
*** 1,23 ****
  #
! # bio/appl/blast/xmlparser.rb - BLAST XML output (-m 7) parser by XMLParser
  # 
! #   Copyright (C) 2001 Mitsuteru C. Nakao <n at bioruby.org>
! #   Copyright (C) 2003 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
  #
! #  $Id$
  #
  
--- 1,31 ----
  #
! # = bio/appl/blast/xmlparser.rb - BLAST XML output (-m 7) parser by XMLParser
  # 
! # Copyright::    Copyright (C) 2001 
! #                Mitsuteru C. Nakao <n at bioruby.org>
! # Copyright::    Copyright (C) 2003 
! #                KATAYAMA Toshiaki <k at bioruby.org>
! # Lisence::      Ruby's
  #
! # $Id$
  #
! # == Description
! # 
! # A parser for blast XML report (format 7) based on the XMLParser.
! # This file is automatically loaded by bio/appl/blast/report.rb if
! # the XMLParser installed.
  #
! # BioRuby provides two implements of the paser for the blast XML format report
! # (format 7) based on the XMLParser and the REXML.
  #
! # == Examples
! #
! # == References
! #
! # * Blast
! #   http://
! #
! # * XMLParser
! #   http://
  #
  
***************
*** 28,217 ****
  
  module Bio
!   class Blast
!     class Report
  
!       private
  
!       def xmlparser_parse(xml)
!         parser = XMLParser.new
!         def parser.default; end
!         
!         begin
!           tag_stack = Array.new
!           hash = Hash.new
  
!           parser.parse(xml) do |type, name, data|
!             #print "type=#{type.inspect} name=#{name.inspect} data=#{data.inspect}\n" # for DEBUG
!             case type
!             when XMLParser::START_ELEM
!               tag_stack.push(name)
!               hash.update(data)
!               case name
!               when 'Iteration'
!                 iteration = Iteration.new
!                 @iterations.push(iteration)
!               when 'Hit'
!                 hit = Hit.new
!                 hit.query_id = @query_id
!                 hit.query_def = @query_def
!                 hit.query_len = @query_len
!                 @iterations.last.hits.push(hit)
!               when 'Hsp'
!                 hsp = Hsp.new
!                 @iterations.last.hits.last.hsps.push(hsp)
!               end
!             when XMLParser::END_ELEM
!               case name
!               when /^BlastOutput/
!                 xmlparser_parse_program(name,hash)
!                 hash = Hash.new
!               when /^Parameters$/
!                 xmlparser_parse_parameters(hash)
!                 hash = Hash.new
!               when /^Iteration/
!                 xmlparser_parse_iteration(name, hash)
!                 hash = Hash.new
!               when /^Hit/
!                 xmlparser_parse_hit(name, hash)
!                 hash = Hash.new
!               when /^Hsp$/
!                 xmlparser_parse_hsp(hash)
!                 hash = Hash.new
!               when /^Statistics$/
!                 xmlparser_parse_statistics(hash)
!                 hash = Hash.new
!               end
!               tag_stack.pop
!             when XMLParser::CDATA
!               if hash[tag_stack.last].nil?
!                 hash[tag_stack.last] = data unless data.strip.empty?
!               else
!                 hash[tag_stack.last].concat(data) if data
!               end
!             when XMLParser::PI
              end
            end
-         rescue XMLParserError
-           line = parser.line
-           column = parser.column
-           print "Parse error at #{line}(#{column}) : #{$!}\n"
          end
        end
  
  
!       def xmlparser_parse_program(tag, hash)
!         case tag
!         when 'BlastOutput_program'
!           @program = hash[tag]
!         when 'BlastOutput_version'
!           @version = hash[tag]
!         when 'BlastOutput_reference'
!           @reference = hash[tag]
!         when 'BlastOutput_db'
!           @db = hash[tag].strip
!         when 'BlastOutput_query-ID'
!           @query_id = hash[tag]
!         when 'BlastOutput_query-def'
!           @query_def = hash[tag]
!         when 'BlastOutput_query-len'
!           @query_len = hash[tag].to_i
!         end
        end
  
!       def xmlparser_parse_parameters(hash)
!         labels = { 
!           'matrix'	=> 'Parameters_matrix',
!           'expect'	=> 'Parameters_expect',
!           'include'	=> 'Parameters_include',
!           'sc-match'	=> 'Parameters_sc-match',
!           'sc-mismatch'	=> 'Parameters_sc-mismatch',
!           'gap-open'	=> 'Parameters_gap-open',
!           'gap-extend'	=> 'Parameters_gap-extend',
!           'filter'	=> 'Parameters_filter',
!           'pattern'	=> 'Parameters_pattern',
!           'entrez-query'=> 'Parameters_entrez-query',
!         }
!         labels.each do |k,v|
!           case k
!           when 'filter', 'matrix'
!             @parameters[k] = hash[v].to_s
!           else
!             @parameters[k] = hash[v].to_i
!           end
          end
        end
  
!       def xmlparser_parse_iteration(tag, hash)
!         case tag
!         when 'Iteration_iter-num'
!           @iterations.last.num = hash[tag].to_i
!         when 'Iteration_message'
!           @iterations.last.message = hash[tag].to_s
!         end
        end
  
!       def xmlparser_parse_hit(tag, hash)
!         hit = @iterations.last.hits.last
!         case tag
!         when 'Hit_num'
!           hit.num = hash[tag].to_i
!         when 'Hit_id'
!           hit.hit_id = hash[tag].clone
!         when 'Hit_def'
!           hit.definition = hash[tag].clone
!         when 'Hit_accession'
!           hit.accession = hash[tag].clone
!         when 'Hit_len'
!           hit.len = hash[tag].clone.to_i
!         end
        end
  
!       def xmlparser_parse_hsp(hash)
!         hsp = @iterations.last.hits.last.hsps.last
!         hsp.num			= hash['Hsp_num'].to_i
!         hsp.bit_score		= hash['Hsp_bit-score'].to_f
!         hsp.score		= hash['Hsp_score'].to_i
!         hsp.evalue		= hash['Hsp_evalue'].to_f
!         hsp.query_from		= hash['Hsp_query-from'].to_i
!         hsp.query_to		= hash['Hsp_query-to'].to_i
!         hsp.hit_from		= hash['Hsp_hit-from'].to_i
!         hsp.hit_to		= hash['Hsp_hit-to'].to_i
!         hsp.pattern_from	= hash['Hsp_pattern-from'].to_i
!         hsp.pattern_to		= hash['Hsp_pattern-to'].to_i
!    	hsp.query_frame		= hash['Hsp_query-frame'].to_i
!         hsp.hit_frame		= hash['Hsp_hit-frame'].to_i
!         hsp.identity		= hash['Hsp_identity'].to_i
!         hsp.positive		= hash['Hsp_positive'].to_i
!         hsp.gaps		= hash['Hsp_gaps'].to_i
!         hsp.align_len		= hash['Hsp_align-len'].to_i
!         hsp.density		= hash['Hsp_density'].to_i
!         hsp.qseq		= hash['Hsp_qseq']
!         hsp.hseq		= hash['Hsp_hseq']
!         hsp.midline		= hash['Hsp_midline']
!       end
  
!       def xmlparser_parse_statistics(hash)
!         labels = {
!           'db-num'	=> 'Statistics_db-num',
!           'db-len'	=> 'Statistics_db-len',
!           'hsp-len'	=> 'Statistics_hsp-len',
!           'eff-space'	=> 'Statistics_eff-space',
!           'kappa'	=> 'Statistics_kappa',
!           'lambda'	=> 'Statistics_lambda',
!           'entropy'	=> 'Statistics_entropy'
!         }
!         labels.each do |k,v|
!           case k
!           when 'db-num', 'db-len', 'hsp-len'
!             @iterations.last.statistics[k] = hash[v].to_i
!           else
!             @iterations.last.statistics[k] = hash[v].to_f
!           end
          end
        end
-         
      end
!   end
! end
  
  
--- 36,224 ----
  
  module Bio
! class Blast
!   class Report
  
!     private
  
!     def xmlparser_parse(xml)
!       parser = XMLParser.new
!       def parser.default; end
!        
!       begin
!         tag_stack = Array.new
!         hash = Hash.new
  
!         parser.parse(xml) do |type, name, data|
!           case type
!           when XMLParser::START_ELEM
!             tag_stack.push(name)
!             hash.update(data)
!             case name
!             when 'Iteration'
!               iteration = Iteration.new
!               @iterations.push(iteration)
!             when 'Hit'
!               hit = Hit.new
!               hit.query_id = @query_id
!               hit.query_def = @query_def
!               hit.query_len = @query_len
!               @iterations.last.hits.push(hit)
!             when 'Hsp'
!               hsp = Hsp.new
!               @iterations.last.hits.last.hsps.push(hsp)
              end
+           when XMLParser::END_ELEM
+             case name
+             when /^BlastOutput/
+               xmlparser_parse_program(name,hash)
+               hash = Hash.new
+             when /^Parameters$/
+               xmlparser_parse_parameters(hash)
+               hash = Hash.new
+             when /^Iteration/
+               xmlparser_parse_iteration(name, hash)
+               hash = Hash.new
+             when /^Hit/
+               xmlparser_parse_hit(name, hash)
+               hash = Hash.new
+             when /^Hsp$/
+               xmlparser_parse_hsp(hash)
+               hash = Hash.new
+             when /^Statistics$/
+               xmlparser_parse_statistics(hash)
+               hash = Hash.new
+             end
+             tag_stack.pop
+           when XMLParser::CDATA
+             if hash[tag_stack.last].nil?
+               hash[tag_stack.last] = data unless data.strip.empty?
+             else
+               hash[tag_stack.last].concat(data) if data
+             end
+           when XMLParser::PI
            end
          end
+       rescue XMLParserError
+         line = parser.line
+         column = parser.column
+         print "Parse error at #{line}(#{column}) : #{$!}\n"
        end
+     end
  
  
!     def xmlparser_parse_program(tag, hash)
!       case tag
!       when 'BlastOutput_program'
!         @program = hash[tag]
!       when 'BlastOutput_version'
!         @version = hash[tag]
!       when 'BlastOutput_reference'
!         @reference = hash[tag]
!       when 'BlastOutput_db'
!         @db = hash[tag].strip
!       when 'BlastOutput_query-ID'
!         @query_id = hash[tag]
!       when 'BlastOutput_query-def'
!         @query_def = hash[tag]
!       when 'BlastOutput_query-len'
!         @query_len = hash[tag].to_i
        end
+     end
  
!     def xmlparser_parse_parameters(hash)
!       labels = { 
!         'matrix'       => 'Parameters_matrix',
!         'expect'       => 'Parameters_expect',
!         'include'      => 'Parameters_include',
!         'sc-match'     => 'Parameters_sc-match',
!         'sc-mismatch'  => 'Parameters_sc-mismatch',
!         'gap-open'     => 'Parameters_gap-open',
!         'gap-extend'   => 'Parameters_gap-extend',
!         'filter'       => 'Parameters_filter',
!         'pattern'      => 'Parameters_pattern',
!         'entrez-query' => 'Parameters_entrez-query',
!       }
!       labels.each do |k,v|
!         case k
!         when 'filter', 'matrix'
!           @parameters[k] = hash[v].to_s
!         else
!           @parameters[k] = hash[v].to_i
          end
        end
+     end
  
!     def xmlparser_parse_iteration(tag, hash)
!       case tag
!       when 'Iteration_iter-num'
!         @iterations.last.num = hash[tag].to_i
!       when 'Iteration_message'
!         @iterations.last.message = hash[tag].to_s
        end
+     end
  
!     def xmlparser_parse_hit(tag, hash)
!       hit = @iterations.last.hits.last
!       case tag
!       when 'Hit_num'
!         hit.num = hash[tag].to_i
!       when 'Hit_id'
!         hit.hit_id = hash[tag].clone
!       when 'Hit_def'
!         hit.definition = hash[tag].clone
!       when 'Hit_accession'
!         hit.accession = hash[tag].clone
!       when 'Hit_len'
!         hit.len = hash[tag].clone.to_i
        end
+     end
  
!     def xmlparser_parse_hsp(hash)
!       hsp = @iterations.last.hits.last.hsps.last
!       hsp.num          = hash['Hsp_num'].to_i
!       hsp.bit_score    = hash['Hsp_bit-score'].to_f
!       hsp.score        = hash['Hsp_score'].to_i
!       hsp.evalue       = hash['Hsp_evalue'].to_f
!       hsp.query_from   = hash['Hsp_query-from'].to_i
!       hsp.query_to     = hash['Hsp_query-to'].to_i
!       hsp.hit_from     = hash['Hsp_hit-from'].to_i
!       hsp.hit_to       = hash['Hsp_hit-to'].to_i
!       hsp.pattern_from = hash['Hsp_pattern-from'].to_i
!       hsp.pattern_to   = hash['Hsp_pattern-to'].to_i
!       hsp.query_frame  = hash['Hsp_query-frame'].to_i
!       hsp.hit_frame    = hash['Hsp_hit-frame'].to_i
!       hsp.identity     = hash['Hsp_identity'].to_i
!       hsp.positive     = hash['Hsp_positive'].to_i
!       hsp.gaps         = hash['Hsp_gaps'].to_i
!       hsp.align_len    = hash['Hsp_align-len'].to_i
!       hsp.density      = hash['Hsp_density'].to_i
!       hsp.qseq         = hash['Hsp_qseq']
!       hsp.hseq         = hash['Hsp_hseq']
!       hsp.midline      = hash['Hsp_midline']
!     end
  
!     def xmlparser_parse_statistics(hash)
!       labels = {
!         'db-num'	=> 'Statistics_db-num',
!         'db-len'	=> 'Statistics_db-len',
!         'hsp-len'	=> 'Statistics_hsp-len',
!         'eff-space'	=> 'Statistics_eff-space',
!         'kappa'	=> 'Statistics_kappa',
!         'lambda'	=> 'Statistics_lambda',
!         'entropy'	=> 'Statistics_entropy'
!       }
!       labels.each do |k,v|
!         case k
!         when 'db-num', 'db-len', 'hsp-len'
!           @iterations.last.statistics[k] = hash[v].to_i
!         else
!           @iterations.last.statistics[k] = hash[v].to_f
          end
        end
      end
!         
!   end # class Report
! end # class Blast
! end # module Bio
  
  



From nakao at dev.open-bio.org  Sun Apr 30 07:11:30 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Sun, 30 Apr 2006 07:11:30 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/psort report.rb,1.12,1.13
Message-ID: <200604300711.k3U7BUtC018673@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/psort
In directory dev.open-bio.org:/tmp/cvs-serv18631/lib/bio/appl/psort

Modified Files:
	report.rb 
Log Message:
* changed license to Ruby's 


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/psort/report.rb,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** report.rb	3 Nov 2005 10:50:58 -0000	1.12
--- report.rb	30 Apr 2006 07:11:28 -0000	1.13
***************
*** 2,7 ****
  # = bio/appl/psort/report.rb - PSORT systems report classes
  #
! # Copyright::   Copyright (C) 2003 Mitsuteru C. Nakao <n at bioruby.org>
! # License::     LGPL
  #
  #  $Id$
--- 2,8 ----
  # = bio/appl/psort/report.rb - PSORT systems report classes
  #
! # Copyright::   Copyright (C) 2003 
! #               Mitsuteru C. Nakao <n at bioruby.org>
! # License::     Ruby's
  #
  #  $Id$
***************
*** 9,30 ****
  # == A Report classes for PSORT Systems
  # 
- #--
- #
- #  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
- #
- # ++
- #
  
  require 'bio/sequence'
--- 10,13 ----



From nakao at dev.open-bio.org  Sun Apr 30 07:11:31 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Sun, 30 Apr 2006 07:11:31 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/targetp report.rb,1.7,1.8
Message-ID: <200604300711.k3U7BVlq018678@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/targetp
In directory dev.open-bio.org:/tmp/cvs-serv18631/lib/bio/appl/targetp

Modified Files:
	report.rb 
Log Message:
* changed license to Ruby's 


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/targetp/report.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** report.rb	18 Dec 2005 15:58:41 -0000	1.7
--- report.rb	30 Apr 2006 07:11:28 -0000	1.8
***************
*** 2,7 ****
  # = bio/appl/targetp/report.rb - TargetP report class
  # 
! # Copyright::  Copyright (C) 2003 Mitsuteru C. Nakao <n at bioruby.org>
! # License::    LGPL
  #
  #  $Id$
--- 2,8 ----
  # = bio/appl/targetp/report.rb - TargetP report class
  # 
! # Copyright::  Copyright (C) 2003 
! #              Mitsuteru C. Nakao <n at bioruby.org>
! # License::    Ruby's
  #
  #  $Id$
***************
*** 13,33 ****
  # == Example
  # == References
- #--
- #
- #  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
- #
- #++
  #
  
--- 14,17 ----



From nakao at dev.open-bio.org  Sun Apr 30 07:11:31 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Sun, 30 Apr 2006 07:11:31 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/genscan report.rb,1.8,1.9
Message-ID: <200604300711.k3U7BVhB018688@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/genscan
In directory dev.open-bio.org:/tmp/cvs-serv18631/lib/bio/appl/genscan

Modified Files:
	report.rb 
Log Message:
* changed license to Ruby's 


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/genscan/report.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** report.rb	18 Dec 2005 15:58:40 -0000	1.8
--- report.rb	30 Apr 2006 07:11:29 -0000	1.9
***************
*** 2,7 ****
  # = bio/appl/genscan/report.rb - Genscan report classes
  #
! # Copyright::  Copyright (C) 2003 Mitsuteru C. Nakao <n at bioruby.org>
! # License::    LGPL
  #
  #  $Id$
--- 2,8 ----
  # = bio/appl/genscan/report.rb - Genscan report classes
  #
! # Copyright::  Copyright (C) 2003 
! #              Mitsuteru C. Nakao <n at bioruby.org>
! # License::    Ruby's
  #
  #  $Id$
***************
*** 11,35 ****
  #
  # == Example
- # == References
- #
- #--
- #
- #  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
! #
! #  $Id$
! #
! #++
  #
  
--- 12,17 ----
  #
  # == Example
  #
! # == References
  #
  



From nakao at dev.open-bio.org  Sun Apr 30 07:11:31 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Sun, 30 Apr 2006 07:11:31 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/tmhmm report.rb,1.6,1.7
Message-ID: <200604300711.k3U7BVdR018683@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/tmhmm
In directory dev.open-bio.org:/tmp/cvs-serv18631/lib/bio/appl/tmhmm

Modified Files:
	report.rb 
Log Message:
* changed license to Ruby's 


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/tmhmm/report.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** report.rb	18 Dec 2005 15:58:41 -0000	1.6
--- report.rb	30 Apr 2006 07:11:29 -0000	1.7
***************
*** 2,7 ****
  # = bio/appl/tmhmm/report.rb - TMHMM report class
  # 
! # Copyright::  Copyright (C) 2003 Mitsuteru C. Nakao <n at bioruby.org>
! # License::    LGPL
  #
  #  $Id$
--- 2,8 ----
  # = bio/appl/tmhmm/report.rb - TMHMM report class
  # 
! # Copyright::  Copyright (C) 2003 
! #              Mitsuteru C. Nakao <n at bioruby.org>
! # License::    Ruby's
  #
  #  $Id$
***************
*** 12,32 ****
  # == Example
  # == References
- #--
- #
- #  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
- #
- #++
  #
  
--- 13,16 ----



From nakao at dev.open-bio.org  Sun Apr 30 07:11:31 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Sun, 30 Apr 2006 07:11:31 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db/embl common.rb,1.10,1.11
Message-ID: <200604300711.k3U7BV2X018693@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db/embl
In directory dev.open-bio.org:/tmp/cvs-serv18631/lib/bio/db/embl

Modified Files:
	common.rb 
Log Message:
* changed license to Ruby's 


Index: common.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/common.rb,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** common.rb	14 Apr 2006 06:04:09 -0000	1.10
--- common.rb	30 Apr 2006 07:11:29 -0000	1.11
***************
*** 2,6 ****
  # = bio/db/embl.rb - Common methods for EMBL style database classes
  #
! # Copyright::   Copyright (C) 2001-2005 Mitsuteru C. Nakao <n at bioruby.org>
  # License::     Ruby's
  #
--- 2,7 ----
  # = bio/db/embl.rb - Common methods for EMBL style database classes
  #
! # Copyright::   Copyright (C) 2001-2006
! #               Mitsuteru C. Nakao <n at bioruby.org>
  # License::     Ruby's
  #



From nakao at dev.open-bio.org  Sun Apr 30 07:11:30 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Sun, 30 Apr 2006 07:11:30 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db go.rb,1.9,1.10
Message-ID: <200604300711.k3U7BU1g018663@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db
In directory dev.open-bio.org:/tmp/cvs-serv18631/lib/bio/db

Modified Files:
	go.rb 
Log Message:
* changed license to Ruby's 


Index: go.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/go.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** go.rb	31 Oct 2005 18:32:36 -0000	1.9
--- go.rb	30 Apr 2006 07:11:28 -0000	1.10
***************
*** 2,7 ****
  # = bio/db/go.rb - Classes for Gene Ontology
  #
! # Copyright::   Copyright (C) 2003 Mitsuteru C. Nakao <n at bioruby.org>
! # License::
  #
  #  $Id$
--- 2,8 ----
  # = bio/db/go.rb - Classes for Gene Ontology
  #
! # Copyright::   Copyright (C) 2003 
! #               Mitsuteru C. Nakao <n at bioruby.org>
! # License::     Ruby's
  #
  #  $Id$
***************
*** 12,32 ****
  #
  # == References
- #--
- #
- #  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
- #
- #++
  #
  
--- 13,16 ----



From nakao at dev.open-bio.org  Sun Apr 30 07:13:41 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Sun, 30 Apr 2006 07:13:41 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/sosui report.rb,1.9,1.10
Message-ID: <200604300713.k3U7DfjR018777@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/sosui
In directory dev.open-bio.org:/tmp/cvs-serv18750/lib/bio/appl/sosui

Modified Files:
	report.rb 
Log Message:
* changed license to Ruby's 


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/sosui/report.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** report.rb	18 Dec 2005 15:58:41 -0000	1.9
--- report.rb	30 Apr 2006 07:13:39 -0000	1.10
***************
*** 2,7 ****
  # = bio/appl/sosui/report.rb - SOSUI report class
  # 
! # Copyright::   Copyright (C) 2003 Mitsuteru C. Nakao <n at bioruby.org>
! # License::     LGPL
  #
  #  $Id$
--- 2,8 ----
  # = bio/appl/sosui/report.rb - SOSUI report class
  # 
! # Copyright::   Copyright (C) 2003 
! #               Mitsuteru C. Nakao <n at bioruby.org>
! # License::     Ruby's
  #
  #  $Id$
***************
*** 10,31 ****
  #
  # == References
- # * http://sosui.proteome.bio.tuat.ac.jp/sosui_submit.html
- #--
- #
- #  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
! #
! #++
  #
  
--- 11,16 ----
  #
  # == References
  #
! # * http://sosui.proteome.bio.tuat.ac.jp/sosui_submit.html
  #
  



From nakao at dev.open-bio.org  Sun Apr 30 07:13:41 2006
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Sun, 30 Apr 2006 07:13:41 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl psort.rb,1.8,1.9
Message-ID: <200604300713.k3U7Dfpp018772@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv18750/lib/bio/appl

Modified Files:
	psort.rb 
Log Message:
* changed license to Ruby's 


Index: psort.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/psort.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** psort.rb	1 Nov 2005 05:15:15 -0000	1.8
--- psort.rb	30 Apr 2006 07:13:39 -0000	1.9
***************
*** 1,8 ****
  #
  # = bio/appl/psort.rb - PSORT, protein sorting site prediction systems
  #
! # Copyright::   Copyright (C) 2003 Mitsuteru C. Nakao <n at bioruby.org>
! # License::     LGPL
! #
  #
  # $Id$
--- 1,10 ----
+ module Bio
+ 
  #
  # = bio/appl/psort.rb - PSORT, protein sorting site prediction systems
  #
! # Copyright::   Copyright (C) 2003-2006
! #               Mitsuteru C. Nakao <n at bioruby.org>
! # License::     Ruby's
  #
  # $Id$
***************
*** 25,59 ****
  #
  #
- #--
- #
- #  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
- #
- #++
- #
  
  require 'bio/sequence'
  require 'bio/db/fasta'
- require 'net/http'
  require 'cgi'
  
  
! module Bio
! 
!   
! 
! 
    class PSORT
      # a Hash for PSORT official hosts:
      #   Key      value (host)
--- 27,40 ----
  #
  #
  
  require 'bio/sequence'
+ require 'bio/command'
  require 'bio/db/fasta'
  require 'cgi'
  
  
!   #
    class PSORT
+ 
      # a Hash for PSORT official hosts:
      #   Key      value (host)
***************
*** 62,78 ****
      #   Okazaki  psort.nibb.ac.jp        
      #   Peking   srs.pku.edu.cn:8088     
!     WWWServer = {
!       'IMSUT'   => {'host' => 'psort.hgc.jp', #'psort.ims.u-tokyo.ac.jp', 
!                     'PSORT1' => '/cgi-bin/okumura.pl',
!                     'PSORT2' => '/cgi-bin/runpsort.pl'},
!       'Okazaki' => {'host' => 'psort.nibb.ac.jp', 
!                     'PSORT1' => '/cgi-bin/okumura.pl',
!                     'PSORT2' => '/cgi-bin/runpsort.pl'},
!       'Peking'  => {'host' => 'srs.pku.edu.en:8088', 
!                     'PSORT1' => '/cgi-bin/okumura.pl',
!                     'PSORT2' => '/cgi-bin/runpsort.pl'}
      }
  
- 
      # = Generic CGI client class
      # A generic CGI client class for Bio::PSORT::* classes.
--- 43,58 ----
      #   Okazaki  psort.nibb.ac.jp        
      #   Peking   srs.pku.edu.cn:8088     
!     ServerURI = {
!       :IMSUT   => {
!         :PSORT1 => URI.parse("http://psort.hgc.jp/cgi-bin/okumura.pl"),
!         :PSORT2 => URI.parse("http://psort.hgc.jp/cgi-bin/runpsort.pl") },
!       :Okazaki => {
!         :PSORT1 => URI.parse("http://psort.nibb.ac.jp/cgi-bin/okumura.pl"),
!         :PSORT2 => URI.parse("http://psort.nibb.ac.jp/cgi-bin/runpsort.pl") },
!       :Peking  => {
!         :PSORT1 => URI.parse("http:///src.pku.edu.cn:8088/cgi-bin/okumura.pl"),
!         :PSORT2 => URI.parse("http://src.pku.edu.cn:8088/cgi-bin/runpsort.pl") },
      }
  
      # = Generic CGI client class
      # A generic CGI client class for Bio::PSORT::* classes.
***************
*** 104,113 ****
  
  
!       # Sets remote ``host'' and cgi ``path''.
!       def initialize(host = '', path = '') 
!         @host = host
!         @path = path
          @args = {}
!         @report
        end
  
--- 84,107 ----
  
  
!       # Sets remote host name and cgi path or uri.
!       #
!       # == Examples
!       #
!       #   CGIDriver.new("localhost", "/cgi-bin/psort_www.pl")
!       #
!       #   CGIDriver.new("http://localhost/cgi-bin/psort_www.pl")
!       #
!       #   CGIDriver.new(URI.parse("http://localhost/cgi-bin/psort_www.pl"))
!       #
!       def initialize(host = '', path = '')
!         case host.to_s
!         when /^http:/
!           uri = host.to_s
!         else
!           uri = 'http://' + host + '/' + path
!         end
!         @uri = URI.parse(uri)
          @args = {}
!         @report = ''
        end
  
***************
*** 118,122 ****
  
          begin
!           result, = Net::HTTP.new(@host).post(@path, data)
            @report = result.body
            output = parse_report(@report)
--- 112,119 ----
  
          begin
!           result = nil
!           Bio::Command::NetTools.net_http_start(@uri.host) {|http|
!             result, = http.post(@uri.path, data)
!           }
            @report = result.body
            output = parse_report(@report)
***************
*** 140,144 ****
        # Erases HTML tags
        def erase_html_tags(str)
!         return str.gsub(/<\S.*?>/,'')
        end
  
--- 137,141 ----
        # Erases HTML tags
        def erase_html_tags(str)
!         return str.gsub(/<\S.*?>/, '')
        end
  
***************
*** 149,153 ****
            tmp << CGI.escape(key.to_s) + '=' + CGI.escape(val.to_s)
          end
!         return tmp.join(delim)  # not ';' but '&' in psort's cgi
        end
  
--- 146,150 ----
            tmp << CGI.escape(key.to_s) + '=' + CGI.escape(val.to_s)
          end
!         return tmp.join(delim)  # not ';' but '&' in the psort cgi script.
        end
  
***************
*** 157,160 ****
--- 154,158 ----
  
      # = Bio::PSORT::PSORT1
+     #
      # Bio::PSORT::PSORT1 is a wapper class for the original PSORT program.
      #
***************
*** 169,175 ****
--- 167,175 ----
      # 
      # == References
+     #
      # 1. Nakai, K. and Kanehisa, M., A knowledge base for predicting protein 
      #    localization sites in eukaryotic cells, Genomics 14, 897-911 (1992).
      #    [PMID:1478671]
+     #
      class PSORT1
  
***************
*** 179,184 ****
        # connecting to the IMSUT server.
        def self.imsut
!         self.new(Remote.new(WWWServer['IMSUT']['host'],
!                             WWWServer['IMSUT']['PSORT1']))
        end
  
--- 179,183 ----
        # connecting to the IMSUT server.
        def self.imsut
!         self.new(Remote.new(ServerURI[:IMSUT][:PSORT1]))
        end
  
***************
*** 187,192 ****
        # connecting to the NIBB server.
        def self.okazaki
!         self.new(Remote.new(WWWServer['Okazaki']['host'],
!                             WWWServer['Okazaki']['PSORT1']))
        end
        
--- 186,190 ----
        # connecting to the NIBB server.
        def self.okazaki
!         self.new(Remote.new(ServerURI[:Okazaki][:PSORT1]))
        end
        
***************
*** 195,209 ****
        # connecting to the Peking server.
        def self.peking
!         self.new(Remote.new(WWWServer['Peking']['host'],
!                             WWWServer['Peking']['PSORT1']))
        end
  
  
!       # Sets a server CGI Driver (Bio::PSORT::PSORT1::Remote).
!       def initialize(driver, origin = 'yeast')
!         @serv     = driver
!         @origin   = origin  # Gram-positive bacterium, Gram-negative bacterium,
!                             # yeast, aminal, plant
!         @title    = 'MYSEQ'
          @sequence = ''
        end
--- 193,207 ----
        # connecting to the Peking server.
        def self.peking
!         self.new(Remote.new(ServerURI[:Peking][:PSORT1]))
        end
  
  
!       # Sets a cgi client (Bio::PSORT::PSORT1::Remote).
!       #
!       def initialize(driver, origin = 'yeast', title = 'MYSEQ')
!         @serv = driver
!         @origin = origin  # Gram-positive bacterium, Gram-negative bacterium,
!                           # yeast, aminal, plant
!         @title = title
          @sequence = ''
        end
***************
*** 237,243 ****
        def exec(faa, parsing = true)
          if faa.class == Bio::FastaFormat
!           @title        = faa.entry_id if @title == 'MYSEQ'
!           @sequence     = faa.seq
!           @serv.args    = {'title' => @title, 'origin' => @origin}
            @serv.parsing = parsing
            return @serv.exec(sequence)
--- 235,241 ----
        def exec(faa, parsing = true)
          if faa.class == Bio::FastaFormat
!           @title = faa.entry_id if @title == 'MYSEQ'
!           @sequence = faa.seq
!           @serv.args = {'title' => @title, 'origin' => @origin}
            @serv.parsing = parsing
            return @serv.exec(sequence)
***************
*** 268,274 ****
          
          # Sets remote ``host'' and cgi ``path''.
!         def initialize(host, path)
!           @origin  = 'yeast'
!           @title   = 'MYSEQ'
            @parsing = true
            super(host, path)
--- 266,272 ----
          
          # Sets remote ``host'' and cgi ``path''.
!         def initialize(host, path = nil, title = 'MYSEQ', origin = 'yeast')
!           @title   = title
!           @origin  = origin
            @parsing = true
            super(host, path)
***************
*** 327,331 ****
        #  Okazaki  psort.nibb.ac.jp         /cgi-bin/runpsort.pl
        #  Peking   srs.pku.edu.cn:8088      /cgi-bin/runpsort.pl
!       def self.remote(host, path)
          self.new(Remote.new(host, path))
        end
--- 325,329 ----
        #  Okazaki  psort.nibb.ac.jp         /cgi-bin/runpsort.pl
        #  Peking   srs.pku.edu.cn:8088      /cgi-bin/runpsort.pl
!       def self.remote(host, path = nil)
          self.new(Remote.new(host, path))
        end
***************
*** 334,339 ****
        # connecting to the IMSUT server.
        def self.imsut
!         self.remote(WWWServer['IMSUT']['host'],
!                     WWWServer['IMSUT']['PSORT2'])
        end
  
--- 332,336 ----
        # connecting to the IMSUT server.
        def self.imsut
!         self.remote(ServerURI[:IMSUT][:PSORT2])
        end
  
***************
*** 341,346 ****
        # connecting to the NIBB server.
        def self.okazaki
!         self.remote(WWWServer['Okazaki']['host'],
!                     WWWServer['Okazaki']['PSORT2'])
        end
  
--- 338,342 ----
        # connecting to the NIBB server.
        def self.okazaki
!         self.remote(ServerURI[:Okazaki][:PSORT2])
        end
  
***************
*** 348,353 ****
        # connecting to the Peking server.
        def self.peking
!         self.remote(WWWServer['Peking']['host'],
!                     WWWServer['Peking']['PSORT2'])
        end
  
--- 344,348 ----
        # connecting to the Peking server.
        def self.peking
!         self.remote(ServerURI[:Peking][:PSORT2])
        end
  
***************
*** 374,380 ****
        def exec(faa, parsing = true)
          if faa.class == Bio::FastaFormat
!           @title        = faa.entry_id if @title == nil
!           @sequence     = faa.seq
!           @serv.args    = {'origin' => @origin, 'title' => @title}
            @serv.parsing = parsing
            return @serv.exec(@sequence)
--- 369,375 ----
        def exec(faa, parsing = true)
          if faa.class == Bio::FastaFormat
!           @title = faa.entry_id if @title == nil
!           @sequence = faa.seq
!           @serv.args = {'origin' => @origin, 'title' => @title}
            @serv.parsing = parsing
            return @serv.exec(@sequence)