From k at dev.open-bio.org  Mon Jul  9 04:48:06 2007
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Mon, 09 Jul 2007 08:48:06 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db/kegg taxonomy.rb,NONE,1.1
Message-ID: <200707090848.l698m6IP029799@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db/kegg
In directory dev.open-bio.org:/tmp/cvs-serv29795

Added Files:
	taxonomy.rb 
Log Message:
* Bio::KEGG::Taxonomy class which treats taxonomyc tree structure of the
  KEGG taxonomy file available at ftp.genome.jp/pub/kegg/genes/taxonomy
  which is a replacement of the previously keggtab file (Bio::KEGG::Keggtab).


--- NEW FILE: taxonomy.rb ---
#
# = bio/db/kegg/taxonomy.rb - KEGG taxonomy parser class
#
# Copyright::  Copyright (C) 2007 Toshiaki Katayama <k at bioruby.org>
# License::    The Ruby License
#
#  $Id: taxonomy.rb,v 1.1 2007/07/09 08:48:03 k Exp $
#

module Bio
class KEGG

# == Description
#
# Parse the KEGG 'taxonomy' file which describes taxonomic classification
# of organisms.
#
# == References
#
# The KEGG 'taxonomy' file is available at
#
# * ftp://ftp.genome.jp/pub/kegg/genes/taxonomy
#
class Taxonomy

  def initialize(filename, orgs = [])
    @tree = Hash.new
    @path = Array.new
    @leaves = Hash.new

    # ?????????????? Genes ??????
    @root = 'Genes'

    hier = Array.new
    level = 0
    label = nil

    File.open(filename).each do |line|
      next if line.strip.empty?

      # ?????????????????? - # ????????????????????????????????
      if line[/^#/]
	level = line[/^#+/].length
	label = line[/[A-z].*/]
	hier[level] = sanitize(label)

      # ?????????????? - ??????????????????????????????????????????
      else
	tax, org, name, desc = line.chomp.split("\t")
        if orgs.nil? or orgs.empty? or orgs.include?(org)
          species, strain, = name.split('_')
          # (0) species ????????????????????????????????????????????????
          #  Gamma/enterobacteria ??????????????????????????????????????
          #  ??????????????????????????????????????????????????????????
          #   ex. E.coli, H.influenzae ????
          # ??????????????????
          #  ???? species ????????????????????### ??????????????????????????????
          #  Tree ?? Hash ??????????????????????????????????????????
          # (1) species ??????????????????????????????????????????
          #   ?? ?????????? species ???? _sp ???????????????????????????? (1-1)
          #      ?????? _sp ???????????????????? strain ???????? (1-2)
          #   ex. Bacteria/Proteobacteria/Beta/T.denitrificans/tbd ??
          #       Bacteria/Proteobacteria/Epsilon/T.denitrificans_ATCC33889/tdn
          #    -> Bacteria/Proteobacteria/Beta/T.denitrificans/tbd ??
          #       Bacteria/Proteobacteria/Epsilon/T.denitrificans_sp/tdn
          # (2) species ??????????????????????????????
          #   ?? ?????????? species ???? _sp ????????????????????????????
          #   ex. Bacteria/Cyanobacgteria/Cyanobacteria_CYA/cya
          #       Bacteria/Cyanobacgteria/Cyanobacteria_CYB/cya
          #       Bacteria/Proteobacteria/Magnetococcus/Magnetococcus_MC1/mgm
          #    -> Bacteria/Cyanobacgteria/Cyanobacteria_sp/cya
          #       Bacteria/Cyanobacgteria/Cyanobacteria_sp/cya
          #       Bacteria/Proteobacteria/Magnetococcus/Magnetococcus_sp/mgm
          sp_group = "#{species}_sp"
          if @tree[species]
            if hier[level+1] == species
              # case (0)
            else
              # case (1-1)
              species = sp_group
              # case (1-2)
              if @tree[sp_group] and hier[level+1] != species
                species = name
              end
            end
          else
            if hier[level] == species
              # case (2)
              species = sp_group
            end
          end
          # hier ?? [nil, Eukaryotes, Fungi, Ascomycetes, Saccharomycetes] ??
          # species ?? org ?? [S_cerevisiae, sce] ????????????
          hier[level+1] = species
          #hier[level+1] = sanitize(species)
          hier[level+2] = org
          ary = hier[1, level+2]
          warn ary.inspect if $DEBUG
          add_to_tree(ary)
          add_to_leaves(ary)
          add_to_path(ary)
        end
      end
    end
    return tree
  end

  attr_reader :tree
  attr_reader :path
  attr_reader :leaves
  attr_accessor :root

  def organisms(group)
    @leaves[group]
  end

  # root ???????????? [node, subnode, subsubnode, ..., leaf] ????????????
  # ????????????????????????????????????
  def add_to_tree(ary)
    parent = @root
    ary.each do |node|
      @tree[parent] ||= Hash.new
      @tree[parent][node] = nil
      parent = node
    end
  end

  # ??????????????????????????????????????????
  def add_to_leaves(ary)
    leaf = ary.last
    ary.each do |node|
      @leaves[node] ||= Array.new
      @leaves[node] << leaf
    end
  end

  # ????????????????????????????
  def add_to_path(ary)
    @path << ary
  end

  # ??????????????????????????????????????????????????????????????
  # ??????????????????????????????????????????????????
  #
  # ex.
  #  Plants / Monocotyledons / grass family / osa --> Plants / Monocotyledons / osa
  #
  def compact(node = root)
    # ??????????????
    if subnodes = @tree[node]
      # ??????????????????????????
      subnodes.keys.each do |subnode|
        # ??????????????
        if subsubnodes = @tree[subnode]
          # ?????????????? 1 ????????
          if subsubnodes.keys.size == 1
            # ????????????????????
            subsubnode = subsubnodes.keys.first
            # ????????????????????
            if subsubsubnodes = @tree[subsubnode]
              # ????????????????????????????????????????
              @tree[subnode] = subsubsubnodes
              # ??????????????
              @tree[subnode].delete(subsubnode)
              warn "--- compact: #{subsubnode} is replaced by #{subsubsubnodes}" if $DEBUG
              # ?????????????????? compact ??????????????????????????????
              retry
            end
          end
        end
        # ????????????????????????????
        compact(subnode)
      end
    end
  end

  # ????????????????????????????????????????????????????????????
  #
  # ex.
  #  Plants / Monocotyledons / osa --> Plants / osa
  #
  def reduce(node = root)
    # ??????????????
    if subnodes = @tree[node]
      # ??????????????????????????
      subnodes.keys.each do |subnode|
        # ??????????????
        if subsubnodes = @tree[subnode]
          # ?????????????? 1 ????????
          if subsubnodes.keys.size == 1
            # ????????????????????
            subsubnode = subsubnodes.keys.first
            # ??????????????????????
            unless @tree[subsubnode]
              # ????????????????????????????
              @tree[node].update(subsubnodes)
              # ??????????????
              @tree[node].delete(subnode)
              warn "--- reduce: #{subnode} is replaced by #{subsubnode}" if $DEBUG
            end
          end
        end
        # ????????????????????????????
        reduce(subnode)
      end
    end
  end

  # ??????????????????????????????????????Hash??????????????
  # ??????????????????????????????????
  def dfs(parent, &block)
    if children = @tree[parent]
      yield parent, children
      children.keys.each do |child|
        dfs(child, &block)
      end
    end
  end

  # ??????????????????????????????????????
  def dfs_with_level(parent, &block)
    @level ||= 0
    if children = @tree[parent]
      yield parent, children, @level
      @level += 1
      children.keys.each do |child|
        dfs_with_level(child, &block)
      end
      @level -= 1
    end
  end

  # ????????????????????????????????????
  def to_s
    result = "#{@root}\n"
    @tree[@root].keys.each do |node|
      result += subtree(node, "  ")
    end
    return result
  end

  private

  # ???? to_s ??????????????????
  def subtree(node, indent)
    result = "#{indent}+- #{node}\n"
    indent += "  "
    @tree[node].keys.each do |child|
      if @tree[child]
        result += subtree(child, indent)
      else
        result += "#{indent}+- #{child}\n"
      end
    end
    return result
  end

  def sanitize(str)
    str.gsub(/[^A-z0-9]/, '_')
  end

end # Taxonomy

end # KEGG
end # Bio



if __FILE__ == $0

  # Usage:
  # % wget ftp://ftp.genome.jp/pub/kegg/genes/taxonomy
  # % ruby taxonomy.rb taxonomy | less -S

  taxonomy = ARGV.shift
  org_list = ARGV.shift || nil

  if org_list
    orgs = File.readlines(org_list).map{|x| x.strip}
  else
    orgs = nil
  end

  tree = Bio::KEGG::Taxonomy.new(taxonomy, orgs)

  puts ">>> tree - original"
  puts tree

  puts ">>> tree - after compact"
  tree.compact
  puts tree

  puts ">>> tree - after reduce"
  tree.reduce
  puts tree

  puts ">>> path - sorted"
  tree.path.sort.each do |path|
    puts path.join("/")
  end

  puts ">>> group : orgs"
  tree.dfs(tree.root) do |parent, children|
    if orgs = tree.organisms(parent)
      puts "#{parent.ljust(30)} (#{orgs.size})\t#{orgs.join(', ')}"
    end
  end

  puts ">>> group : subgroups"
  tree.dfs_with_level(tree.root) do |parent, children, level|
    subgroups = children.keys.sort
    indent = " " * level
    label  = "#{indent} #{level} #{parent}"
    puts "#{label.ljust(35)}\t#{subgroups.join(', ')}"
  end

end


From k at dev.open-bio.org  Mon Jul  9 04:49:17 2007
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Mon, 09 Jul 2007 08:49:17 +0000
Subject: [BioRuby-cvs] bioruby/lib bio.rb,1.84,1.85
Message-ID: <200707090849.l698nHpo029821@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib
In directory dev.open-bio.org:/tmp/cvs-serv29817

Modified Files:
	bio.rb 
Log Message:
* Bio:KEGG::Keggtab is obsoleted. Use Bio::KEGG::Taxonomy instead.


Index: bio.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio.rb,v
retrieving revision 1.84
retrieving revision 1.85
diff -C2 -d -r1.84 -r1.85
*** bio.rb	5 Apr 2007 23:35:39 -0000	1.84
--- bio.rb	9 Jul 2007 08:49:15 -0000	1.85
***************
*** 97,101 ****
      autoload :ORTHOLOGY,    'bio/db/kegg/orthology'
      autoload :KGML,         'bio/db/kegg/kgml'
!     autoload :Keggtab,      'bio/db/kegg/keggtab'
    end
  
--- 97,101 ----
      autoload :ORTHOLOGY,    'bio/db/kegg/orthology'
      autoload :KGML,         'bio/db/kegg/kgml'
!     autoload :Taxonomy,     'bio/db/kegg/taxonomy'
    end
  


From k at dev.open-bio.org  Mon Jul  9 06:29:18 2007
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Mon, 09 Jul 2007 10:29:18 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db/kegg taxonomy.rb,1.1,1.2
Message-ID: <200707091029.l69ATIbX029957@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db/kegg
In directory dev.open-bio.org:/tmp/cvs-serv29953

Modified Files:
	taxonomy.rb 
Log Message:
* Comments translated into English.


Index: taxonomy.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/taxonomy.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** taxonomy.rb	9 Jul 2007 08:48:03 -0000	1.1
--- taxonomy.rb	9 Jul 2007 10:29:16 -0000	1.2
***************
*** 25,33 ****
  
    def initialize(filename, orgs = [])
      @tree = Hash.new
      @path = Array.new
      @leaves = Hash.new
  
!     # ?????????????? Genes ??????
      @root = 'Genes'
  
--- 25,39 ----
  
    def initialize(filename, orgs = [])
+     # Stores the taxonomic tree as a linked list (implemented in Hash), so
+     # every node need to have unique name (key) to work correctly
      @tree = Hash.new
+ 
+     # Also stores the taxonomic tree as a list of arrays (full path)
      @path = Array.new
+ 
+     # Also stores all leaf nodes (organism codes) of every intermediate nodes
      @leaves = Hash.new
  
!     # tentative name for the root node (use accessor to change)
      @root = 'Genes'
  
***************
*** 39,43 ****
        next if line.strip.empty?
  
!       # ?????????????????? - # ????????????????????????????????
        if line[/^#/]
  	level = line[/^#+/].length
--- 45,49 ----
        next if line.strip.empty?
  
!       # line for taxonomic hierarchy (indent according to the number of # marks)
        if line[/^#/]
  	level = line[/^#+/].length
***************
*** 45,69 ****
  	hier[level] = sanitize(label)
  
!       # ?????????????? - ??????????????????????????????????????????
        else
  	tax, org, name, desc = line.chomp.split("\t")
          if orgs.nil? or orgs.empty? or orgs.include?(org)
            species, strain, = name.split('_')
!           # (0) species ????????????????????????????????????????????????
!           #  Gamma/enterobacteria ??????????????????????????????????????
!           #  ??????????????????????????????????????????????????????????
!           #   ex. E.coli, H.influenzae ????
!           # ??????????????????
!           #  ???? species ????????????????????### ??????????????????????????????
!           #  Tree ?? Hash ??????????????????????????????????????????
!           # (1) species ??????????????????????????????????????????
!           #   ?? ?????????? species ???? _sp ???????????????????????????? (1-1)
!           #      ?????? _sp ???????????????????? strain ???????? (1-2)
!           #   ex. Bacteria/Proteobacteria/Beta/T.denitrificans/tbd ??
            #       Bacteria/Proteobacteria/Epsilon/T.denitrificans_ATCC33889/tdn
!           #    -> Bacteria/Proteobacteria/Beta/T.denitrificans/tbd ??
            #       Bacteria/Proteobacteria/Epsilon/T.denitrificans_sp/tdn
!           # (2) species ??????????????????????????????
!           #   ?? ?????????? species ???? _sp ????????????????????????????
            #   ex. Bacteria/Cyanobacgteria/Cyanobacteria_CYA/cya
            #       Bacteria/Cyanobacgteria/Cyanobacteria_CYB/cya
--- 51,79 ----
  	hier[level] = sanitize(label)
  
!       # line for organims name (unify different strains of a species)
        else
  	tax, org, name, desc = line.chomp.split("\t")
          if orgs.nil? or orgs.empty? or orgs.include?(org)
            species, strain, = name.split('_')
!           # (0) Grouping of the strains of the same species.
!           #  If the name of species is the same as the previous line,
!           #  add the species to the same species group.
!           #   ex. Gamma/enterobacteria has a large number of organisms,
!           #       so sub grouping of strains is needed for E.coli strains etc.
!           #
!           # However, if the species name is already used, need to avoid
!           # collision of species name as the current implementation stores
!           # the tree as a Hash, which may cause the infinite loop.
!           #
!           # (1) If species name == the intermediate node of other lineage
!           #  Add '_sp' to the species name to avoid the conflict (1-1), and if
!           #  'species_sp' is already taken, use 'species_strain' instead (1-2).
!           #   ex. Bacteria/Proteobacteria/Beta/T.denitrificans/tbd
            #       Bacteria/Proteobacteria/Epsilon/T.denitrificans_ATCC33889/tdn
!           #    -> Bacteria/Proteobacteria/Beta/T.denitrificans/tbd
            #       Bacteria/Proteobacteria/Epsilon/T.denitrificans_sp/tdn
!           #
!           # (2) If species name == the intermediate node of the same lineage
!           #  Add '_sp' to the species name to avoid the conflict.
            #   ex. Bacteria/Cyanobacgteria/Cyanobacteria_CYA/cya
            #       Bacteria/Cyanobacgteria/Cyanobacteria_CYB/cya
***************
*** 90,97 ****
              end
            end
!           # hier ?? [nil, Eukaryotes, Fungi, Ascomycetes, Saccharomycetes] ??
!           # species ?? org ?? [S_cerevisiae, sce] ????????????
!           hier[level+1] = species
!           #hier[level+1] = sanitize(species)
            hier[level+2] = org
            ary = hier[1, level+2]
--- 100,107 ----
              end
            end
!           # 'hier' is an array of the taxonomic tree + species and strain name.
!           #  ex. [nil, Eukaryotes, Fungi, Ascomycetes, Saccharomycetes] +
!           #      [S_cerevisiae, sce]
!           hier[level+1] = species	# sanitize(species)
            hier[level+2] = org
            ary = hier[1, level+2]
***************
*** 115,120 ****
    end
  
!   # root ???????????? [node, subnode, subsubnode, ..., leaf] ????????????
!   # ????????????????????????????????????
    def add_to_tree(ary)
      parent = @root
--- 125,130 ----
    end
  
!   # Add a new path [node, subnode, subsubnode, ..., leaf] under the root node
!   # and every intermediate nodes stores their child nodes as a Hash.
    def add_to_tree(ary)
      parent = @root
***************
*** 126,130 ****
    end
  
!   # ??????????????????????????????????????????
    def add_to_leaves(ary)
      leaf = ary.last
--- 136,141 ----
    end
  
!   # Add a new path [node, subnode, subsubnode, ..., leaf] under the root node
!   # and stores leaf nodes to the every intermediate nodes as an Array.
    def add_to_leaves(ary)
      leaf = ary.last
***************
*** 135,173 ****
    end
  
!   # ????????????????????????????
    def add_to_path(ary)
      @path << ary
    end
  
!   # ??????????????????????????????????????????????????????????????
!   # ??????????????????????????????????????????????????
!   #
!   # ex.
!   #  Plants / Monocotyledons / grass family / osa --> Plants / Monocotyledons / osa
    #
    def compact(node = root)
!     # ??????????????
      if subnodes = @tree[node]
!       # ??????????????????????????
        subnodes.keys.each do |subnode|
-         # ??????????????
          if subsubnodes = @tree[subnode]
!           # ?????????????? 1 ????????
            if subsubnodes.keys.size == 1
!             # ????????????????????
              subsubnode = subsubnodes.keys.first
!             # ????????????????????
              if subsubsubnodes = @tree[subsubnode]
!               # ????????????????????????????????????????
                @tree[subnode] = subsubsubnodes
!               # ??????????????
                @tree[subnode].delete(subsubnode)
                warn "--- compact: #{subsubnode} is replaced by #{subsubsubnodes}" if $DEBUG
!               # ?????????????????? compact ??????????????????????????????
                retry
              end
            end
          end
!         # ????????????????????????????
          compact(subnode)
        end
--- 146,185 ----
    end
  
!   # Add a new path [node, subnode, subsubnode, ..., leaf] under the root node
!   # and stores the path itself in an Array.
    def add_to_path(ary)
      @path << ary
    end
  
!   # Compaction of intermediate nodes of the resulted taxonomic tree.
!   #  - If child node has only one child node (grandchild), make the child of
!   #    grandchild as a grandchild.
!   #  ex.
!   #    Plants / Monocotyledons / grass family / osa
!   #    --> Plants / Monocotyledons / osa
    #
    def compact(node = root)
!     # if the node has children
      if subnodes = @tree[node]
!       # obtain grandchildren for each child
        subnodes.keys.each do |subnode|
          if subsubnodes = @tree[subnode]
!           # if the number of grandchild node is 1
            if subsubnodes.keys.size == 1
!             # obtain the name of the grandchild node
              subsubnode = subsubnodes.keys.first
!             # obtain the child of the grandchlid node
              if subsubsubnodes = @tree[subsubnode]
!               # make the child of grandchild node as a chlid of child node
                @tree[subnode] = subsubsubnodes
!               # delete grandchild node
                @tree[subnode].delete(subsubnode)
                warn "--- compact: #{subsubnode} is replaced by #{subsubsubnodes}" if $DEBUG
!               # retry until new grandchild also needed to be compacted.
                retry
              end
            end
          end
!         # repeat recurseively
          compact(subnode)
        end
***************
*** 175,199 ****
    end
  
!   # ????????????????????????????????????????????????????????????
!   #
!   # ex.
!   #  Plants / Monocotyledons / osa --> Plants / osa
    #
    def reduce(node = root)
!     # ??????????????
      if subnodes = @tree[node]
!       # ??????????????????????????
        subnodes.keys.each do |subnode|
-         # ??????????????
          if subsubnodes = @tree[subnode]
!           # ?????????????? 1 ????????
            if subsubnodes.keys.size == 1
!             # ????????????????????
              subsubnode = subsubnodes.keys.first
!             # ??????????????????????
              unless @tree[subsubnode]
!               # ????????????????????????????
                @tree[node].update(subsubnodes)
!               # ??????????????
                @tree[node].delete(subnode)
                warn "--- reduce: #{subnode} is replaced by #{subsubnode}" if $DEBUG
--- 187,212 ----
    end
  
!   # Reduction of the leaf node of the resulted taxonomic tree.
!   #  - If the parent node have only one leaf node, replace parent node
!   #    with the leaf node.
!   #  ex.
!   #   Plants / Monocotyledons / osa
!   #   --> Plants / osa
    #
    def reduce(node = root)
!     # if the node has children
      if subnodes = @tree[node]
!       # obtain grandchildren for each child
        subnodes.keys.each do |subnode|
          if subsubnodes = @tree[subnode]
!           # if the number of grandchild node is 1
            if subsubnodes.keys.size == 1
!             # obtain the name of the grandchild node
              subsubnode = subsubnodes.keys.first
!             # if the grandchild node is a leaf node
              unless @tree[subsubnode]
!               # make the grandchild node as a child node
                @tree[node].update(subsubnodes)
!               # delete child node
                @tree[node].delete(subnode)
                warn "--- reduce: #{subnode} is replaced by #{subsubnode}" if $DEBUG
***************
*** 201,205 ****
            end
          end
!         # ????????????????????????????
          reduce(subnode)
        end
--- 214,218 ----
            end
          end
!         # repeat recursively
          reduce(subnode)
        end
***************
*** 207,212 ****
    end
  
!   # ??????????????????????????????????????Hash??????????????
!   # ??????????????????????????????????
    def dfs(parent, &block)
      if children = @tree[parent]
--- 220,225 ----
    end
  
!   # Traverse the taxonomic tree by the depth first search method
!   # under the given (root or intermediate) node.
    def dfs(parent, &block)
      if children = @tree[parent]
***************
*** 218,222 ****
    end
  
!   # ??????????????????????????????????????
    def dfs_with_level(parent, &block)
      @level ||= 0
--- 231,236 ----
    end
  
!   # Similar to the dfs method but also passes the current level of the nest
!   # to the iterator.
    def dfs_with_level(parent, &block)
      @level ||= 0
***************
*** 231,239 ****
    end
  
!   # ????????????????????????????????????
    def to_s
      result = "#{@root}\n"
      @tree[@root].keys.each do |node|
!       result += subtree(node, "  ")
      end
      return result
--- 245,253 ----
    end
  
!   # Convert the taxonomic tree structure to a simple ascii art.
    def to_s
      result = "#{@root}\n"
      @tree[@root].keys.each do |node|
!       result += ascii_tree(node, "  ")
      end
      return result
***************
*** 242,252 ****
    private
  
!   # ???? to_s ??????????????????
!   def subtree(node, indent)
      result = "#{indent}+- #{node}\n"
      indent += "  "
      @tree[node].keys.each do |child|
        if @tree[child]
!         result += subtree(child, indent)
        else
          result += "#{indent}+- #{child}\n"
--- 256,266 ----
    private
  
!   # Helper method for the to_s method.
!   def ascii_tree(node, indent)
      result = "#{indent}+- #{node}\n"
      indent += "  "
      @tree[node].keys.each do |child|
        if @tree[child]
!         result += ascii_tree(child, indent)
        else
          result += "#{indent}+- #{child}\n"


From k at dev.open-bio.org  Mon Jul  9 07:14:31 2007
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Mon, 09 Jul 2007 11:14:31 +0000
Subject: [BioRuby-cvs]
	bioruby/lib/bio/shell/rails/vendor/plugins/generators/bioruby
	bioruby_generator.rb, 1.3, 1.4
Message-ID: <200707091114.l69BEVEW030108@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/shell/rails/vendor/plugins/generators/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv30101

Modified Files:
	bioruby_generator.rb 
Log Message:
* Completely new design for BioRuby shell on Rails translated from
  the 'DibdoltRed' theme on www.openwebdesign.org which is created by
  Darjan Panic and Brian Green as a public domain work.


Index: bioruby_generator.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/rails/vendor/plugins/generators/bioruby/bioruby_generator.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** bioruby_generator.rb	28 Jun 2007 10:56:25 -0000	1.3
--- bioruby_generator.rb	9 Jul 2007 11:14:29 -0000	1.4
***************
*** 21,24 ****
--- 21,26 ----
        m.file 'bioruby.png',           'public/images/bioruby.png'
        m.file 'bioruby.gif',           'public/images/bioruby.gif'
+       m.file 'bg.gif',                'public/images/bg.gif'
+       m.file 'console.png',           'public/images/console.png'
        m.file 'bioruby.css',           'public/stylesheets/bioruby.css'
      end


From k at dev.open-bio.org  Mon Jul  9 07:14:31 2007
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Mon, 09 Jul 2007 11:14:31 +0000
Subject: [BioRuby-cvs]
	bioruby/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates
	bg.gif, NONE, 1.1 console.png, NONE, 1.1 _classes.rhtml, 1.1,
	1.2 _log.rhtml, 1.1, 1.2 _methods.rhtml, 1.2,
	1.3 _modules.rhtml, 1.1, 1.2 bioruby.css, 1.4,
	1.5 bioruby.rhtml, 1.3, 1.4 bioruby_controller.rb, 1.5,
	1.6 commands.rhtml, 1.1, 1.2 index.rhtml, 1.3, 1.4
Message-ID: <200707091114.l69BEV4Z030111@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates
In directory dev.open-bio.org:/tmp/cvs-serv30101/templates

Modified Files:
	_classes.rhtml _log.rhtml _methods.rhtml _modules.rhtml 
	bioruby.css bioruby.rhtml bioruby_controller.rb commands.rhtml 
	index.rhtml 
Added Files:
	bg.gif console.png 
Log Message:
* Completely new design for BioRuby shell on Rails translated from
  the 'DibdoltRed' theme on www.openwebdesign.org which is created by
  Darjan Panic and Brian Green as a public domain work.


Index: _classes.rhtml
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_classes.rhtml,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** _classes.rhtml	24 Dec 2006 08:27:15 -0000	1.1
--- _classes.rhtml	9 Jul 2007 11:14:29 -0000	1.2
***************
*** 1,2 ****
--- 1,4 ----
  [ <%= @class %> ]
+ <div id="class_list">
  <%= @classes.map{ |x| reference_link(x) }.join(" > ") %>
+ </div>
\ No newline at end of file

Index: commands.rhtml
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/commands.rhtml,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** commands.rhtml	24 Dec 2006 08:27:15 -0000	1.1
--- commands.rhtml	9 Jul 2007 11:14:29 -0000	1.2
***************
*** 1,2 ****
--- 1,3 ----
+ <div id="command">
  <h2>BioRuby shell commands</h2>
  <ul>
***************
*** 5,7 ****
    <% end %>
  </ul>
! 
--- 6,8 ----
    <% end %>
  </ul>
! </div>
\ No newline at end of file

Index: bioruby_controller.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby_controller.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** bioruby_controller.rb	28 Jun 2007 10:56:25 -0000	1.5
--- bioruby_controller.rb	9 Jul 2007 11:14:29 -0000	1.6
***************
*** 4,17 ****
  
    HIDE_MODULES = [
!     ActiveSupport::CoreExtensions::String::Iterators,
!     ActiveSupport::CoreExtensions::String::StartsEndsWith,
!     ActiveSupport::CoreExtensions::String::Inflections,
!     ActiveSupport::CoreExtensions::String::Conversions,
!     ActiveSupport::CoreExtensions::String::Access,
!     ActiveSupport::CoreExtensions::String::Unicode,
!     ActiveSupport::CoreExtensions::Numeric::Bytes,
!     ActiveSupport::CoreExtensions::Numeric::Time,
!     Base64::Deprecated, Base64, PP::ObjectMixin,
!     Bio::Shell
    ]
    HIDE_MODULES << WEBrick if defined?(WEBrick)
--- 4,8 ----
  
    HIDE_MODULES = [
!     Base64::Deprecated, Base64, PP::ObjectMixin, Bio::Shell,
    ]
    HIDE_MODULES << WEBrick if defined?(WEBrick)
***************
*** 63,67 ****
      script, result, output = Bio::Shell.cache[:results].restore(number)
      @class = result.class
!     @methods = result.methods - HIDE_METHODS
  
      render :update do |page|
--- 54,58 ----
      script, result, output = Bio::Shell.cache[:results].restore(number)
      @class = result.class
!     @methods = (result.methods - HIDE_METHODS).sort
  
      render :update do |page|

Index: _modules.rhtml
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_modules.rhtml,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** _modules.rhtml	24 Dec 2006 08:27:15 -0000	1.1
--- _modules.rhtml	9 Jul 2007 11:14:29 -0000	1.2
***************
*** 1,2 ****
  [ <%= @class %> ]
! <%= @modules.map {|x| reference_link(x) }.join(" | ") %>
--- 1,4 ----
  [ <%= @class %> ]
! <div id="module_list">
! <%= @modules.map {|x| reference_link(x) }.sort.join("<br>") %>
! </div>
\ No newline at end of file

Index: bioruby.css
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.css,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** bioruby.css	28 Mar 2007 09:21:45 -0000	1.4
--- bioruby.css	9 Jul 2007 11:14:29 -0000	1.5
***************
*** 2,8 ****
  
  body {
! 	color: #6e8377;
! 	background-color: #ffffff;
! 	font-family: verdana, arial, helvetica, sans-serif;
  }
  
--- 2,50 ----
  
  body {
! 	margin: 0;
! 	color: #555555;
! 	background: url("/images/bg.gif") repeat-y center;
! 	font-family: "trebuchet ms", verdana, arial, helvetica, sans-serif;
! 	font-size: 12px;
! }
! 
! div#content {
! 	width: 750px;
! 	height: auto;
! 	margin: 0 auto 0 auto;
! 	text-align: left;
! }
! 
! /* title */
! 
! div#title {
! 	width: 550px;
! 	padding-right: 200px;
! 	margin-bottom: 20px;
! 	text-align: left;
! 	background: url("/images/bioruby.png") no-repeat left bottom;
! }
! 
! div#title .titletop {
! 	color: #736451;
! 	font-size: 30px;
! 	font-weight: normal;
! 	text-align: left;
! 	text-indent: 70px;
! 	margin: 0;
! 	padding: 0;
! 	padding-top: 20px;
! 	margin-bottom: 10px;
! }
! 
! div#title .titlesub {
! 	color: #000000;
! 	font-size: 15px;
! 	font-weight: normal;
! 	text-align: left;
! 	text-indent: 70px;
! 	margin: 0;
! 	padding: 0;
! 	border-bottom: 1px solid #eeeeee;
  }
  
***************
*** 10,14 ****
  
  div#main {
! 	width: 700px;
  	background-color: #ffffff;
  	padding-top: 0px;
--- 52,56 ----
  
  div#main {
! 	width: 550px;
  	background-color: #ffffff;
  	padding-top: 0px;
***************
*** 20,23 ****
--- 62,66 ----
  	border: 1px solid #f00;
  }
+ 
  div#notice p {
  	margin: 0;
***************
*** 32,38 ****
--- 75,89 ----
  	border-width: 1px;
  	padding: 5px;
+ 	width: 500px;
  	overflow: auto;
  }
  
+ div.log {
+ 	width: 500px;
+ 	margin-top: 15px;
+ 	padding-top: 5px;
+ 	border-top: 1px dotted #333333;
+ }
+ 
  div.log div.input pre.script {
  	background-color: #ffffeb;
***************
*** 66,73 ****
  }
  
! div.log hr.result {
  	border-style: dotted none none none;
  	border-top-width: 1px;
  	border-color: #6e8377;
  	height: 1px;
  }
--- 117,125 ----
  }
  
! div.log hr.log {
  	border-style: dotted none none none;
  	border-top-width: 1px;
  	border-color: #6e8377;
+ 	width: 200px;
  	height: 1px;
  }
***************
*** 77,88 ****
  div#side {
  	width: 150px;
! 	background-color: #ffffff;
! 	position: absolute;
! 	top: 10px;
! 	left: 10px;
  }
  
  div#side div.title {
  	border-width: 0px 0px 1px 0px;
  }
  
--- 129,169 ----
  div#side {
  	width: 150px;
! 	float: right;
! 	margin-top: 20px;
! 	text-align: left;
! 	font-size: 12px;
! 	color: #e44268;
  }
  
  div#side div.title {
+ 	font-weight: normal;
+ 	color: #e44268;
+ 	text-align: left;
  	border-width: 0px 0px 1px 0px;
+ 	border-bottom: 1px solid #e44268;
+ }
+ 
+ div#side a:link {
+ 	color: #ffffff;
+ 	text-decoration: none;
+ }
+ 
+ div#side a:visited {
+ 	color: #ffffff;
+ 	text-decoration: none;
+ }
+ 
+ div#side a:hover {
+ 	color: #cccccc;
+ 	text-decoration: underline;
+ }
+ 
+ div#side ol,ul {
+ 	margin: 10px;
+ 	padding-left: 10px;
+ }
+ 
+ div#side li {
+ 	color: #e44268;
  }
  
***************
*** 93,97 ****
  /* history */
  
! div#history { 
  }
  
--- 174,179 ----
  /* history */
  
! div#history {
! 	width: 500px;
  }
  
***************
*** 108,111 ****
--- 190,199 ----
  }
  
+ /* command */
+ 
+ div#command {
+ 	width: 500px;
+ }
+ 
  /* image */
  
***************
*** 115,118 ****
--- 203,207 ----
  	margin-left: auto;
  	margin-right: auto;
+ 	border: 0px;
  }
  
***************
*** 208,216 ****
  }
  
- table#list_methods {
- 	width: 680px;
- 	border: none;
- }
- 
  th {
  	vertical-align: top;
--- 297,300 ----
***************
*** 223,234 ****
  }
  
  
  /* textarea */
  
  textarea {
  	font-family: monospace;
! 	font-size: 100%;
  	overflow: auto;
! 	width: 80%;
  }
  
--- 307,346 ----
  }
  
+ div#method_list table {
+ 	border: none;
+ }
+ 
+ 
+ /* form */
+ 
+ input {
+ 	background-color: #FFFFFF;
+ 	padding: 2px;
+ 	font-size: 10px;
+ 	color: #666666;
+ 	border: 1px solid #611022;
+ 	margin-bottom: 2px;
+ }
+ 
+ input[type=submit] {
+ 	background-color: #FFFFFF;
+ 	padding: 2px;
+ 	font-size: 10px;
+ 	color: #ffffff;
+ 	border: 1px solid #611022;
+ 	background-color: #E44268;
+ 	margin-bottom: 2px;
+ }
  
  /* textarea */
  
  textarea {
+ 	background: url("/images/console.png") no-repeat center;
+ 	background-color: #eaedeb;
  	font-family: monospace;
! 	font-size: 12px;
  	overflow: auto;
! 	width: 500px;
! 	padding: 5px;
  }
  
***************
*** 252,256 ****
  
  @media screen {
! 	div#main	{ margin-left: 150px; }
  	div#side	{ display: block; }
  }
--- 364,368 ----
  
  @media screen {
! 	div#main	{ margin-left: 0px; }
  	div#side	{ display: block; }
  }

--- NEW FILE: console.png ---
(This appears to be a binary file; contents omitted.)

Index: _methods.rhtml
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_methods.rhtml,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** _methods.rhtml	16 Jan 2007 05:47:05 -0000	1.2
--- _methods.rhtml	9 Jul 2007 11:14:29 -0000	1.3
***************
*** 1,9 ****
  [ <%= @class %> ]
! <table id="list_methods">
  <tr>
  <%- step = @methods.size / 4 + 1 -%>
  <%- 0.step(@methods.size, step) do |i| -%>
! <td><%= @methods.sort[i, step].join("<br>") %></td>
  <%- end -%>
  </tr>
! </table>
\ No newline at end of file
--- 1,11 ----
  [ <%= @class %> ]
! <div id="method_list">
! <table>
  <tr>
  <%- step = @methods.size / 4 + 1 -%>
  <%- 0.step(@methods.size, step) do |i| -%>
! <td><%= @methods[i, step].join("<br>") %></td>
  <%- end -%>
  </tr>
! </table>
! </div>

Index: index.rhtml
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/index.rhtml,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** index.rhtml	28 Mar 2007 09:21:45 -0000	1.3
--- index.rhtml	9 Jul 2007 11:14:29 -0000	1.4
***************
*** 4,8 ****
  <%- end -%>
  <%= form_remote_tag(:url => {:action => "evaluate"}, :position => "top") %>
! <b>BioRuby script</b>
  <input type="submit" value="Evaluate">
  <input type="reset" value="Clear">
--- 4,9 ----
  <%- end -%>
  <%= form_remote_tag(:url => {:action => "evaluate"}, :position => "top") %>
! <b>BioRuby script:</b>
! <textarea id="script" name="script" rows=10 cols=80></textarea><br>
  <input type="submit" value="Evaluate">
  <input type="reset" value="Clear">
***************
*** 12,19 ****
  <%= link_to_remote "Last 5",   :url => {:action => "results", :limit => 5} %> |
  <%= link_to_remote "Previous", :url => {:action => "results", :limit => 1} %>
! ] or [
! <%= link_to "Clear", :action => "index" %>
! ] results<br>
! <textarea id="script" name="script" rows=10 cols=80></textarea><br>
  <%= end_form_tag %>
  </div>
--- 13,19 ----
  <%= link_to_remote "Last 5",   :url => {:action => "results", :limit => 5} %> |
  <%= link_to_remote "Previous", :url => {:action => "results", :limit => 1} %>
! ] or
! <%= link_to "Hide", :action => "index" %>
! results<br>
  <%= end_form_tag %>
  </div>

Index: _log.rhtml
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_log.rhtml,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** _log.rhtml	16 Jan 2007 05:35:37 -0000	1.1
--- _log.rhtml	9 Jul 2007 11:14:29 -0000	1.2
***************
*** 1,4 ****
  <div id="log_<%= @number %>" class="log">
- <hr class="log">
  <div class="input">
  Input: [<%= link_to_remote @number, :url => {:action => "reload_script", :number => @number} %>]
--- 1,3 ----

--- NEW FILE: bg.gif ---
(This appears to be a binary file; contents omitted.)

Index: bioruby.rhtml
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.rhtml,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** bioruby.rhtml	28 Jun 2007 10:56:25 -0000	1.3
--- bioruby.rhtml	9 Jul 2007 11:14:29 -0000	1.4
***************
*** 1,41 ****
! <html>
  <head>
  <title>BioRuby shell on Rails</title>
  <%= stylesheet_link_tag "bioruby.css" %>
  <%= javascript_include_tag :defaults %>
  </head>
- <body>
- 
- <div id="side">
-  <img src="/images/bioruby.png">
-  <br>
  
!  <div class="title">Project</div>
!  <ul>
!   <li><%= link_to "#{File.basename(project_workdir)}", "file://#{project_workdir}" %>
!  </ul>
  
!  <div class="title">Functions</div>
!  <ul>
!    <li><%= link_to "Console", :action => "index" %></li>
!    <li><%= link_to "History", :action => "history" %></li>
!    <li><%= link_to "Commands", :action => "commands" %></li>
!  </ul>
  
!  <div class="title">Local variables</div>
!  <%= render :partial => "variables" %>
  
!  <br>
!  <a href="http://bioruby.org/"><img src="/images/bioruby.gif" border=0></a>
! </div>
  
  
! <div id="main">
  
! <h1>BioRuby shell on Rails</h1>
  
  <%= yield %>
  
! </div>
  
  </body>
--- 1,47 ----
! <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
! <html xmlns="http://www.w3.org/1999/xhtml">
  <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />	
  <title>BioRuby shell on Rails</title>
  <%= stylesheet_link_tag "bioruby.css" %>
  <%= javascript_include_tag :defaults %>
  </head>
  
! <body>
  
! <div id="content">
  
!  <div id="side">
!   <div class="title">Project</div>
!   <ul>
!    <li><%= link_to "#{File.basename(project_workdir)}", "file://#{project_workdir}" %>
!   </ul>
  
!   <div class="title">Functions</div>
!   <ul>
!     <li><%= link_to "Console", :action => "index" %></li>
!     <li><%= link_to "History", :action => "history" %></li>
!     <li><%= link_to "Commands", :action => "commands" %></li>
!   </ul>
  
+   <div class="title">Local variables</div>
+   <%= render :partial => "variables" %>
  
!   <br>
!   <a href="http://bioruby.org/"><img src="/images/bioruby.gif" border=0></a>
!  </div><!-- side -->
  
!  <div id="title">
!   <p class="titletop">BioRuby shell on Rails</p>
!   <p class="titlesub">Web interface for the BioRuby library</p>
!  </div><!-- title -->
  
+  <div id="main">
  <%= yield %>
+  </div><!-- main -->
  
! </div><!-- content -->
  
  </body>
+ 
+ </html>


From k at dev.open-bio.org  Mon Jul  9 07:17:11 2007
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Mon, 09 Jul 2007 11:17:11 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio shell.rb,1.19,1.20
Message-ID: <200707091117.l69BHB2V030190@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv30184/lib/bio

Modified Files:
	shell.rb 
Log Message:
* added NCBI, EBI, DDBJ web services


Index: shell.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell.rb,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** shell.rb	5 Apr 2007 23:45:10 -0000	1.19
--- shell.rb	9 Jul 2007 11:17:09 -0000	1.20
***************
*** 33,36 ****
--- 33,37 ----
    require 'bio/shell/plugin/das'
    require 'bio/shell/plugin/keggapi'
+   require 'bio/shell/plugin/soap'
    require 'bio/shell/plugin/emboss'
    require 'bio/shell/plugin/blast'


From k at dev.open-bio.org  Mon Jul  9 07:17:11 2007
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Mon, 09 Jul 2007 11:17:11 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/shell/plugin soap.rb,NONE,1.1
Message-ID: <200707091117.l69BHB3x030195@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/shell/plugin
In directory dev.open-bio.org:/tmp/cvs-serv30184/lib/bio/shell/plugin

Added Files:
	soap.rb 
Log Message:
* added NCBI, EBI, DDBJ web services


--- NEW FILE: soap.rb ---
#
# = bio/shell/plugin/soap.rb - web services
#
# Copyright::   Copyright (C) 2006
#               Toshiaki Katayama <k at bioruby.org>
# License::     Ruby's
#
# $Id: soap.rb,v 1.1 2007/07/09 11:17:09 k Exp $
#

module Bio::Shell

  private

  def ncbisoap(wsdl = nil)
    if wsdl
      @ncbisoap = Bio::NCBI::SOAP.new(wsdl)
    else
      @ncbisoap ||= Bio::NCBI::SOAP.new
    end
    return @ncbisoap
  end

  def ebisoap(wsdl = nil)
    case wsdl
    when :ipscan
      @ebisoap = Bio::EBI::SOAP::InterProScan.new(wsdl)
    when :emboss
      @ebisoap = Bio::EBI::SOAP::Emboss.new(wsdl)
    when :clustalw
      @ebisoap = Bio::EBI::SOAP::ClustalW.new(wsdl)
    when :tcoffee
      @ebisoap = Bio::EBI::SOAP::TCoffee.new(wsdl)
    when :muscle
      @ebisoap = Bio::EBI::SOAP::Muscle.new(wsdl)
    when :fasta
      @ebisoap = Bio::EBI::SOAP::Fasta.new(wsdl)
    when :wublast
      @ebisoap = Bio::EBI::SOAP::WUBlast.new(wsdl)
    when :mpsrch
      @ebisoap = Bio::EBI::SOAP::MPsrch.new(wsdl)
    when :scanps
      @ebisoap = Bio::EBI::SOAP::ScanPS.new(wsdl)
    when :msd
      @ebisoap = Bio::EBI::SOAP::MSD.new(wsdl)
    when :ontology
      @ebisoap = Bio::EBI::SOAP::Ontology.new(wsdl)
    when :citation
      @ebisoap = Bio::EBI::SOAP::Citation.new(wsdl)
    when /^http/
      @ebisoap = Bio::EBI::SOAP.new(wsdl)
    else
      @ebisoap ||= Bio::EBI::SOAP.new
    end
    return @ebisoap
  end

  def ddbjsoap(wsdl = nil)
    case wsdl
    when :blast
      @ddbjsoap = Bio::DDBJ::XML::Blast.new
    when :fasta
      @ddbjsoap = Bio::DDBJ::XML::Fasta.new
    when :clustalw
      @ddbjsoap = Bio::DDBJ::XML::ClustalW.new
    when :ddbj
      @ddbjsoap = Bio::DDBJ::XML::DDBJ.new
    when :gib
      @ddbjsoap = Bio::DDBJ::XML::Gib.new
    when :gtop
      @ddbjsoap = Bio::DDBJ::XML::Gtop.new
    when :pml
      @ddbjsoap = Bio::DDBJ::XML::PML.new
    when :srs
      @ddbjsoap = Bio::DDBJ::XML::SRS.new
    when :txsearch
      @ddbjsoap = Bio::DDBJ::XML::TxSearch.new
    when /^http/
      @ddbjsoap = Bio::DDBJ::XML.new(wsdl)
    else
      @ddbjsoap ||= Bio::DDBJ::XML.new
    end
    return @ddbjsoap
  end

end



From k at dev.open-bio.org  Mon Jul  9 07:44:11 2007
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Mon, 09 Jul 2007 11:44:11 +0000
Subject: [BioRuby-cvs]
	bioruby/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates
	bg.gif, 1.1, NONE bioruby.png, 1.1, NONE bioruby.gif, 1.1,
	NONE console.png, 1.1, NONE
Message-ID: <200707091144.l69BiBfw030272@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates
In directory dev.open-bio.org:/tmp/cvs-serv30268

Removed Files:
	bg.gif bioruby.png bioruby.gif console.png 
Log Message:
* images are renamed to be prefixed with bioruby-


--- bioruby.gif DELETED ---

--- bg.gif DELETED ---

--- bioruby.png DELETED ---

--- console.png DELETED ---


From k at dev.open-bio.org  Mon Jul  9 07:46:02 2007
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Mon, 09 Jul 2007 11:46:02 +0000
Subject: [BioRuby-cvs]
	bioruby/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates
	bioruby-bg.gif, NONE, 1.1 bioruby-console.png, NONE,
	1.1 bioruby-gem.png, NONE, 1.1 bioruby-link.gif, NONE,
	1.1 bioruby.css, 1.5, 1.6 bioruby.rhtml, 1.4, 1.5
Message-ID: <200707091146.l69Bk2CU030345@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates
In directory dev.open-bio.org:/tmp/cvs-serv30339/d

Modified Files:
	bioruby.css bioruby.rhtml 
Added Files:
	bioruby-bg.gif bioruby-console.png bioruby-gem.png 
	bioruby-link.gif 
Log Message:
* images are renamed to be prefixed by 'bioruby-' to avoid confliction
  with already existing files in /public/images


--- NEW FILE: bioruby-bg.gif ---
(This appears to be a binary file; contents omitted.)

--- NEW FILE: bioruby-console.png ---
(This appears to be a binary file; contents omitted.)

--- NEW FILE: bioruby-link.gif ---
(This appears to be a binary file; contents omitted.)

Index: bioruby.css
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.css,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** bioruby.css	9 Jul 2007 11:14:29 -0000	1.5
--- bioruby.css	9 Jul 2007 11:46:00 -0000	1.6
***************
*** 4,8 ****
  	margin: 0;
  	color: #555555;
! 	background: url("/images/bg.gif") repeat-y center;
  	font-family: "trebuchet ms", verdana, arial, helvetica, sans-serif;
  	font-size: 12px;
--- 4,8 ----
  	margin: 0;
  	color: #555555;
! 	background: url("/images/bioruby-bg.gif") repeat-y center;
  	font-family: "trebuchet ms", verdana, arial, helvetica, sans-serif;
  	font-size: 12px;
***************
*** 23,27 ****
  	margin-bottom: 20px;
  	text-align: left;
! 	background: url("/images/bioruby.png") no-repeat left bottom;
  }
  
--- 23,27 ----
  	margin-bottom: 20px;
  	text-align: left;
! 	background: url("/images/bioruby-gem.png") no-repeat left bottom;
  }
  
***************
*** 336,340 ****
  
  textarea {
! 	background: url("/images/console.png") no-repeat center;
  	background-color: #eaedeb;
  	font-family: monospace;
--- 336,340 ----
  
  textarea {
! 	background: url("/images/bioruby-console.png") no-repeat center;
  	background-color: #eaedeb;
  	font-family: monospace;

--- NEW FILE: bioruby-gem.png ---
(This appears to be a binary file; contents omitted.)

Index: bioruby.rhtml
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.rhtml,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** bioruby.rhtml	9 Jul 2007 11:14:29 -0000	1.4
--- bioruby.rhtml	9 Jul 2007 11:46:00 -0000	1.5
***************
*** 29,33 ****
  
    <br>
!   <a href="http://bioruby.org/"><img src="/images/bioruby.gif" border=0></a>
   </div><!-- side -->
  
--- 29,33 ----
  
    <br>
!   <a href="http://bioruby.org/"><img src="/images/bioruby-link.gif" border=0></a>
   </div><!-- side -->
  


From k at dev.open-bio.org  Mon Jul  9 07:46:02 2007
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Mon, 09 Jul 2007 11:46:02 +0000
Subject: [BioRuby-cvs]
	bioruby/lib/bio/shell/rails/vendor/plugins/generators/bioruby
	bioruby_generator.rb, 1.4, 1.5
Message-ID: <200707091146.l69Bk2Dw030351@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/shell/rails/vendor/plugins/generators/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv30339

Modified Files:
	bioruby_generator.rb 
Log Message:
* images are renamed to be prefixed by 'bioruby-' to avoid confliction
  with already existing files in /public/images


Index: bioruby_generator.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/rails/vendor/plugins/generators/bioruby/bioruby_generator.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** bioruby_generator.rb	9 Jul 2007 11:14:29 -0000	1.4
--- bioruby_generator.rb	9 Jul 2007 11:46:00 -0000	1.5
***************
*** 19,26 ****
        m.file 'index.rhtml',           'app/views/bioruby/index.rhtml'
        m.file 'bioruby.rhtml',         'app/views/layouts/bioruby.rhtml'
!       m.file 'bioruby.png',           'public/images/bioruby.png'
!       m.file 'bioruby.gif',           'public/images/bioruby.gif'
!       m.file 'bg.gif',                'public/images/bg.gif'
!       m.file 'console.png',           'public/images/console.png'
        m.file 'bioruby.css',           'public/stylesheets/bioruby.css'
      end
--- 19,26 ----
        m.file 'index.rhtml',           'app/views/bioruby/index.rhtml'
        m.file 'bioruby.rhtml',         'app/views/layouts/bioruby.rhtml'
!       m.file 'bioruby-gem.png',       'public/images/bioruby-gem.png'
!       m.file 'bioruby-link.gif',      'public/images/bioruby-link.gif'
!       m.file 'bioruby-bg.gif',        'public/images/bioruby-bg.gif'
!       m.file 'bioruby-console.png',   'public/images/bioruby-console.png'
        m.file 'bioruby.css',           'public/stylesheets/bioruby.css'
      end


From ngoto at dev.open-bio.org  Mon Jul  9 10:08:36 2007
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Mon, 09 Jul 2007 14:08:36 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/io flatfile.rb,1.59,1.60
Message-ID: <200707091408.l69E8aAC030730@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv30708/lib/bio/io

Modified Files:
	flatfile.rb 
Log Message:
Bio::FlatFile.foreach is added (which is suggested by IO.foreach).


Index: flatfile.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/flatfile.rb,v
retrieving revision 1.59
retrieving revision 1.60
diff -C2 -d -r1.59 -r1.60
*** flatfile.rb	14 Apr 2007 02:29:45 -0000	1.59
--- flatfile.rb	9 Jul 2007 14:08:34 -0000	1.60
***************
*** 509,512 ****
--- 509,526 ----
      end
  
+     # Executes the block for every entry in the stream.
+     # Same as FlatFile.open(*arg) { |ff| ff.each { |entry| ... }}.
+     # 
+     # * Example
+     #     Bio::FlatFile.foreach('test.fst') { |e| puts e.definition }
+     #
+     def self.foreach(*arg)
+       self.open(*arg) do |flatfileobj|
+         flatfileobj.each do |entry|
+           yield entry
+         end
+       end
+     end
+ 
      # Same as FlatFile.open, except that 'stream' should be a opened
      # stream object (IO, File, ..., who have the 'gets' method).


From ngoto at dev.open-bio.org  Mon Jul  9 10:08:36 2007
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Mon, 09 Jul 2007 14:08:36 +0000
Subject: [BioRuby-cvs] bioruby ChangeLog,1.63,1.64
Message-ID: <200707091408.l69E8a7M030733@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv30708

Modified Files:
	ChangeLog 
Log Message:
Bio::FlatFile.foreach is added (which is suggested by IO.foreach).


Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.63
retrieving revision 1.64
diff -C2 -d -r1.63 -r1.64
*** ChangeLog	2 Apr 2007 12:55:26 -0000	1.63
--- ChangeLog	9 Jul 2007 14:08:34 -0000	1.64
***************
*** 1,2 ****
--- 1,8 ----
+ 2007-07-09  Naohisa Goto <ng at bioruby.org>
+ 
+ 	* lib/bio/io/flatfile.rb
+ 
+ 	Bio::FlatFile.foreach is added (which is suggested by IO.foreach).
+ 
  2007-04-02  Naohisa Goto <ng at bioruby.org>
  


From ngoto at dev.open-bio.org  Tue Jul 10 06:44:49 2007
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Tue, 10 Jul 2007 10:44:49 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db/pdb pdb.rb,1.22,1.23
Message-ID: <200707101044.l6AAinvO001327@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db/pdb
In directory dev.open-bio.org:/tmp/cvs-serv1303/lib/bio/db/pdb

Modified Files:
	pdb.rb 
Log Message:
Pdb_LString.new is changed not to raise error for nil.

Fixed a bug when below records does not exist in a PDB entry:
REMARK (remark), JRNL (jrnl), HELIX (helix),
TURN (turn), SHEET (sheet), SSBOND (ssbond), SEQRES (seqres),
DBREF (dbref), KEYWDS (keywords), AUTHOR (authors),
HEADER (entry_id, accession, classification),
TITLE (definition), and REVDAT (version) records (methods).

Incompatible change: Bio::PDB#record is changed to return
an empty array for nonexistent record.

Thanks to Dr. Mikael Borg. (Re: [BioRuby] Preparing for 1.1 release)



Index: pdb.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/pdb.rb,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** pdb.rb	19 Apr 2007 13:59:29 -0000	1.22
--- pdb.rb	10 Jul 2007 10:44:46 -0000	1.23
***************
*** 120,124 ****
          end
          def self.new(str)
!           String.new(str)
          end
        end
--- 120,124 ----
          end
          def self.new(str)
!           String.new(str.to_s)
          end
        end
***************
*** 1675,1679 ****
      #
      def record(name = nil)
!       name ? @hash[name] : @hash
      end
  
--- 1675,1679 ----
      #
      def record(name = nil)
!       name ? (@hash[name] || []) : @hash
      end
  
***************
*** 1838,1847 ****
      # Classification in "HEADER".
      def classification
!       self.record('HEADER').first.classification
      end
  
      # Get authors in "AUTHOR".
      def authors
!       self.record('AUTHOR').first.authorList
      end
  
--- 1838,1848 ----
      # Classification in "HEADER".
      def classification
!       f = self.record('HEADER').first
!       f ? f.classification : nil
      end
  
      # Get authors in "AUTHOR".
      def authors
!       self.record('AUTHOR').collect { |f| f.authorList }.flatten
      end
  
***************
*** 1852,1856 ****
      # PDB identifier written in "HEADER". (e.g. 1A00)
      def entry_id
!       @id = self.record('HEADER').first.idCode unless @id
        @id
      end
--- 1853,1860 ----
      # PDB identifier written in "HEADER". (e.g. 1A00)
      def entry_id
!       unless @id
!         f = self.record('HEADER').first
!         @id = f ? f.idCode : nil
!       end
        @id
      end
***************
*** 1863,1872 ****
      # Title of this entry in "TITLE".
      def definition
!       self.record('TITLE').first.title
      end
  
      # Current modification number in "REVDAT".
      def version
!       self.record('REVDAT').first.modNum
      end
  
--- 1867,1878 ----
      # Title of this entry in "TITLE".
      def definition
!       f = self.record('TITLE').first
!       f ? f.title : nil
      end
  
      # Current modification number in "REVDAT".
      def version
!       f = self.record('REVDAT').first
!       f ? f.modNum : nil
      end
  


From ngoto at dev.open-bio.org  Tue Jul 10 06:44:49 2007
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Tue, 10 Jul 2007 10:44:49 +0000
Subject: [BioRuby-cvs] bioruby/doc Changes-0.7.rd,1.21,1.22
Message-ID: <200707101044.l6AAine2001333@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/doc
In directory dev.open-bio.org:/tmp/cvs-serv1303/doc

Modified Files:
	Changes-0.7.rd 
Log Message:
Pdb_LString.new is changed not to raise error for nil.

Fixed a bug when below records does not exist in a PDB entry:
REMARK (remark), JRNL (jrnl), HELIX (helix),
TURN (turn), SHEET (sheet), SSBOND (ssbond), SEQRES (seqres),
DBREF (dbref), KEYWDS (keywords), AUTHOR (authors),
HEADER (entry_id, accession, classification),
TITLE (definition), and REVDAT (version) records (methods).

Incompatible change: Bio::PDB#record is changed to return
an empty array for nonexistent record.

Thanks to Dr. Mikael Borg. (Re: [BioRuby] Preparing for 1.1 release)



Index: Changes-0.7.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Changes-0.7.rd,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** Changes-0.7.rd	23 Apr 2007 16:03:24 -0000	1.21
--- Changes-0.7.rd	10 Jul 2007 10:44:47 -0000	1.22
***************
*** 259,262 ****
--- 259,264 ----
    name field for selecting atoms, because the element field is not useful
    for selecting atoms and is not used in many pdb files.
+ * Bio::PDB#record is changed to return an empty array instead of nil
+   for a nonexistent record.
  
  --- Bio::FlatFile


From ngoto at dev.open-bio.org  Tue Jul 10 06:44:49 2007
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Tue, 10 Jul 2007 10:44:49 +0000
Subject: [BioRuby-cvs] bioruby ChangeLog,1.64,1.65
Message-ID: <200707101044.l6AAin4J001330@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv1303

Modified Files:
	ChangeLog 
Log Message:
Pdb_LString.new is changed not to raise error for nil.

Fixed a bug when below records does not exist in a PDB entry:
REMARK (remark), JRNL (jrnl), HELIX (helix),
TURN (turn), SHEET (sheet), SSBOND (ssbond), SEQRES (seqres),
DBREF (dbref), KEYWDS (keywords), AUTHOR (authors),
HEADER (entry_id, accession, classification),
TITLE (definition), and REVDAT (version) records (methods).

Incompatible change: Bio::PDB#record is changed to return
an empty array for nonexistent record.

Thanks to Dr. Mikael Borg. (Re: [BioRuby] Preparing for 1.1 release)



Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.64
retrieving revision 1.65
diff -C2 -d -r1.64 -r1.65
*** ChangeLog	9 Jul 2007 14:08:34 -0000	1.64
--- ChangeLog	10 Jul 2007 10:44:47 -0000	1.65
***************
*** 1,4 ****
--- 1,22 ----
  2007-07-09  Naohisa Goto <ng at bioruby.org>
  
+ 	* lib/bio/db/pdb/pdb.rb
+ 
+ 	Pdb_LString.new is changed not to raise error for nil.
+ 
+ 	Fixed a bug when below records does not exist in a PDB entry:
+ 	REMARK (remark), JRNL (jrnl), HELIX (helix),
+ 	TURN (turn), SHEET (sheet), SSBOND (ssbond), SEQRES (seqres),
+ 	DBREF (dbref), KEYWDS (keywords), AUTHOR (authors),
+ 	HEADER (entry_id, accession, classification),
+ 	TITLE (definition), and REVDAT (version) records (methods).
+ 
+ 	Incompatible change: Bio::PDB#record is changed to return
+ 	an empty array for nonexistent record.
+ 
+ 	(reported by Mikael Borg)
+ 
+ 2007-07-09  Naohisa Goto <ng at bioruby.org>
+ 
  	* lib/bio/io/flatfile.rb
  


From ngoto at dev.open-bio.org  Mon Jul 16 08:15:44 2007
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Mon, 16 Jul 2007 12:15:44 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/appl/mafft - New directory
Message-ID: <200707161215.l6GCFiOG019861@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/appl/mafft
In directory dev.open-bio.org:/tmp/cvs-serv19841/test/unit/bio/appl/mafft

Log Message:
Directory /home/repository/bioruby/bioruby/test/unit/bio/appl/mafft added to the repository



From ngoto at dev.open-bio.org  Mon Jul 16 08:21:41 2007
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Mon, 16 Jul 2007 12:21:41 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio alignment.rb,1.22,1.23
Message-ID: <200707161221.l6GCLfRO019956@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv19932/lib/bio

Modified Files:
	alignment.rb 
Log Message:
* lib/bio/mafft/report.rb
  For generic multi-fasta formatted sequence alignment,
  Bio::Alignment::MultiFastaFormat is newly added based on
  Bio::MAFFT::Report class, and Bio::MAFFT::Report is
  changed to inherit the new class.
  Tests are added in test/unit/bio/appl/mafft/test_report.rb.
* lib/bio/alignment.rb
  added autoload of Bio::Alignment::MultiFastaFormat.
  New modules and classes Bio::Alignment::FactoryTemplate::* are added.


Index: alignment.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/alignment.rb,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** alignment.rb	5 Apr 2007 23:35:39 -0000	1.22
--- alignment.rb	16 Jul 2007 12:21:39 -0000	1.23
***************
*** 22,25 ****
--- 22,27 ----
  #
  
+ require 'tempfile'
+ require 'bio/command'
  require 'bio/sequence'
  
***************
*** 71,74 ****
--- 73,78 ----
    module Alignment
  
+     autoload :MultiFastaFormat, 'bio/appl/mafft/report'
+ 
      # Bio::Alignment::PropertyMethods is a set of methods to treat
      # the gap character and so on.
***************
*** 2195,2198 ****
--- 2199,2514 ----
        OriginalAlignment.readfiles(*files)
      end
+ 
+     #---
+     # Service classes for multiple alignment applications
+     #+++
+     #---
+     # Templates of alignment application factory
+     #+++
+ 
+     # Namespace for templates for alignment application factory
+     module FactoryTemplate
+ 
+       # Template class for alignment application factory.
+       # The program acts:
+       # input: stdin or file, format = fasta format
+       # output: stdout (parser should be specified by DEFAULT_PARSER)
+       class Simple
+ 
+         # Creates a new alignment factory
+         def initialize(program = self.class::DEFAULT_PROGRAM, options = [])
+           @program = program
+           @options = options
+           @command = nil
+           @output = nil
+           @report = nil
+           @exit_status = nil
+           @data_stdout = nil
+         end
+ 
+         # program name
+         attr_accessor :program
+ 
+         # options
+         attr_accessor :options
+ 
+         # Last command-line string. Returns nil or an array of String.
+         # Note that filenames described in the command-line may already
+         # be removed because these files may be temporary files.
+         attr_reader :command
+ 
+         # Last raw result of the program.
+         # Return a string (or nil).
+         attr_reader :output
+ 
+         # Last result object performed by the factory.
+         attr_reader :report
+ 
+         # Last exit status
+         attr_reader :exit_status
+ 
+         # Last output to the stdout.
+         attr_accessor :data_stdout
+ 
+         # Clear the internal data and status, except program and options.
+         def reset
+           @command = nil
+           @output = nil
+           @report = nil
+           @exit_status = nil
+           @data_stdout = nil
+         end
+ 
+         # Executes the program.
+         # If +seqs+ is not nil, perform alignment for seqs.
+         # If +seqs+ is nil, simply executes the program.
+         #
+         # Compatibility note: When seqs is nil,
+         # returns true if the program exits normally, and
+         # returns false if the program exits abnormally.
+         def query(seqs)
+           if seqs then
+             query_alignment(seqs)
+           else
+             exec_local(@options)
+             @exit_status.exitstatus == 0 ? true : false
+           end
+         end
+ 
+         # Performs alignment for seqs.
+         # +seqs+ should be Bio::Alignment or Array of sequences or nil.
+         def query_alignment(seqs)
+           unless seqs.respond_to?(:output_fasta) then
+             seqs = Bio::Alignment.new(seqs)
+           end
+           query_string(seqs.output_fasta(:width => 70))
+         end
+ 
+         # alias of query_alignment.
+         #
+         # Compatibility Note: query_align will renamed to query_alignment.
+         def query_align(seqs)
+           #warn 'query_align is renamed to query_alignment.'
+           query_alignment(seqs)
+         end
+ 
+         # Performs alignment for +str+.
+         # The +str+ should be a string that can be recognized by the program.
+         def query_string(str)
+           _query_string(str, @options)
+           @report
+         end
+ 
+         # Performs alignment of sequences in the file named +fn+.
+         def query_by_filename(filename_in)
+           _query_local(filename_in, @options)
+           @report
+         end
+ 
+         private
+         # Executes a program in the local machine.
+         def exec_local(opt, data_stdin = nil)
+           @exit_status = nil
+           @command = [ @program, *opt ]
+           #STDERR.print "DEBUG: ", @command.join(" "), "\n"
+           @data_stdout = Bio::Command.query_command(@command, data_stdin)
+           @exit_status = $?
+         end
+ 
+         # prepare temporary file
+         def _prepare_tempfile(str = nil)
+           tf_in = Tempfile.open(str ? 'alignment_i' :'alignment_o')
+           tf_in.print str if str
+           tf_in.close(false)
+           tf_in
+         end
+ 
+         # generates options specifying input/output filename.
+         # nil for filename means stdin or stdout.
+         # +options+ must not contain specify filenames.
+         # returns an array of string.
+         def _generate_options(infile, outfile, options)
+           options +
+             (infile ? _option_input_file(infile) : _option_input_stdin) +
+             (outfile ? _option_output_file(outfile) : _option_output_stdout)
+         end
+ 
+         # generates options specifying input filename.
+         # returns an array of string
+         def _option_input_file(fn)
+           [ fn ]
+         end
+ 
+         # generates options specifying output filename.
+         # returns an array of string
+         def _option_output_file(fn)
+           raise 'can not specify output file: always stdout'
+         end
+ 
+         # generates options specifying that input is taken from stdin.
+         # returns an array of string
+         def _option_input_stdin
+           []
+         end
+ 
+         # generates options specifying output to stdout.
+         # returns an array of string
+         def _option_output_stdout
+           []
+         end
+       end #class Simple
+ 
+       # mix-in module
+       module WrapInputStdin
+         private
+         # Performs alignment for +str+.
+         # The +str+ should be a string that can be recognized by the program.
+         def _query_string(str, opt)
+           _query_local(nil, opt, str)
+         end
+       end #module WrapInputStdin
+ 
+       # mix-in module
+       module WrapInputTempfile
+         private
+         # Performs alignment for +str+.
+         # The +str+ should be a string that can be recognized by the program.
+         def _query_string(str, opt)
+           begin
+             tf_in = _prepare_tempfile(str)
+             ret = _query_local(tf_in.path, opt, nil)
+           ensure
+             tf_in.close(true) if tf_in
+           end
+           ret
+         end
+       end #module WrapInputTempfile
+ 
+       # mix-in module
+       module WrapOutputStdout
+         private
+         # Performs alignment by specified filenames
+         def _query_local(fn_in, opt, data_stdin = nil)
+           opt = _generate_options(fn_in, nil, opt)
+           exec_local(opt, data_stdin)
+           @output = @data_stdout
+           @report = self.class::DEFAULT_PARSER.new(@output)
+           @report
+         end
+       end #module WrapOutputStdout
+ 
+       # mix-in module
+       module WrapOutputTempfile
+         private
+         # Performs alignment
+         def _query_local(fn_in, opt, data_stdin = nil)
+           begin
+             tf_out = _prepare_tempfile()
+             opt = _generate_options(fn_in, tf_out.path, opt)
+             exec_local(opt, data_stdin)
+             tf_out.open
+             @output = tf_out.read
+           ensure
+             tf_out.close(true) if tf_out
+           end
+           @report = self.class::DEFAULT_PARSER.new(@output)
+           @report
+         end
+       end #module WrapOutputTempfile
+ 
+       # Template class for alignment application factory.
+       # The program needs:
+       # input: file (cannot accept stdin), format = fasta format
+       # output: stdout (parser should be specified by DEFAULT_PARSER)
+       class FileInStdoutOut < Simple
+         include Bio::Alignment::FactoryTemplate::WrapInputTempfile
+         include Bio::Alignment::FactoryTemplate::WrapOutputStdout
+ 
+         private
+         # generates options specifying that input is taken from stdin.
+         # returns an array of string
+         def _option_input_stdin
+           raise 'input is always a file'
+         end
+       end #class FileInStdoutOut
+ 
+       # Template class for alignment application factory.
+       # The program needs:
+       # input: stdin or file, format = fasta format
+       # output: file (parser should be specified by DEFAULT_PARSER)
+       class StdinInFileOut < Simple
+         include Bio::Alignment::FactoryTemplate::WrapInputStdin
+         include Bio::Alignment::FactoryTemplate::WrapOutputTempfile
+ 
+         private
+         # generates options specifying output to stdout.
+         # returns an array of string
+         def _option_output_stdout
+           raise 'output is always a file'
+         end
+       end #class StdinInFileOut
+ 
+       # Template class for alignment application factory.
+       # The program needs:
+       # input: file (cannot accept stdin), format = fasta format
+       # output: file (parser should be specified by DEFAULT_PARSER)
+       class FileInFileOut < Simple
+         include Bio::Alignment::FactoryTemplate::WrapInputTempfile
+         include Bio::Alignment::FactoryTemplate::WrapOutputTempfile
+ 
+         private
+         # generates options specifying that input is taken from stdin.
+         # returns an array of string
+         def _option_input_stdin
+           raise 'input is always a file'
+         end
+ 
+         # generates options specifying output to stdout.
+         # returns an array of string
+         def _option_output_stdout
+           raise 'output is always a file'
+         end
+       end #class FileInFileOut
+ 
+       # Template class for alignment application factory.
+       # The program needs:
+       # input: file (cannot accept stdin), format = fasta format
+       # output: file (parser should be specified by DEFAULT_PARSER)
+       # Tree (*.dnd) output is also supported.
+       class FileInFileOutWithTree < FileInFileOut
+ 
+         # alignment guide tree generated by the program (*.dnd file)
+         attr_reader :output_dnd
+ 
+         def reset
+           @output_dnd = nil
+           super
+         end
+ 
+         private
+         # Performs alignment
+         def _query_local(fn_in, opt, data_stdin = nil)
+           begin
+             tf_dnd = _prepare_tempfile()
+             opt = opt + _option_output_dndfile(tf_dnd.path)
+             ret = super(fn_in, opt, data_stdin)
+             tf_dnd.open
+             @output_dnd = tf_dnd.read
+           ensure
+             tf_dnd.close(true) if tf_dnd
+           end
+           ret
+         end
+ 
+         # generates options specifying output tree file (*.dnd).
+         # returns an array of string
+         def _option_output_dndfile
+           raise NotImplementedError
+         end
+       end #class FileInFileOutWithTree
+ 
+     end #module FactoryTemplate
+ 
+ 
    end #module Alignment
  


From ngoto at dev.open-bio.org  Mon Jul 16 08:21:41 2007
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Mon, 16 Jul 2007 12:21:41 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/appl/mafft test_report.rb, NONE,
	1.1
Message-ID: <200707161221.l6GCLfbB019966@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/appl/mafft
In directory dev.open-bio.org:/tmp/cvs-serv19932/test/unit/bio/appl/mafft

Added Files:
	test_report.rb 
Log Message:
* lib/bio/mafft/report.rb
  For generic multi-fasta formatted sequence alignment,
  Bio::Alignment::MultiFastaFormat is newly added based on
  Bio::MAFFT::Report class, and Bio::MAFFT::Report is
  changed to inherit the new class.
  Tests are added in test/unit/bio/appl/mafft/test_report.rb.
* lib/bio/alignment.rb
  added autoload of Bio::Alignment::MultiFastaFormat.
  New modules and classes Bio::Alignment::FactoryTemplate::* are added.


--- NEW FILE: test_report.rb ---
#
# test/unit/bio/appl/mafft/test_report.rb - Unit test for Bio::Alignment::MultiFastaFormat
#
# Copyright::  Copyright (C) 2007
#              2005 Naohisa Goto <ng at bioruby.org>
# License::    The Ruby License
#
#  $Id: test_report.rb,v 1.1 2007/07/16 12:21:39 ngoto Exp $
#

require 'pathname'
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
$:.unshift(libpath) unless $:.include?(libpath)

require 'test/unit'

require 'bio'

module Bio
  class TestAlignmentMultiFastaFormat < Test::Unit::TestCase
    def setup
      @na = Bio::Alignment::MultiFastaFormat.new <<__END_OF_NASEQS__
>naseq1
TAGATTTCGAATTTCTAGnGAACCGAACCGkACAGCCTTACATyATTCAGACCAATGTGT
TACCAATTCGAGTATACAAGAACAGTGATAAGGTACCAAACAACGACTTCTTCCCGAACC
>naseq2
TAGATTTCGAATCTAGGGAATCCGATACGGACAGCCTTACATTATTCAGACCAATGTGTA
TACCAATTCGAGAATACAAGAACGTGATAAGGTACCCAAACAACGACTTCTTCCCGAACC
>naseq3
TAGATTTCGAATCTAGGGAATCCGATACCGGACAGCCTTACATTATTCAGACCAATGTGT
TACCAATTCGAGAATACAAGAACGTGATAAGGTACCCAAACAACGACTTCTTCCCGAACC
__END_OF_NASEQS__

      @aa = Bio::Alignment::MultiFastaFormat.new <<__END_OF_AASEQS__
>aaseq1
MVHWTAEEKQLITGLWGKVNVAECGAEALARLLIVYPWTQRFFASFGNLSSPTAILGNPMVRAHGKKVLT
>aaseq2
MLTAEEKAAVTGFWGKVKVDEVGAEALGRLLVVYPWTQRFFEHFGDLSSADAVMNNAKVKAHGKKVLDSF
>aaseq3
MVHLTDAEKSAVSCLWAKVNPDEVGGEALGRLLVVYPWTQRYFDSFGDLSSASAIMGNPKVKAHGKKVIT
>aaseq4
MVHLTDAEKAAVNGLWGKVNPDDVGGEALGRLLVVYPWTQRYFDSFGDLSSASAIMGNPKVKAHGKKVIN
__END_OF_AASEQS__
    end #def setup

    def test_alignment
      assert_equal(120, @na.alignment.alignment_length)
      assert_equal(70, @aa.alignment.alignment_length)
    end

    def test_entries
      assert_equal(3, @na.entries.size)
      assert_equal(4, @aa.entries.size)
    end

    def test_determine_seq_method
      @na.alignment
      assert_equal(:naseq, @na.instance_eval { @seq_method })
      @aa.alignment
      assert_equal(:aaseq, @aa.instance_eval { @seq_method })
    end
  end #class TestAlignmentMultiFastaFormat
end #module Bio


From ngoto at dev.open-bio.org  Mon Jul 16 08:21:41 2007
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Mon, 16 Jul 2007 12:21:41 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/mafft report.rb,1.12,1.13
Message-ID: <200707161221.l6GCLftT019961@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/mafft
In directory dev.open-bio.org:/tmp/cvs-serv19932/lib/bio/appl/mafft

Modified Files:
	report.rb 
Log Message:
* lib/bio/mafft/report.rb
  For generic multi-fasta formatted sequence alignment,
  Bio::Alignment::MultiFastaFormat is newly added based on
  Bio::MAFFT::Report class, and Bio::MAFFT::Report is
  changed to inherit the new class.
  Tests are added in test/unit/bio/appl/mafft/test_report.rb.
* lib/bio/alignment.rb
  added autoload of Bio::Alignment::MultiFastaFormat.
  New modules and classes Bio::Alignment::FactoryTemplate::* are added.


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/mafft/report.rb,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** report.rb	5 Apr 2007 23:35:40 -0000	1.12
--- report.rb	16 Jul 2007 12:21:39 -0000	1.13
***************
*** 2,6 ****
  # = bio/appl/mafft/report.rb - MAFFT report class
  #
! # Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
  # License::   The Ruby License
  #
--- 2,6 ----
  # = bio/appl/mafft/report.rb - MAFFT report class
  #
! # Copyright:: Copyright (C) 2003, 2007  Naohisa Goto <ng at bioruby.org>
  # License::   The Ruby License
  #
***************
*** 14,17 ****
--- 14,21 ----
  # interface between Bio::ClustalW::Report.
  #
+ # Bio::Alignment::MultiFastaFormat is a generic data class for
+ # fasta-formatted multiple sequence alignment data.
+ # Bio::MAFFT::Report inherits Bio::Alignment::MultiFastaFormat.
+ #
  # == References
  #
***************
*** 26,32 ****
--- 30,121 ----
  require 'bio/db/fasta'
  require 'bio/io/flatfile'
+ require 'bio/alignment'
  require 'bio/appl/mafft'
  
  module Bio
+   module Alignment
+     # Data class for fasta-formatted multiple sequence alignment data,
+     # which is simply multiple entiries of fasta formatted sequences.
+     class MultiFastaFormat
+ 
+       # delimiter for flatfile
+       DELIMITER = RS = nil
+ 
+       # Creates a new data object.
+       # +str+ should be a (multi-)fasta formatted string.
+       def initialize(str)
+         ff = Bio::FlatFile.new(Bio::FastaFormat, StringIO.new(str))
+         @data = ff.to_a
+         @alignment = nil
+         @seq_method = nil
+       end
+ 
+       # Gets an multiple alignment.
+       # Returns a Bio::Alignment object.
+       # +method+ should be one of :naseq, :aaseq, :seq, or nil (default).
+       # nil means to automatically determine nucleotide or amino acid.
+       #
+       # This method returns previously parsed object
+       # if the same method is given (or guessed method is the same).
+       def alignment(method = nil)
+         m = determine_seq_method(@data, method)
+         if !@alignment or m != @seq_method then
+           @seq_method = m
+           @alignment = do_parse(@data, @seq_method)
+         end
+         @alignment
+       end
+ 
+       # Gets an array of the fasta formatted sequence objects.
+       # Returns an array of Bio::FastaFormat objects.
+       def entries
+         @data
+       end
+ 
+       private
+       # determines seqtype.
+       # if nil is given, try to guess DNA or protein.
+       def determine_seq_method(data, m = nil)
+         case m
+         when :aaseq
+           :aaseq
+         when :naseq
+           :naseq
+         when :seq
+           :seq
+         when nil
+           # auto-detection
+           score = 0
+           data[0, 3].each do |e|
+             k = e.to_seq.guess
+             if k == Bio::Sequence::NA then
+               score += 1
+             elsif k == Bio::Sequence::AA then
+               score -= 1
+             end
+           end
+           if score > 0 then
+             :naseq
+           elsif score < 0 then
+             :aaseq
+           else
+             :seq
+           end
+         else
+           raise 'one of :naseq, :aaseq, :seq, or nil should be given'
+         end
+       end
+ 
+       # Parses a result.
+       def do_parse(ary, seqmethod)
+         a = Bio::Alignment.new
+         a.add_sequences(ary) do |x|
+           [ x.__send__(seqmethod), x.definition ]
+         end
+         a
+       end
+     end #class MultiFastaFormat
+   end #module Alignment
+ 
    class MAFFT
  
***************
*** 37,50 ****
      # the significance of this class is to keep standard form and
      # interface between Bio::ClustalW::Report.
!     class Report
  
        # Creates a new Report object.
        # +str+ should be multi-fasta formatted text as a string.
-       # +seqclass+ should on of following:
-       # Class:  Bio::Sequence::AA, Bio::Sequence::NA, ...
-       # String: 'PROTEIN', 'DNA', ...
        #
        # Compatibility Note: the old usage (to get array of Bio::FastaFormat
        # objects) is deprecated.
        def initialize(str, seqclass = nil)
          if str.is_a?(Array) then
--- 126,143 ----
      # the significance of this class is to keep standard form and
      # interface between Bio::ClustalW::Report.
!     class Report < Bio::Alignment::MultiFastaFormat
  
        # Creates a new Report object.
        # +str+ should be multi-fasta formatted text as a string.
        #
        # Compatibility Note: the old usage (to get array of Bio::FastaFormat
        # objects) is deprecated.
+       #
+       # Compatibility Note 2: the argument +seqclass+ is deprecated.
+       #
+       # +seqclass+ should be one of following:
+       # Class:  Bio::Sequence::AA, Bio::Sequence::NA, ...
+       # String: 'PROTEIN', 'DNA', ...
+       #
        def initialize(str, seqclass = nil)
          if str.is_a?(Array) then
***************
*** 52,69 ****
            @data = str
          else
!           ff = Bio::FlatFile.new(Bio::FastaFormat, StringIO.new(str))
!           @data = ff.to_a
          end
!         @align = nil
!         case seqclass
!         when /PROTEIN/i
!           @seqclass = Bio::Sequence::AA
!         when /[DR]NA/i
!           @seqclass = Bio::Sequence::NA
!         else
!           if seqclass.is_a?(Module) then
!             @seqclass = seqclass
            else
!             @seqclass = Bio::Sequence
            end
          end
--- 145,164 ----
            @data = str
          else
!           super(str)
          end
! 
!         if seqclass then
!           warn "the 2nd argument (seqclass) will be no deprecated."
!           case seqclass
!           when /PROTEIN/i
!             @seqclass = Bio::Sequence::AA
!           when /[DR]NA/i
!             @seqclass = Bio::Sequence::NA
            else
!             if seqclass.is_a?(Module) then
!               @seqclass = seqclass
!             else
!               @seqclass = nil
!             end
            end
          end
***************
*** 74,103 ****
  
        # Sequence class (Bio::Sequence::AA, Bio::Sequence::NA, ...)
        attr_reader :seqclass
  
        # Gets an multiple alignment.
        # Returns a Bio::Alignment object.
!       def alignment
!         do_parse() unless @align
!         @align
        end
  
!       # This will be deprecated. Instead, please use alignment.
        #
        # Gets an multiple alignment.
        # Returns a Bio::Alignment object.
        def align
!         warn "align method will be deprecated. Please use \'alignment\'."
          alignment
        end
  
        # Gets an fasta-format string of the sequences.
        # Returns a string.
        # Same as align.to_fasta.
!       # Please refer to Bio::Alignment#to_fasta for arguments.
        def to_fasta(*arg)
!         alignment.to_fasta(*arg)
        end
  
        # Gets an array of the sequences.
        # Returns an array of Bio::FastaFormat instances.
--- 169,205 ----
  
        # Sequence class (Bio::Sequence::AA, Bio::Sequence::NA, ...)
+       #
+       # Compatibility note: This method will be removed in the tufure.
        attr_reader :seqclass
  
        # Gets an multiple alignment.
        # Returns a Bio::Alignment object.
!       def alignment(method = nil)
!         super
        end
  
!       # This method will be deprecated. Instead, please use alignment.
        #
        # Gets an multiple alignment.
        # Returns a Bio::Alignment object.
        def align
!         warn "Bio::MAFFT::Report#align is deprecated. Please use \'alignment\'."
          alignment
        end
  
+       # This will be deprecated. Instead, please use alignment.output_fasta.
+       #
        # Gets an fasta-format string of the sequences.
        # Returns a string.
        # Same as align.to_fasta.
!       # Please refer to Bio::Alignment#output_fasta for arguments.
        def to_fasta(*arg)
!         warn "Bio::MAFFT::report#to_fasta is deprecated. Please use \'alignment.output_fasta\'"
!         alignment.output_fasta(*arg)
        end
  
+       # Compatibility note: Behavior of the method will be changed
+       # in the future.
+       #
        # Gets an array of the sequences.
        # Returns an array of Bio::FastaFormat instances.
***************
*** 108,117 ****
        private
        # Parsing a result.
!       def do_parse
!         return nil if @align
!         @align = Bio::Alignment.new(@data) do |x|
!           [ @seqclass.new(x.seq), x.definition ]
          end
-         nil
        end
  
--- 210,222 ----
        private
        # Parsing a result.
!       def do_parse(ary, seqmethod)
!         if @seqclass then
!           a = Bio::Alignment.new
!           a.add_sequences(ary) do |x|
!             [ @seqclass.new(x.seq), x.definition ]
!           end
!         else
!           super(ary, seqmethod)
          end
        end
  


From ngoto at dev.open-bio.org  Mon Jul 16 08:25:52 2007
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Mon, 16 Jul 2007 12:25:52 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl muscle.rb, NONE, 1.1 probcons.rb,
	NONE, 1.1 tcoffee.rb, NONE, 1.1
Message-ID: <200707161225.l6GCPqYD020015@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv19995/lib/bio/appl

Added Files:
	muscle.rb probcons.rb tcoffee.rb 
Log Message:
New classess Bio::Muscle, Bio::Probcons, and Bio::Tcoffee are added
for MUSCLE, ProbCons, and T-Coffee multiple alignment programs.
Contributed by Jeffrey Blakeslee and colleagues.


--- NEW FILE: tcoffee.rb ---
#
# = bio/appl/tcoffee.rb - T-Coffee application wrapper class
#
# Copyright:: Copyright (C) 2006-2007
#             Jeffrey Blakeslee and John Conery University of Oregon <jeffb at uoregon.edu>
#             Naohisa Goto <ng at bioruby.org>
# License::   The Ruby License
#
#  $Id: tcoffee.rb,v 1.1 2007/07/16 12:25:50 ngoto Exp $
#
# Bio::Tcoffee is a wrapper class to execute T-Coffee.
#
# == References
#
# * http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
# * Notredame, C., Higgins, D.G. and Heringa, J.
#   T-Coffee: A novel method for fast and accurate multiple sequence
#   alignment. J. Mol. Biol. 302: 205-217, 2000.
#


module Bio

  # Bio::Tcoffee is a wrapper class to execute t-coffee.
  #
  # Please refer documents in bio/apple/tcoffee.rb for references.
  class Tcoffee < Bio::Alignment::FactoryTemplate::FileInFileOutWithTree

    # default program name
    DEFAULT_PROGRAM = 't_coffee'.freeze

    # default report parser
    DEFAULT_PARSER = Bio::ClustalW::Report

    private
    # generates options specifying input filename.
    # returns an array of string
    def _option_input_file(fn)
      [ '-infile', fn ]
    end

    # generates options specifying output filename.
    # returns an array of string
    def _option_output_file(fn)
      [ '-outfile', fn ]
    end

    # generates options specifying output filename.
    # returns an array of string
    def _option_output_dndfile(fn)
      [ '-newtree', fn ]
    end
  end #class TCoffee

end #module Bio

--- NEW FILE: muscle.rb ---
#
# = bio/appl/muscle.rb - MUSCLE application wrapper class
#
# Copyright:: Copyright (C) 2006-2007
#             Jeffrey Blakeslee and John Conery University of Oregon <jeffb at uoregon.edu>
#             Naohisa Goto <ng at bioruby.org>
# License::   The Ruby License
#
#  $Id: muscle.rb,v 1.1 2007/07/16 12:25:50 ngoto Exp $
#
#
# Bio::Muscle is a wrapper class to execute MUSCLE.
#
# == References
#
# * http://www.drive5.com/muscle/
# * Edgar R.C.
#   MUSCLE: multiple sequence alignment with high accuracy and
#   high throughput. Nucleic Acids Res. 32: 1792-1797, 2004.
# * Edgar, R.C.
#   MUSCLE: a multiple sequence alignment method with reduced time
#   and space complexity. BMC Bioinformatics 5: 113, 2004.
#

module Bio

  # Bio::Muscle is a wrapper class to execute MUSCLE.
  #
  # Please refer documents in bio/apple/muscle.rb for references.
  class Muscle < Bio::Alignment::FactoryTemplate::StdinInFileOut

    # default program name
    DEFAULT_PROGRAM = 'muscle'.freeze

    # default report parser
    DEFAULT_PARSER = Bio::Alignment::MultiFastaFormat

    private
    # generates options specifying input filename.
    # returns an array of string
    def _option_input_file(fn)
      [ '-in', fn ]
    end

    # generates options specifying output filename.
    # returns an array of string
    def _option_output_file(fn)
      [ '-out', fn ]
    end
  end #class Muscle

end #module Bio

--- NEW FILE: probcons.rb ---
#
# = bio/appl/probcons.rb - ProbCons application wrapper class
#
# Copyright:: Copyright (C) 2006-2007
#             Jeffrey Blakeslee and John Conery University of Oregon <jeffb at uoregon.edu>
#             Naohisa Goto <ng at bioruby.org>
# License::   The Ruby License
#
#  $Id: probcons.rb,v 1.1 2007/07/16 12:25:50 ngoto Exp $
#
# Bio::Probcons is a wrapper class to execute ProbCons
# (Probabilistic Consistency-based Multiple Alignment
# of Amino Acid Sequences).
#
# == References
# 
# * http://probcons.stanford.edu/
# * Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S.
#   ProbCons: Probabilistic Consistency-based Multiple Sequence Alignment.
#   Genome Research 15: 330-340, 2005.
#


module Bio

  # Bio::Probcons is a wrapper class to execute PROBCONS
  # (Probabilistic Consistency-based Multiple Alignment
  # of Amino Acid Sequences).
  #
  # Please refer documents in bio/apple/probcons.rb for references.
  class Probcons < Bio::Alignment::FactoryTemplate::FileInStdoutOut

    # default program name
    DEFAULT_PROGRAM = 'probcons'.freeze

    # default report parser
    DEFAULT_PARSER = Bio::Alignment::MultiFastaFormat

  end #class Probcons

end #module Bio


From ngoto at dev.open-bio.org  Mon Jul 16 08:26:30 2007
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Mon, 16 Jul 2007 12:26:30 +0000
Subject: [BioRuby-cvs] bioruby/lib bio.rb,1.85,1.86
Message-ID: <200707161226.l6GCQUHD020045@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib
In directory dev.open-bio.org:/tmp/cvs-serv20025/lib

Modified Files:
	bio.rb 
Log Message:
added autoload for Bio::Muscle, Bio::Probcons, and Bio::Tcoffee


Index: bio.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio.rb,v
retrieving revision 1.85
retrieving revision 1.86
diff -C2 -d -r1.85 -r1.86
*** bio.rb	9 Jul 2007 08:49:15 -0000	1.85
--- bio.rb	16 Jul 2007 12:26:28 -0000	1.86
***************
*** 227,230 ****
--- 227,234 ----
    #end
  
+   autoload :Tcoffee,        'bio/appl/tcoffee'
+   autoload :Muscle,         'bio/appl/muscle'
+   autoload :Probcons,       'bio/appl/probcons'
+ 
    autoload :Sim4,           'bio/appl/sim4'
    ## below are described in bio/appl/sim4.rb


From ngoto at dev.open-bio.org  Mon Jul 16 08:27:31 2007
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Mon, 16 Jul 2007 12:27:31 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl clustalw.rb, 1.18, 1.19 mafft.rb,
	1.17, 1.18
Message-ID: <200707161227.l6GCRV41020073@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv20053/lib/bio/appl

Modified Files:
	clustalw.rb mafft.rb 
Log Message:
Interfaces of Bio::ClustalW and Bio::MAFFT are added/modified
to follow Bio::Alignment::FactoryTemplate (but not yet changed to use it).


Index: clustalw.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/clustalw.rb,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** clustalw.rb	5 Apr 2007 23:35:39 -0000	1.18
--- clustalw.rb	16 Jul 2007 12:27:29 -0000	1.19
***************
*** 8,12 ****
  #
  # Bio::ClustalW is a CLUSTAL W execution wrapper class.
! # Its object is also called an alignment factory.
  # CLUSTAL W is a very popular software for multiple sequence alignment.
  #
--- 8,12 ----
  #
  # Bio::ClustalW is a CLUSTAL W execution wrapper class.
! # It can also be called as an alignment factory.
  # CLUSTAL W is a very popular software for multiple sequence alignment.
  #
***************
*** 45,49 ****
        @output = nil
        @report = nil
!       @log = nil
      end
  
--- 45,51 ----
        @output = nil
        @report = nil
!       @data_stdout = nil
!       @exit_status = nil
!       @output_dnd = nil
      end
  
***************
*** 56,60 ****
      # option is deprecated. Instead, please use options.
      def option
!       warn "option is deprecated. Please use options."
        options
      end
--- 58,62 ----
      # option is deprecated. Instead, please use options.
      def option
!       warn "Bio::ClustalW#option is deprecated. Please use options."
        options
      end
***************
*** 66,73 ****
      attr_reader :command
  
      # Returns last messages of CLUSTAL W execution.
!     attr_reader :log
  
!     # Returns last raw alignment result (String).
      attr_reader :output
  
--- 68,80 ----
      attr_reader :command
  
+     # This method will be deprecated.
+     #
      # Returns last messages of CLUSTAL W execution.
!     def log
!       #warn 'Bio::ClustalW#log will be deprecated.'
!       @data_stdout
!     end
  
!     # Returns last raw alignment result (String or nil).
      attr_reader :output
  
***************
*** 76,82 ****
--- 83,109 ----
      attr_reader :report
  
+     # Last exit status
+     attr_reader :exit_status
+ 
+     # Last output to the stdout.
+     attr_accessor :data_stdout
+     
+     # Clear the internal data and status, except program and options.
+     def reset
+       @command = nil
+       @output = nil
+       @report = nil
+       @exit_status = nil
+       @data_stdout = nil
+       @output_dnd = nil
+     end
+ 
      # Executes the program(clustalw).
      # If +seqs+ is not nil, perform alignment for seqs.
      # If +seqs+ is nil, simply executes CLUSTAL W.
+     #
+     # Compatibility note: When seqs is nil,
+     # returns true if the program exits normally, and
+     # returns false if the program exits abnormally.
      def query(seqs)
        if seqs then
***************
*** 84,112 ****
        else
          exec_local(@options)
        end
      end
  
      # Performs alignment for +seqs+.
      # +seqs+ should be Bio::Alignment or Array of sequences or nil.
      def query_align(seqs)
-       seqtype = nil
        unless seqs.is_a?(Bio::Alignment)
          seqs = Bio::Alignment.new(seqs)
        end
-       seqs.each do |s|
-         if    s.is_a?(Bio::Sequence::AA) then
-           seqtype = 'PROTEIN'
-         elsif s.is_a?(Bio::Sequence::NA) then
-           seqtype = 'DNA'
-         end
-         break if seqtype
-       end
        query_string(seqs.output_fasta(:width => 70,
!                                      :avoid_same_name => true), seqtype)
      end
  
      # Performs alignment for +str+.
      # +str+ should be a string that can be recognized by CLUSTAL W.
      def query_string(str, *arg)
        begin
          tf_in = Tempfile.open('align')
--- 111,146 ----
        else
          exec_local(@options)
+         @exit_status.exitstatus == 0 ? true : false
        end
      end
  
+     # Note that this method will be renamed to query_alignment.
+     #
      # Performs alignment for +seqs+.
      # +seqs+ should be Bio::Alignment or Array of sequences or nil.
+     #
+     # Compatibility Note: Nucleic or amino is not determined by this method.
      def query_align(seqs)
        unless seqs.is_a?(Bio::Alignment)
          seqs = Bio::Alignment.new(seqs)
        end
        query_string(seqs.output_fasta(:width => 70,
!                                      :avoid_same_name => true))
!     end
! 
!     # Performs alignment for +seqs+.
!     # +seqs+ should be Bio::Alignment or Array of sequences or nil.
!     def query_alignment(seqs)
!       query_align(seqs)
      end
  
      # Performs alignment for +str+.
      # +str+ should be a string that can be recognized by CLUSTAL W.
+     #
+     # Compatibility Note: 2nd argument is deprecated and ignored.
      def query_string(str, *arg)
+       if arg.size > 0 then
+         warn '2nd argument of Bio::ClustalW#query_string is ignored'
+       end
        begin
          tf_in = Tempfile.open('align')
***************
*** 115,119 ****
          tf_in.close(false)
        end
!       r = query_by_filename(tf_in.path, *arg)
        tf_in.close(true)
        r
--- 149,153 ----
          tf_in.close(false)
        end
!       r = query_by_filename(tf_in.path)
        tf_in.close(true)
        r
***************
*** 121,126 ****
  
      # Performs alignment of sequences in the file named +path+.
!     def query_by_filename(path, seqtype = nil)
!       require 'bio/appl/clustalw/report'
  
        tf_out = Tempfile.open('clustalout')
--- 155,164 ----
  
      # Performs alignment of sequences in the file named +path+.
!     #
!     # Compatibility Note: 2nd argument (seqtype) is deprecated and ignored.
!     def query_by_filename(path, *arg)
!       if arg.size > 0 then
!         warn '2nd argument of Bio::ClustalW#query_by_filename is ignored'
!       end
  
        tf_out = Tempfile.open('clustalout')
***************
*** 135,139 ****
          "-outorder=input"
        ]
!       opt << "-type=#{seqtype}" if seqtype
        opt.concat(@options)
        exec_local(opt)
--- 173,177 ----
          "-outorder=input"
        ]
!       #opt << "-type=#{seqtype}" if seqtype
        opt.concat(@options)
        exec_local(opt)
***************
*** 144,148 ****
        @output_dnd = tf_dnd.read
        tf_dnd.close(true)
!       @report = Report.new(@output, seqtype)
        @report
      end
--- 182,186 ----
        @output_dnd = tf_dnd.read
        tf_dnd.close(true)
!       @report = Report.new(@output)
        @report
      end
***************
*** 166,176 ****
        @command = [ @program,  *opt ]
        #STDERR.print "DEBUG: ", @command.join(" "), "\n"
!       @log = nil
  
        Bio::Command.call_command(@command) do |io|
          io.close_write
!         @log = io.read
        end
!       @log
      end
  
--- 204,215 ----
        @command = [ @program,  *opt ]
        #STDERR.print "DEBUG: ", @command.join(" "), "\n"
!       @data_stdout = nil
!       @exit_status = nil
  
        Bio::Command.call_command(@command) do |io|
          io.close_write
!         @data_stdout = io.read
        end
!       @exit_status = $?
      end
  

Index: mafft.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/mafft.rb,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** mafft.rb	5 Apr 2007 23:35:39 -0000	1.17
--- mafft.rb	16 Jul 2007 12:27:29 -0000	1.18
***************
*** 106,110 ****
      # +program+ is the name of the program.
      # +opt+ is options of the program.
!     def initialize(program, opt)
        @program = program
        @options = opt
--- 106,110 ----
      # +program+ is the name of the program.
      # +opt+ is options of the program.
!     def initialize(program = 'mafft', opt = [])
        @program = program
        @options = opt
***************
*** 112,118 ****
        @output = nil
        @report = nil
      end
  
!     # program name
      attr_accessor :program
  
--- 112,120 ----
        @output = nil
        @report = nil
+       @data_stdout = nil
+       @exit_status = nil
      end
  
!     # program name (usually 'mafft' in UNIX)
      attr_accessor :program
  
***************
*** 122,126 ****
      # option is deprecated. Instead, please use options.
      def option
!       warn "option is deprecated. Please use options."
        options
      end
--- 124,128 ----
      # option is deprecated. Instead, please use options.
      def option
!       warn "Bio::MAFFT#option is deprecated. Please use options."
        options
      end
***************
*** 138,142 ****
      #log is deprecated (no replacement) and returns empty string.
      def log
!       warn "log is deprecated (no replacement) and returns empty string."
        ''
      end
--- 140,144 ----
      #log is deprecated (no replacement) and returns empty string.
      def log
!       warn "Bio::MAFFT#log is deprecated (no replacement) and returns empty string."
        ''
      end
***************
*** 153,159 ****
--- 155,180 ----
      attr_reader :report
  
+     # Last exit status
+     attr_reader :exit_status
+ 
+     # Last output to the stdout.
+     attr_accessor :data_stdout
+     
+     # Clear the internal data and status, except program and options.
+     def reset
+       @command = nil
+       @output = nil
+       @report = nil
+       @exit_status = nil
+       @data_stdout = nil
+     end
+ 
      # Executes the program.
      # If +seqs+ is not nil, perform alignment for seqs.
      # If +seqs+ is nil, simply executes the program.
+     #
+     # Compatibility note: When seqs is nil,
+     # returns true if the program exits normally, and
+     # returns false if the program exits abnormally.
      def query(seqs)
        if seqs then
***************
*** 161,179 ****
        else
          exec_local(@options)
        end
      end
  
      # Performs alignment for seqs.
      # +seqs+ should be Bio::Alignment or Array of sequences or nil.
      def query_align(seqs, *arg)
        unless seqs.is_a?(Bio::Alignment)
!         seqs = Bio::Alignment.new(seqs, *arg)
        end
        query_string(seqs.output_fasta(:width => 70))
      end
  
      # Performs alignment for +str+.
      # Str should be a string that can be recognized by the program.
      def query_string(str, *arg)
        begin
          tf_in = Tempfile.open('align')
--- 182,219 ----
        else
          exec_local(@options)
+         @exit_status.exitstatus == 0 ? true : false
        end
      end
  
+     # Note that this method will be renamed to query_alignment.
+     #
      # Performs alignment for seqs.
      # +seqs+ should be Bio::Alignment or Array of sequences or nil.
+     #
+     # Compatibility Note: arg is deprecated and ignored.
      def query_align(seqs, *arg)
+       if arg.size > 0 then
+         warn '2nd and other arguments of Bio::MAFFT#query_align is ignored'
+       end
        unless seqs.is_a?(Bio::Alignment)
!         seqs = Bio::Alignment.new(seqs)
        end
        query_string(seqs.output_fasta(:width => 70))
      end
  
+     # Performs alignment for seqs.
+     # +seqs+ should be Bio::Alignment or Array of sequences or nil.
+     def query_alignment(seqs)
+       query_align(seqs)
+     end
+ 
      # Performs alignment for +str+.
      # Str should be a string that can be recognized by the program.
+     #
+     # Compatibility Note: arg is deprecated and ignored.
      def query_string(str, *arg)
+       if arg.size > 0 then
+         warn '2nd and other arguments of Bio::MAFFT#query_string is ignored'
+       end
        begin
          tf_in = Tempfile.open('align')
***************
*** 188,195 ****
  
      # Performs alignment of sequences in the file named +fn+.
!     def query_by_filename(fn, seqtype = nil)
        opt = @options + [ fn ]
        exec_local(opt)
!       @report = Report.new(@output, seqtype)
        @report
      end
--- 228,240 ----
  
      # Performs alignment of sequences in the file named +fn+.
!     #
!     # Compatibility Note: 2nd argument (seqtype) is deprecated and ignored.
!     def query_by_filename(fn, *arg)
!       if arg.size > 0 then
!         warn '2nd argument of Bio::MAFFT#query_filename is ignored'
!       end
        opt = @options + [ fn ]
        exec_local(opt)
!       @report = Report.new(@output)
        @report
      end
***************
*** 200,208 ****
        @command = [ @program, *opt ]
        #STDERR.print "DEBUG: ", @command.join(" "), "\n"
!       @output = nil
        Bio::Command.call_command(@command) do |io|
          io.close_write
!         @output = io.read
        end
      end
  
--- 245,256 ----
        @command = [ @program, *opt ]
        #STDERR.print "DEBUG: ", @command.join(" "), "\n"
!       @data_stdout = nil
!       @exit_status = nil
        Bio::Command.call_command(@command) do |io|
          io.close_write
!         @data_stdout = io.read
        end
+       @output = @data_stdout
+       @exit_status = $?
      end
  


From ngoto at dev.open-bio.org  Mon Jul 16 08:44:06 2007
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Mon, 16 Jul 2007 12:44:06 +0000
Subject: [BioRuby-cvs] bioruby ChangeLog,1.65,1.66
Message-ID: <200707161244.l6GCi6NT020232@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv20210

Modified Files:
	ChangeLog 
Log Message:
documents are added


Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.65
retrieving revision 1.66
diff -C2 -d -r1.65 -r1.66
*** ChangeLog	10 Jul 2007 10:44:47 -0000	1.65
--- ChangeLog	16 Jul 2007 12:44:04 -0000	1.66
***************
*** 1,2 ****
--- 1,32 ----
+ 2007-07-16  Naohisa Goto <ng at bioruby.org>
+ 
+ 	* lib/bio/mafft/report.rb
+ 
+ 	For generic multi-fasta formatted sequence alignment,
+ 	Bio::Alignment::MultiFastaFormat is newly added based on
+ 	Bio::MAFFT::Report class, and Bio::MAFFT::Report is
+ 	changed to inherit the new class.
+ 	Tests are added in test/unit/bio/appl/mafft/test_report.rb.
+ 
+ 	* lib/bio/alignment.rb
+ 
+ 	New modules and classes Bio::Alignment::FactoryTemplate::* are added.
+ 	They are used by following three new classes.
+ 	
+ 	* lib/bio/appl/muscle.rb
+ 	* lib/bio/appl/probcons.rb
+ 	* lib/bio/appl/tcoffee.rb
+ 
+ 	New classess Bio::Muscle, Bio::Probcons, and Bio::Tcoffee are added
+ 	for MUSCLE, ProbCons, and T-Coffee multiple alignment programs.
+ 	Contributed by Jeffrey Blakeslee and colleagues.
+ 
+ 	* lib/bio/appl/clustalw.rb
+ 	* lib/bio/appl/mafft.rb
+ 
+ 	Interfaces of Bio::ClustalW and Bio::MAFFT are added/modified
+ 	to follow Bio::Alignment::FactoryTemplate (but not yet changed to
+ 	use it).
+ 
  2007-07-09  Naohisa Goto <ng at bioruby.org>
  


From ngoto at dev.open-bio.org  Mon Jul 16 08:44:06 2007
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Mon, 16 Jul 2007 12:44:06 +0000
Subject: [BioRuby-cvs] bioruby/doc Changes-0.7.rd,1.22,1.23
Message-ID: <200707161244.l6GCi6nF020237@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/doc
In directory dev.open-bio.org:/tmp/cvs-serv20210/doc

Modified Files:
	Changes-0.7.rd 
Log Message:
documents are added


Index: Changes-0.7.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Changes-0.7.rd,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** Changes-0.7.rd	10 Jul 2007 10:44:47 -0000	1.22
--- Changes-0.7.rd	16 Jul 2007 12:44:04 -0000	1.23
***************
*** 297,300 ****
--- 297,312 ----
    No replacements/alternatives are available.
  
+ --- Bio::ClustalW, Bio::MAFFT
+ 
+ In 1.1.0:
+ 
+ * Bio::(ClustalW|MAFFT)#query_align, #query_string, #query_by_filename
+   are changed not to get second (and third, ...) arguments.
+ * Bio::(ClustalW|MAFFT)#query, #query_string, #query_by_filename
+   are changed not trying to guess whether given data is nucleotide or protein.
+ * Return value of Bio::(ClustalW|MAFFT)#query with no arguments is changed.
+   If the program exists normally (exit status is 0), returns true.
+   Otherwise, returns false.
+ 
  --- Bio::MAFFT
  


From k at dev.open-bio.org  Mon Jul 16 14:06:14 2007
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Mon, 16 Jul 2007 18:06:14 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/io das.rb,1.16,1.17
Message-ID: <200707161806.l6GI6Eln020711@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv20684/lib/bio/io

Modified Files:
	das.rb 
Log Message:
* fixed that get_dsn.each {|dsn| dsn.mapmaster} to return correct
  value (mapmaster URL). This bug is fixed and reported by Dave Thorne
  on bioruby list on June 7, 2007.


Index: das.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/das.rb,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** das.rb	5 Apr 2007 23:35:41 -0000	1.16
--- das.rb	16 Jul 2007 18:06:12 -0000	1.17
***************
*** 59,63 ****
            dsn.source_version = e.attributes['version']
          when 'MAPMASTER'
!           dsn.mapmaster = e.name
          when 'DESCRIPTION'
            dsn.description = e.text
--- 59,63 ----
            dsn.source_version = e.attributes['version']
          when 'MAPMASTER'
!           dsn.mapmaster = e.text
          when 'DESCRIPTION'
            dsn.description = e.text


From nakao at dev.open-bio.org  Mon Jul 16 15:21:35 2007
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Mon, 16 Jul 2007 19:21:35 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/appl/iprscan test_report.rb, 1.4,
	1.5
Message-ID: <200707161921.l6GJLZJW021139@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/appl/iprscan
In directory dev.open-bio.org:/tmp/cvs-serv21101/test/unit/bio/appl/iprscan

Modified Files:
	test_report.rb 
Log Message:
* Fixed go terms parsing in the raw format. (Thanks ngoto-san).


Index: test_report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/appl/iprscan/test_report.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** test_report.rb	22 Feb 2007 10:15:01 -0000	1.4
--- test_report.rb	16 Jul 2007 19:21:33 -0000	1.5
***************
*** 213,229 ****
        @obj = []
        while line = test_raw.gets
!         if entry != '' and entry.split("\t").first == line.split("\t").first
            entry << line
!         elsif entry != ''
            @obj << Bio::Iprscan::Report.parse_in_raw(entry)
!           entry = line
          else
            entry << line
          end
        end
      end
      
      def test_obj
!       assert_equal(2, @obj.size)
      end
      
--- 213,230 ----
        @obj = []
        while line = test_raw.gets
!         if entry.split("\t").first == line.split("\t").first
            entry << line
!         elsif entry != '' and entry.split("\t").first != line.split("\t").first
            @obj << Bio::Iprscan::Report.parse_in_raw(entry)
!           entry = ''
          else
            entry << line
          end
        end
+       @obj << Bio::Iprscan::Report.parse_in_raw(entry)
      end
      
      def test_obj
!       assert_equal(3, @obj.size)
      end
      
***************
*** 293,297 ****
  
      def test_match_go_terms
!       assert_equal(["Molecular Function:RNA binding (GO:0003723)"], @obj.first.matches.first.go_terms)
      end
  
--- 294,301 ----
  
      def test_match_go_terms
!       ary = ["Biological Process:phosphorylation (GO:0016310)", 
!              "Molecular Function:transferase activity, transferring phosphorus-containing groups (GO:0016772)"]
!       assert_equal(ary,
!                    @obj.last.matches.last.go_terms)
      end
  


From nakao at dev.open-bio.org  Mon Jul 16 15:21:35 2007
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Mon, 16 Jul 2007 19:21:35 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/iprscan report.rb,1.6,1.7
Message-ID: <200707161921.l6GJLZ0O021138@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/iprscan
In directory dev.open-bio.org:/tmp/cvs-serv21101/lib/bio/appl/iprscan

Modified Files:
	report.rb 
Log Message:
* Fixed go terms parsing in the raw format. (Thanks ngoto-san).


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/iprscan/report.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** report.rb	5 Apr 2007 23:35:40 -0000	1.6
--- report.rb	16 Jul 2007 19:21:32 -0000	1.7
***************
*** 105,109 ****
              report.matches.last.ipr_description = line[12]
            end
!           report.matches.last.go_terms = line[13].split(', ') if line[13]          
          end
          report.query_id = report.matches.first.query_id
--- 105,109 ----
              report.matches.last.ipr_description = line[12]
            end
!           report.matches.last.go_terms = line[13].scan(/(\w+ \w+\:.+? \(GO:\d+\))/).flatten if line[13]          
          end
          report.query_id = report.matches.first.query_id


From k at dev.open-bio.org  Mon Jul 16 15:28:50 2007
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Mon, 16 Jul 2007 19:28:50 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/util restriction_enzyme.rb, 1.15, 1.16
Message-ID: <200707161928.l6GJSoN8021258@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/util
In directory dev.open-bio.org:/tmp/cvs-serv21244

Modified Files:
	restriction_enzyme.rb 
Log Message:
* autoloadified


Index: restriction_enzyme.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme.rb,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** restriction_enzyme.rb	13 May 2007 04:08:02 -0000	1.15
--- restriction_enzyme.rb	16 Jul 2007 19:28:48 -0000	1.16
***************
*** 9,27 ****
  #
  
- require 'bio/db/rebase'
- require 'bio/util/restriction_enzyme/double_stranded'
- require 'bio/util/restriction_enzyme/single_strand'
- require 'bio/util/restriction_enzyme/cut_symbol'
- require 'bio/util/restriction_enzyme/analysis'
- 
  module Bio #:nodoc:
  
! #
! # bio/util/restriction_enzyme.rb - Digests DNA based on restriction enzyme cut patterns
! #
! # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
! # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   The Ruby License
! #
  # = Description
  # 
--- 9,16 ----
  #
  
  module Bio #:nodoc:
  
!   autoload :REBASE, 'bio/db/rebase'
! 
  # = Description
  # 
***************
*** 124,129 ****
  # * Circular DNA cutting
  #
!   
! class Bio::RestrictionEnzyme
    include CutSymbol
    extend CutSymbol
--- 113,129 ----
  # * Circular DNA cutting
  #
! 
! class RestrictionEnzyme
! 
!   #require 'bio/util/restriction_enzyme/cut_symbol'
! 
!   autoload :CutSymbol,               'bio/util/restriction_enzyme/cut_symbol'
!   autoload :StringFormatting,        'bio/util/restriction_enzyme/string_formatting'
!   autoload :SingleStrand,            'bio/util/restriction_enzyme/single_strand'
!   autoload :SingleStrandComplement,  'bio/util/restriction_enzyme/single_strand_complement'
!   autoload :DoubleStranded,          'bio/util/restriction_enzyme/double_stranded'
!   autoload :Analysis,                'bio/util/restriction_enzyme/analysis'
!   autoload :Range,                   'bio/util/restriction_enzyme/range/sequence_range'
! 
    include CutSymbol
    extend CutSymbol
***************
*** 226,228 ****
    end
  end # RestrictionEnzyme
! end # Bio
\ No newline at end of file
--- 226,228 ----
    end
  end # RestrictionEnzyme
! end # Bio


From k at dev.open-bio.org  Mon Jul 16 15:28:50 2007
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Mon, 16 Jul 2007 19:28:50 +0000
Subject: [BioRuby-cvs]
	bioruby/lib/bio/util/restriction_enzyme/double_stranded
	aligned_strands.rb, 1.5, 1.6 cut_location_pair.rb, 1.8,
	1.9 cut_location_pair_in_enzyme_notation.rb, 1.6,
	1.7 cut_locations.rb, 1.5,
	1.6 cut_locations_in_enzyme_notation.rb, 1.6, 1.7
Message-ID: <200707161928.l6GJSoRx021270@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/double_stranded
In directory dev.open-bio.org:/tmp/cvs-serv21244/restriction_enzyme/double_stranded

Modified Files:
	aligned_strands.rb cut_location_pair.rb 
	cut_location_pair_in_enzyme_notation.rb cut_locations.rb 
	cut_locations_in_enzyme_notation.rb 
Log Message:
* autoloadified


Index: aligned_strands.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** aligned_strands.rb	5 Apr 2007 23:35:42 -0000	1.5
--- aligned_strands.rb	16 Jul 2007 19:28:48 -0000	1.6
***************
*** 1,4 ****
  #
! # bio/util/restrction_enzyme/double_stranded/aligned_strands.rb - Align two SingleStrand objects
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
--- 1,4 ----
  #
! # bio/util/restriction_enzyme/double_stranded/aligned_strands.rb - Align two SingleStrand objects
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
***************
*** 9,27 ****
  #
  
! require 'bio/util/restriction_enzyme/single_strand'
! require 'bio/util/restriction_enzyme/cut_symbol'
! require 'bio/util/restriction_enzyme/string_formatting'
  
! module Bio; end
! class Bio::RestrictionEnzyme
  class DoubleStranded
  
- #
- # bio/util/restrction_enzyme/double_stranded/aligned_strands.rb - Align two SingleStrand objects
- #
- # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
- # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
- # License::   The Ruby License
- #
  # Align two SingleStrand objects and return a Result
  # object with +primary+ and +complement+ accessors.
--- 9,18 ----
  #
  
! require 'bio/util/restriction_enzyme'
  
! module Bio
! class RestrictionEnzyme
  class DoubleStranded
  
  # Align two SingleStrand objects and return a Result
  # object with +primary+ and +complement+ accessors.
***************
*** 136,138 ****
  end # AlignedStrands
  end # DoubleStranded
! end # Bio::RestrictionEnzyme
--- 127,130 ----
  end # AlignedStrands
  end # DoubleStranded
! end # RestrictionEnzyme
! end # Bio

Index: cut_locations.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** cut_locations.rb	5 Apr 2007 23:35:42 -0000	1.5
--- cut_locations.rb	16 Jul 2007 19:28:48 -0000	1.6
***************
*** 1,4 ****
  #
! # bio/util/restrction_enzyme/double_stranded/cut_locations.rb - Contains an Array of CutLocationPair objects
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
--- 1,4 ----
  #
! # bio/util/restriction_enzyme/double_stranded/cut_locations.rb - Contains an Array of CutLocationPair objects
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
***************
*** 9,25 ****
  #
  
! require 'bio/util/restriction_enzyme/double_stranded/cut_location_pair'
  
! module Bio; end
! class Bio::RestrictionEnzyme
  class DoubleStranded
  
- #
- # bio/util/restrction_enzyme/double_stranded/cut_locations.rb - Contains an Array of CutLocationPair objects
- #
- # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
- # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
- # License::   The Ruby License
- #
  # Contains an +Array+ of CutLocationPair objects.
  #
--- 9,18 ----
  #
  
! require 'bio/util/restriction_enzyme'
  
! module Bio
! class RestrictionEnzyme
  class DoubleStranded
  
  # Contains an +Array+ of CutLocationPair objects.
  #
***************
*** 80,82 ****
  end # CutLocations
  end # DoubleStranded
! end # Bio::RestrictionEnzyme
--- 73,76 ----
  end # CutLocations
  end # DoubleStranded
! end # RestrictionEnzyme
! end # Bio

Index: cut_locations_in_enzyme_notation.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** cut_locations_in_enzyme_notation.rb	5 Apr 2007 23:35:42 -0000	1.6
--- cut_locations_in_enzyme_notation.rb	16 Jul 2007 19:28:48 -0000	1.7
***************
*** 1,4 ****
  #
! # bio/util/restrction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb - Inherits from DoubleStrand::CutLocations
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
--- 1,4 ----
  #
! # bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb - Inherits from DoubleStrand::CutLocations
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
***************
*** 9,26 ****
  #
  
! require 'bio/util/restriction_enzyme/double_stranded/cut_locations'
! require 'bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation'
  
! module Bio; end
! class Bio::RestrictionEnzyme
  class DoubleStranded
  
- #
- # bio/util/restrction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb - Inherits from DoubleStrand::CutLocations
- #
- # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
- # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
- # License::   The Ruby License
- #
  # Inherits from DoubleStranded::CutLocations.  Contains CutLocationPairInEnzymeNotation objects.
  # Adds helper methods to convert from enzyme index notation to 0-based array index notation.
--- 9,18 ----
  #
  
! require 'bio/util/restriction_enzyme'
  
! module Bio
! class RestrictionEnzyme
  class DoubleStranded
  
  # Inherits from DoubleStranded::CutLocations.  Contains CutLocationPairInEnzymeNotation objects.
  # Adds helper methods to convert from enzyme index notation to 0-based array index notation.
***************
*** 112,114 ****
  end # CutLocationsInEnzymeNotation
  end # DoubleStranded
! end # Bio::RestrictionEnzyme
--- 104,107 ----
  end # CutLocationsInEnzymeNotation
  end # DoubleStranded
! end # RestrictionEnzyme
! end # Bio

Index: cut_location_pair_in_enzyme_notation.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** cut_location_pair_in_enzyme_notation.rb	5 Apr 2007 23:35:42 -0000	1.6
--- cut_location_pair_in_enzyme_notation.rb	16 Jul 2007 19:28:48 -0000	1.7
***************
*** 1,4 ****
  #
! # bio/util/restrction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb - Inherits from DoubleStranded::CutLocationPair
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
--- 1,4 ----
  #
! # bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb - Inherits from DoubleStranded::CutLocationPair
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
***************
*** 9,25 ****
  #
  
! require 'bio/util/restriction_enzyme/double_stranded/cut_location_pair'
  
! module Bio; end
! class Bio::RestrictionEnzyme
  class DoubleStranded
  
- #
- # bio/util/restrction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb - Inherits from DoubleStranded::CutLocationPair
- #
- # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
- # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
- # License::   The Ruby License
- #
  # Inherits from DoubleStranded::CutLocationPair , stores the cut location pair in
  # enzyme notation instead of 0-based.
--- 9,18 ----
  #
  
! require 'bio/util/restriction_enzyme'
  
! module Bio
! class RestrictionEnzyme
  class DoubleStranded
  
  # Inherits from DoubleStranded::CutLocationPair , stores the cut location pair in
  # enzyme notation instead of 0-based.
***************
*** 42,44 ****
  end # CutLocationPair
  end # DoubleStranded
! end # Bio::RestrictionEnzyme
--- 35,38 ----
  end # CutLocationPair
  end # DoubleStranded
! end # RestrictionEnzyme
! end # Bio

Index: cut_location_pair.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** cut_location_pair.rb	5 Apr 2007 23:35:42 -0000	1.8
--- cut_location_pair.rb	16 Jul 2007 19:28:48 -0000	1.9
***************
*** 1,4 ****
  #
! # bio/util/restrction_enzyme/double_stranded/cut_location_pair.rb - Stores a cut location pair in 0-based index notation
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
--- 1,4 ----
  #
! # bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb - Stores a cut location pair in 0-based index notation
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
***************
*** 9,25 ****
  #
  
! require 'bio/util/restriction_enzyme/cut_symbol'
  
! module Bio; end
! class Bio::RestrictionEnzyme
  class DoubleStranded
    
- #
- # bio/util/restrction_enzyme/double_stranded/cut_location_pair.rb - Stores a cut location pair in 0-based index notation
- #
- # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
- # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
- # License::   The Ruby License
- #
  # Stores a single cut location pair in 0-based index notation for use with
  # DoubleStranded enzyme sequences.
--- 9,18 ----
  #
  
! require 'bio/util/restriction_enzyme'
  
! module Bio
! class RestrictionEnzyme
  class DoubleStranded
    
  # Stores a single cut location pair in 0-based index notation for use with
  # DoubleStranded enzyme sequences.
***************
*** 107,109 ****
  end # CutLocationPair
  end # DoubleStranded
! end # Bio::RestrictionEnzyme
--- 100,103 ----
  end # CutLocationPair
  end # DoubleStranded
! end # RestrictionEnzyme
! end # Bio


From k at dev.open-bio.org  Mon Jul 16 15:28:50 2007
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Mon, 16 Jul 2007 19:28:50 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme/single_strand
	cut_locations_in_enzyme_notation.rb, 1.6, 1.7
Message-ID: <200707161928.l6GJSoc4021293@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/single_strand
In directory dev.open-bio.org:/tmp/cvs-serv21244/restriction_enzyme/single_strand

Modified Files:
	cut_locations_in_enzyme_notation.rb 
Log Message:
* autoloadified


Index: cut_locations_in_enzyme_notation.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** cut_locations_in_enzyme_notation.rb	5 Apr 2007 23:35:42 -0000	1.6
--- cut_locations_in_enzyme_notation.rb	16 Jul 2007 19:28:48 -0000	1.7
***************
*** 9,26 ****
  #
  
! require 'bio/util/restriction_enzyme/cut_symbol'
! require 'bio/sequence'
  
! module Bio; end
! class Bio::RestrictionEnzyme
! class SingleStrand < Bio::Sequence::NA
  
- #
- # bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb - The cut locations, in enzyme notation
- #
- # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
- # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
- # License::   The Ruby License
- #
  # Stores the cut location in thier enzyme index notation
  # 
--- 9,18 ----
  #
  
! require 'bio/util/restriction_enzyme'
  
! module Bio
! class RestrictionEnzyme
! class SingleStrand
  
  # Stores the cut location in thier enzyme index notation
  # 
***************
*** 140,142 ****
  end # CutLocationsInEnzymeNotation
  end # SingleStrand
! end # Bio::RestrictionEnzyme
\ No newline at end of file
--- 132,135 ----
  end # CutLocationsInEnzymeNotation
  end # SingleStrand
! end # RestrictionEnzyme
! end # Bio


From k at dev.open-bio.org  Mon Jul 16 15:28:50 2007
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Mon, 16 Jul 2007 19:28:50 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme/range
	cut_range.rb, 1.3, 1.4 cut_ranges.rb, 1.4,
	1.5 horizontal_cut_range.rb, 1.4, 1.5 sequence_range.rb, 1.8,
	1.9 vertical_cut_range.rb, 1.4, 1.5
Message-ID: <200707161928.l6GJSoH9021277@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range
In directory dev.open-bio.org:/tmp/cvs-serv21244/restriction_enzyme/range

Modified Files:
	cut_range.rb cut_ranges.rb horizontal_cut_range.rb 
	sequence_range.rb vertical_cut_range.rb 
Log Message:
* autoloadified


Index: vertical_cut_range.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** vertical_cut_range.rb	5 Apr 2007 23:35:42 -0000	1.4
--- vertical_cut_range.rb	16 Jul 2007 19:28:48 -0000	1.5
***************
*** 1,4 ****
  #
! # bio/util/restrction_enzyme/range/vertical_cut_range.rb - 
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
--- 1,4 ----
  #
! # bio/util/restriction_enzyme/range/vertical_cut_range.rb - 
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
***************
*** 9,25 ****
  #
  
! require 'bio/util/restriction_enzyme/range/cut_range'
  
! module Bio; end
! class Bio::RestrictionEnzyme
  class Range
  
- #
- # bio/util/restrction_enzyme/range/vertical_cut_range.