bio 1.4.3.0001 → 1.5.0

data/lib/bio/io/ddbjrest.rb

@@ -1,344 +0,0 @@
-#
-# = bio/io/ddbjrest.rb - DDBJ Web API for Biology (WABI) access class via REST
-#
-# Copyright::	Copyright (C) 2011
-#		Naohisa Goto <ng@bioruby.org>
-# License::	The Ruby License
-#
-# == Description
-# 
-# This file contains Bio::DDBJ::REST, DDBJ Web API for Biology (WABI) access
-# classes via REST (Representational State Transfer) protocol.
-#
-# == References
-#
-# * http://xml.nig.ac.jp/
-#
-
-require 'bio/command'
-require 'bio/db/genbank/ddbj'
-
-module Bio
-class DDBJ
-
-  # == Description
-  #
-  # The module Bio::DDBJ::REST is the namespace for the DDBJ Web API for
-  # Biology (WABI) via REST protocol. Under the Bio::DDBJ::REST,
-  # following classes are available.
-  #
-  # * Bio::DDBJ::REST::DDBJ
-  # * Bio::DDBJ::REST::Blast
-  # * Bio::DDBJ::REST::ClustalW
-  # * Bio::DDBJ::REST::Mafft
-  # * Bio::DDBJ::REST::RequestManager
-  #
-  # Following classes are NOT available, but will be written in the future.
-  #
-  # * Bio::DDBJ::REST::GetEntry
-  # * Bio::DDBJ::REST::ARSA
-  # * Bio::DDBJ::REST::VecScreen
-  # * Bio::DDBJ::REST::PhylogeneticTree
-  # * Bio::DDBJ::REST::Gib
-  # * Bio::DDBJ::REST::Gtop
-  # * Bio::DDBJ::REST::GTPS
-  # * Bio::DDBJ::REST::GIBV
-  # * Bio::DDBJ::REST::GIBIS
-  # * Bio::DDBJ::REST::SPS
-  # * Bio::DDBJ::REST::TxSearch
-  # * Bio::DDBJ::REST::Ensembl
-  # * Bio::DDBJ::REST::NCBIGenomeAnnotation
-  #
-  # Read the document of each class for details.
-  #
-  # In addition, there is a private class Bio::DDBJ::REST::WABItemplate,
-  # basic class for the above classes. Normal users should not use the
-  # WABItemplate class directly.
-  #
-  module REST
-
-    # Bio::DDBJ::REST::WABItemplate is a private class to provide common
-    # methods to access DDBJ Web API for Biology (WABI) services by using
-    # REST protocol.
-    #
-    # Normal users should not use the class directly.
-    #
-    class WABItemplate
-
-      # hostname for the WABI service
-      WABI_HOST = 'xml.nig.ac.jp'
-
-      # path for the WABI service
-      WABI_PATH = '/rest/Invoke'
-
-      private
-
-      # Creates a new object.
-      def initialize
-        @http = Bio::Command.new_http(WABI_HOST)
-        @service = self.class.to_s.split(/\:\:/)[-1]
-      end
-
-      # (private) query to the service by using POST method
-      def _wabi_post(method_name, param)
-        parameters = {
-          'service' => @service,
-          'method' => method_name
-        }
-        parameters.update(param)
-        #$stderr.puts parameters.inspect
-        r = Bio::Command.http_post_form(@http, WABI_PATH, parameters)
-        #$stderr.puts r.inspect
-        #$stderr.puts "-"*78
-        #$stderr.puts r.body
-        #$stderr.puts "-"*78
-        r.body
-      end
-
-      def self.define_wabi_method(array,
-                                  ruby_method_name = nil,
-                                  public_method_name = nil)
-        wabi_method_name = array[0]
-        ruby_method_name ||= wabi_method_name
-        public_method_name ||= wabi_method_name
-        arg = array[1..-1]
-        arguments = arg.join(', ')
-        parameters = "{" +
-          arg.collect { |x| "#{x.dump} => #{x}" }.join(", ") + "}"
-        module_eval "def #{ruby_method_name}(#{arguments})
-                       param = #{parameters}
-                       _wabi_post(#{wabi_method_name.dump}, param)
-                     end
-                     def self.#{public_method_name}(#{arguments})
-                       self.new.#{public_method_name}(#{arguments})
-                     end"
-        self
-      end
-      private_class_method :define_wabi_method
-
-      def self.def_wabi(array)
-        define_wabi_method(array)
-      end
-      private_class_method :def_wabi
-
-      def self.def_wabi_custom(array)
-        ruby_method_name = '_' + array[0]
-        define_wabi_method(array, ruby_method_name)
-        module_eval "private :#{ruby_method_name}"
-        self
-      end
-      private_class_method :def_wabi_custom
-
-      def self.def_wabi_async(array)
-        m = array[0]
-        def_wabi_custom(array)
-        module_eval "def #{m}(*arg)
-            ret = _#{m}(*arg)
-            if /Your +requestId +is\s*\:\s*(.+)\s*/i =~ ret.to_s then
-              return $1
-            else
-              raise \"unknown return value: \#\{ret.inspect\}\"
-            end
-          end"
-        self
-      end
-      private_class_method :def_wabi_async
-    end #class WABItemplate
-
-    # === Description
-    #
-    # DDBJ (DNA DataBank of Japan) entry retrieval functions.
-    #
-    # * http://xml.nig.ac.jp/wabi/Method?serviceName=DDBJ&mode=methodList&lang=en
-    #
-    # === Examples
-    #
-    # see http://xml.nig.ac.jp/wabi/Method?serviceName=DDBJ&mode=methodList&lang=en
-    #
-    class DDBJ < WABItemplate
-
-      # Number and ratio of each base such as A,T,G,C.
-      #
-      # see http://xml.nig.ac.jp/wabi/Method?&lang=en&serviceName=DDBJ&methodName=countBasePair&mode=methodDetail
-      # ---
-      # *Arguments*:
-      # * (required) _accession_: (String) accession
-      # *Returns*:: (String) tab-deliminated text
-      def countBasePair(accession); end if false #dummy
-      def_wabi %w( countBasePair accession )
-
-      # see http://xml.nig.ac.jp/wabi/Method?&lang=en&serviceName=DDBJ&methodName=get&mode=methodDetail
-      def get(accessionList, paramList); end if false #dummy
-      def_wabi %w( get accessionList paramList )
-
-      # see http://xml.nig.ac.jp/wabi/Method?&lang=en&serviceName=DDBJ&methodName=getAllFeatures&mode=methodDetail
-      def getAllFeatures(accession); end if false #dummy
-      def_wabi %w( getAllFeatures accession )
-
-      # see http://xml.nig.ac.jp/wabi/Method?&lang=en&serviceName=DDBJ&methodName=getFFEntry&mode=methodDetail
-      def getFFEntry(accession); end if false #dummy
-      def_wabi %w( getFFEntry accession )
-
-      # http://xml.nig.ac.jp/wabi/Method?&lang=en&serviceName=DDBJ&methodName=getRelatedFeatures&mode=methodDetail
-      def getRelatedFeatures(accession, start, stop); end if false #dummy
-      def_wabi %w( getRelatedFeatures accession start stop )
-
-      # see http://xml.nig.ac.jp/wabi/Method?&lang=en&serviceName=DDBJ&methodName=getRelatedFeaturesSeq&mode=methodDetail
-      def getRelatedFeaturesSeq(accession, start, stop); end if false #dummy
-      def_wabi %w( getRelatedFeaturesSeq accession start stop )
-    end #class DDBJ
-
-    # === Description
-    #
-    # DDBJ (DNA DataBank of Japan) BLAST web service.
-    # See below for details and examples.
-    #
-    # Users normally would want to use searchParamAsync or
-    # searchParallelAsync with RequestManager.
-    #
-    # * http://xml.nig.ac.jp/wabi/Method?serviceName=Blast&mode=methodList&lang=en
-    class Blast < WABItemplate
-
-      # see http://xml.nig.ac.jp/wabi/Method?&lang=en&serviceName=Blast&methodName=extractPosition&mode=methodDetail
-      def extractPosition(result); end if false #dummy
-      def_wabi %w( extractPosition result )
-
-      # see http://xml.nig.ac.jp/wabi/Method?&lang=en&serviceName=Blast&methodName=getSupportDatabaseList&mode=methodDetail
-      def getSupportDatabaseList(); end if false #dummy
-      def_wabi %w( getSupportDatabaseList )
-
-      # see http://xml.nig.ac.jp/wabi/Method?&lang=en&serviceName=Blast&methodName=searchParallel&mode=methodDetail
-      def searchParallel(program, database, query, param); end if false #dummy
-      def_wabi %w( searchParallel program database query param )
-
-      # see http://xml.nig.ac.jp/wabi/Method?&lang=en&serviceName=Blast&methodName=searchParallelAsync&mode=methodDetail
-      def searchParallelAsync(program, database,
-                              query, param); end if false #dummy
-      def_wabi_async %w( searchParallelAsync program database query param )
-
-      # see http://xml.nig.ac.jp/wabi/Method?&lang=en&serviceName=Blast&methodName=searchParam&mode=methodDetail
-      def searchParam(program, database, query, param); end if false #dummy
-      def_wabi %w( searchParam program database query param )
-
-      # see http://xml.nig.ac.jp/wabi/Method?&lang=en&serviceName=Blast&methodName=searchParamAsync&mode=methodDetail
-      def searchParamAsync(program, database,
-                           query, param); end if false #dummy
-      def_wabi_async %w( searchParamAsync program database query param )
-
-      # see http://xml.nig.ac.jp/wabi/Method?&lang=en&serviceName=Blast&methodName=searchSimple&mode=methodDetail
-      def searchSimple(program, database, query); end if false #dummy
-      def_wabi %w( searchSimple program database query )
-
-      # see http://xml.nig.ac.jp/wabi/Method?&lang=en&serviceName=Blast&methodName=searchSimpleAsync&mode=methodDetail
-      def searchSimpleAsync(program, database, query); end if false #dummy
-      def_wabi_async %w( searchSimpleAsync program database query )
-
-    end #class Blast
-
-    # === Description
-    #
-    # DDBJ (DNA DataBank of Japan) web service of ClustalW multiple sequence
-    # alignment software.
-    # See below for details and examples.
-    #
-    # * http://xml.nig.ac.jp/wabi/Method?serviceName=ClustalW&mode=methodList&lang=en
-    class ClustalW < WABItemplate
-      # see http://xml.nig.ac.jp/wabi/Method?&lang=en&serviceName=ClustalW&methodName=analyzeParam&mode=methodDetail
-      def analyzeParam(query, param); end if false #dummy
-      def_wabi %w( analyzeParam query param )
-
-      # see http://xml.nig.ac.jp/wabi/Method?&lang=en&serviceName=ClustalW&methodName=analyzeParamAsync&mode=methodDetail
-      def analyzeParamAsync(query, param); end if false #dummy
-      def_wabi_async %w( analyzeParamAsync query param )
-
-      # http://xml.nig.ac.jp/wabi/Method?&lang=en&serviceName=ClustalW&methodName=analyzeSimple&mode=methodDetail
-      def analyzeSimple(query); end if false #dummy
-      def_wabi %w( analyzeSimple query )
-
-      # http://xml.nig.ac.jp/wabi/Method?&lang=en&serviceName=ClustalW&methodName=analyzeSimpleAsync&mode=methodDetail
-      def analyzeSimpleAsync(query); end if false #dummy
-      def_wabi_async %w( analyzeSimpleAsync query )
-    end #lcass ClustalW
-
-    # === Description
-    #
-    # DDBJ (DNA DataBank of Japan) web service of MAFFT multiple sequence
-    # alignment software.
-    # See below for details and examples.
-    #
-    # * http://xml.nig.ac.jp/wabi/Method?serviceName=Mafft&mode=methodList&lang=en
-    class Mafft < WABItemplate
-      # see http://xml.nig.ac.jp/wabi/Method?&lang=en&serviceName=Mafft&methodName=analyzeParam&mode=methodDetail
-      def analyzeParam(query, param); end if false #dummy
-      def_wabi %w( analyzeParam query param )
-
-      # see http://xml.nig.ac.jp/wabi/Method?&lang=en&serviceName=Mafft&methodName=analyzeParamAsync&mode=methodDetail
-      def analyzeParamAsync(query, param); end if false #dummy
-      def_wabi_async %w( analyzeParamAsync query param )
-
-      # see http://xml.nig.ac.jp/wabi/Method?&lang=en&serviceName=Mafft&methodName=analyzeSimple&mode=methodDetail
-      def analyzeSimple(query); end if false #dummy
-      def_wabi %w( analyzeSimple query )
-
-      # see http://xml.nig.ac.jp/wabi/Method?&lang=en&serviceName=Mafft&methodName=analyzeSimpleAsync&mode=methodDetail
-      def analyzeSimpleAsync(query); end if false #dummy
-      def_wabi_async %w( analyzeSimpleAsync query )
-    end #lcass Mafft
-
-
-    # === Description
-    #
-    # DDBJ (DNA DataBank of Japan) special web service to get result of
-    # asynchronous web service.
-    # See below for details and examples.
-    #
-    # * http://xml.nig.ac.jp/wabi/Method?serviceName=RequestManager&mode=methodList&lang=en
-    class RequestManager < WABItemplate
-
-      # see http://xml.nig.ac.jp/wabi/Method?&lang=en&serviceName=RequestManager&methodName=getAsyncResult&mode=methodDetail
-      def getAsyncResult(requestId); end if false #dummy
-      def_wabi %w( getAsyncResult requestId )
-
-      # Waits until the query is finished and the result is returnd,
-      # with calling getAsyncResult.
-      # 
-      # This is BioRuby original method.
-      # ---
-      # *Arguments*:
-      # * (required) _requestID_: (String) requestId
-      # *Returns*:: (String) result
-      def wait_getAsyncResult(requestId)
-        sleeptime = 2
-        while true
-          result = getAsyncResult(requestId)
-          case result.to_s
-          when /The search and analysis service by WWW is very busy now/
-            raise result.to_s.strip + '(Alternatively, wrong options may be given.)'
-          when /\AYour job has not (?:been )?completed yet/
-            sleeptime = 2 + rand(4)
-          when /\AERROR:/
-            raise result.to_s.strip
-          else
-            return result
-          end #case
-          if $VERBOSE then
-            $stderr.puts "DDBJ REST: requestId: #{requestId} -- waitng #{sleeptime} sec."
-          end
-          sleep(sleeptime)
-        end
-        # will never be reached here
-        raise "Bug?"
-      end
-
-      # the same as Bio::DDBJ::REST::RequestManager#wait_getAsyncResult
-      def self.wait_getAsyncResult(requestId)
-        self.new.wait_getAsyncResult(requestId)
-      end
-
-    end #class RequestManager
-
-  end #module REST
-end #class DDBJ
-end #module Bio
-
-

data/lib/bio/io/ddbjxml.rb

@@ -1,458 +0,0 @@
-#
-# = bio/io/ddbjxml.rb - DDBJ SOAP server access class
-#
-# Copyright::	Copyright (C) 2003, 2004
-#		Toshiaki Katayama <k@bioruby.org>
-# License::	The Ruby License
-#
-# $Id:$
-#
-
-require 'bio/io/soapwsdl'
-require 'bio/db/genbank/ddbj'
-
-
-module Bio
-class DDBJ
-
-
-# = Bio::DDBJ::XML
-#
-# Accessing the DDBJ web services.
-#
-# * http://xml.nig.ac.jp/
-# * http://xml.nig.ac.jp/wsdl/index.jsp
-#
-class XML < Bio::SOAPWSDL
-
-  BASE_URI = "http://xml.nig.ac.jp/wsdl/"
-
-  # set default to GetEntry
-  SERVER_URI = BASE_URI + "GetEntry.wsdl"
-
-  def initialize(wsdl = nil)
-    super(wsdl || self.class::SERVER_URI)
-  end
-
-  # === Description
-  #
-  # DDBJ XML BLAST Database Search 
-  #
-  # * http://xml.nig.ac.jp/doc/Blast.txt
-  #
-  # === Examples
-  #
-  #   serv = Bio::DDBJ::XML::Blast.new
-  #   program = 'blastp'
-  #   database = 'SWISS'
-  #   query = "MSSRIARALALVVTLLHLTRLALSTCPAACHCPLEAPKCAPGVGLVRDGCGCCKVCAKQL"
-  #   
-  #   report = serv.searchSimple(program, database, query)
-  #   Bio::Blast::Default::Report.new(report).each_hit do |hit|
-  #     hit.hsps.find_all {|x| x.evalue < 0.1 }.each do |hsp|
-  #       p [hsps.evalue, hsps.identity, hsps.definition]
-  #     end
-  #   end
-  #  
-  #   program = 'tblastn'
-  #   database = 'ddbjvrl'
-  #   param = '-m 8 -e 0.001'
-  #   puts serv.searchParam(program, database, query, param)
-  # 
-  # === WSDL Methods
-  # 
-  # * searchSimple(program, database, query)
-  #
-  # Returns a blast report in the default format.
-  #
-  # * searchParam(program, database, query, param)
-  #
-  # Blasts with param and returns a blast report.
-  #
-  # === References
-  #
-  # * http://xml.nig.ac.jp/doc/Blast.txt
-  #
-  class Blast < XML
-    SERVER_URI = BASE_URI + "Blast.wsdl"
-  end
-
-
-  # === ClustalW
-  # 
-  # Multiple seaquece alignment using ClustalW.
-  #
-  # * http://xml.nig.ac.jp/doc/ClustalW.txt
-  #
-  # === Examples
-  #
-  #   serv = Bio::DDBJ::XML::ClustalW.new
-  #
-  #   query = <<END
-  #   > RABSTOUT   rabbit Guinness receptor
-  #   LKMHLMGHLKMGLKMGLKGMHLMHLKHMHLMTYTYTTYRRWPLWMWLPDFGHAS
-  #   ADSCVCAHGFAVCACFAHFDVCFGAVCFHAVCFAHVCFAAAVCFAVCAC
-  #   > MUSNOSE   mouse nose drying factor
-  #   mhkmmhkgmkhmhgmhmhglhmkmhlkmgkhmgkmkytytytryrwtqtqwtwyt
-  #   fdgfdsgafdagfdgfsagdfavdfdvgavfsvfgvdfsvdgvagvfdv
-  #   > HSHEAVEN    human Guinness receptor repeat
-  #   mhkmmhkgmkhmhgmhmhg   lhmkmhlkmgkhmgkmk  ytytytryrwtqtqwtwyt
-  #   fdgfdsgafdagfdgfsag   dfavdfdvgavfsvfgv  dfsvdgvagvfdv
-  #   mhkmmhkgmkhmhgmhmhg   lhmkmhlkmgkhmgkmk  ytytytryrwtqtqwtwyt
-  #   fdgfdsgafdagfdgfsag   dfavdfdvgavfsvfgv  dfsvdgvagvfdv
-  #   END
-  #
-  #   puts serv.analyzeSimple(query)
-  #   puts serv.analyzeParam(query, '-align -matrix=blosum')
-  #
-  # === WSDL Methods
-  #
-  # * analyzeSimple(query)
-  # * analyzeParam(query, param)
-  #
-  # === References
-  #
-  # * http://xml.nig.ac.jp/doc/ClustalW.txt
-  #
-  class ClustalW < XML
-    SERVER_URI = BASE_URI + "ClustalW.wsdl"
-  end
-
-
-  # == DDBJ
-  #
-  # Retrieves a sequence entry from the DDBJ DNA Data Bank Japan.
-  #
-  # * http://xml.nig.ac.jp/doc/DDBJ.txt
-  #
-  # === Examples
-  #
-  #   serv = Bio::DDBJ::XML::DDBJ.new
-  #   puts serv.getFFEntry('AB000050')
-  #   puts serv.getXMLEntry('AB000050')
-  #   puts serv.getFeatureInfo('AB000050', 'cds')
-  #   puts serv.getAllFeatures('AB000050')
-  #   puts serv.getRelatedFeatures('AL121903', '59000', '64000')
-  #   puts serv.getRelatedFeaturesSeq('AL121903', '59000', '64000')
-  #
-  # === WSDL Methods 
-  #
-  # * getFFEntry(accession)
-  # * getXMLEntry(accession)
-  # * getFeatureInfo(accession, feature)
-  # * getAllFeatures(accession)
-  # * getRelatedFeatures(accession, start, stop)
-  # * getRelatedFeaturesSeq(accession, start, stop)
-  #
-  # === References
-  #
-  # * http://xml.nig.ac.jp/doc/DDBJ.txt
-  #
-  class DDBJ < XML
-    SERVER_URI = BASE_URI + "DDBJ.wsdl"
-  end
-
-
-  # == Fasta
-  # 
-  # Searching database using the Fasta package.
-  #
-  # * http://xml.nig.ac.jp/doc/Fasta.txt
-  # 
-  # === Examples
-  #
-  #   serv = Bio::DDBJ::XML::Fasta.new
-  #   query = ">Test\nMSDGAVQPDG GQPAVRNERA TGSGNGSGGG GGGGSGGVGI"
-  #    
-  #   puts serv.searchSimple('fasta34', 'PDB', query)
-  #   query = ">Test\nAGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC"
-  #   puts serv.searchParam('fastx34_t', 'PDB', query, '-n')
-  #
-  # === WSDL Methods
-  #
-  # * searchSimple(program, database, query)
-  # * searchParam(program, database, query, param)
-  #
-  # === References
-  #
-  # * http://xml.nig.ac.jp/doc/Fasta.txt
-  #
-  class Fasta < XML
-    SERVER_URI = BASE_URI + "Fasta.wsdl"
-  end
-
-
-  # == GetEntry
-  #
-  # Retrieves database entries.
-  #
-  # * http://xml.nig.ac.jp/doc/GetEntry.txt
-  #
-  # === Examples
-  #
-  #  serv = Bio::DDBJ::XML::GetEntry.new
-  #  puts serv.getDDBJEntry('AB000050')
-  #  puts serv. getPDBEntry('1AAR')
-  #
-  # === WSDL Methods
-  #
-  # * getEntry(database, var, param1, param2)
-  # * getEntry(database, var)
-  # * getDDBJEntry(accession)
-  # * getDDBJCONEntry(accession)
-  # * getDDBJVerEntry(accession)
-  # * getLocus_DDBJEntry(locus)
-  # * getGene_DDBJEntry(gene)
-  # * getProd_DDBJEntry(products)
-  # * getPID_DDBJEntry(pid)
-  # * getClone_DDBJEntry(clone)
-  # * getXML_DDBJEntry(accession)
-  # * getEMBLEntry(accession)
-  # * getSWISSEntry(accession)
-  # * getPIREntry(accession)
-  # * getPRFEntry(accession)
-  # * getPDBEntry(accession)
-  # * getQVEntry(accession)
-  # * getDADEntry(accession)
-  # * getPID_DADEntry(pid)
-  # * getFASTA_DDBJEntry(accession)
-  # * getFASTA_DDBJCONEntry(accession)
-  # * getFASTA_DDBJVerEntry(accession)
-  # * getFASTA_DDBJSeqEntry(accession, start, end)
-  # * getFASTA_DADEntry(accession)
-  # * getFASTA_PIREntry(accession)
-  # * getFASTA_SWISSEntry(accession)
-  # * getFASTA_PDBEntry(accession)
-  # * getFASTA_PRFEntry(accession)
-  # * getFASTA_CDSEntry(accession)
-  #
-  # === References
-  #
-  # * http://xml.nig.ac.jp/doc/GetEntry.txt
-  #
-  class GetEntry < XML
-    SERVER_URI = BASE_URI + "GetEntry.wsdl"
-  end
-
-
-  # === Gib
-  # 
-  # Genome Information broker
-  #
-  # * http://xml.nig.ac.jp/doc/Gib.txt
-  #
-  # === Examples
-  #
-  #   serv = Bio::DDBJ::XML::Gib.new
-  #   puts serv.getOrganismList
-  #   puts serv.getChIDList
-  #   puts serv.getOrganismNameFromChid('Sent_CT18:')
-  #   puts serv.getChIDFromOrganismName('Aquifex aeolicus VF5')
-  #   puts serv.getAccession('Ecol_K12_MG1655:')
-  #   puts serv.getPieceNumber('Mgen_G37:')
-  #   puts serv.getDivision('Mgen_G37:')
-  #   puts serv.getType('Mgen_G37:')
-  #   puts serv.getCDS('Aaeo_VF5:ece1')
-  #   puts serv.getFlatFile('Nost_PCC7120:pCC7120zeta')
-  #   puts serv.getFastaFile('Nost_PCC7120:pCC7120zeta', 'cdsaa')
-  #
-  # === WSDL Methods
-  #
-  # * getOrganismList
-  # * getChIDList
-  # * getOrganismNameFromChid(chid)
-  # * getChIDFromOrganismName(orgName)
-  # * getAccession(chid)
-  # * getPieceNumber(chid)
-  # * getDivision(chid)
-  # * getType(chid)
-  # * getFlatFile(chid)
-  # * getFastaFile(chid, type)
-  # * getCDS(chid)
-  #
-  # === References
-  #
-  # * http://xml.nig.ac.jp/doc/Gib.txt
-  #
-  class Gib < XML
-    SERVER_URI = BASE_URI + "Gib.wsdl"
-  end
-
-  
-  # === Gtop
-  #
-  # GTOP: Gene to protein.
-  #
-  # * http://xml.nig.ac.jp/doc/Gtop.txt
-  #
-  # === Examples
-  #
-  #   serv = Bio::DDBJ::XML::Gtop.new
-  #   puts serv.getOrganismList
-  #   puts serv.getMasterInfo('thrA', 'ecol0')
-  #
-  # === WSDL Methods
-  #
-  # * getOrganismList
-  # * getMasterInfo(orfID, organism)
-  #
-  # === References
-  #
-  # * http://xml.nig.ac.jp/doc/Gtop.txt
-  #
-  class Gtop < XML
-    SERVER_URI = BASE_URI + "Gtop.wsdl"
-  end
-
-
-  # === PML
-  #
-  # Variation database
-  #
-  # * http://xml.nig.ac.jp/doc/PML.txt
-  # 
-  # === Examples
-  #
-  #   serv = Bio::DDBJ::XML::PML.new
-  #   puts serv.getVariation('1')
-  #
-  # === WSDL Methods
-  #
-  # * searchVariation(field, query, order)
-  # * searchVariationSimple(field, query)
-  # * searchFrequency(field, query, order)
-  # * searchFrequencySimple(field, query)
-  # * getVariation(variation_id)
-  # * getFrequency(variation_id, population_id)
-  #
-  # === References
-  #
-  # * http://xml.nig.ac.jp/doc/PML.txt
-  #
-  class PML < XML
-    SERVER_URI = BASE_URI + "PML.wsdl"
-  end
-
-  # === RequestManager
-  #
-  # Sequence Retrieving System
-  # 
-  # * http://xml.nig.ac.jp/doc/RequestManager.txt
-  # 
-  # === Examples
-  #
-  #   serv = Bio::DDBJ::XML::RequestManager.new
-  #   puts serv.getAsyncResult('20070420102828140')
-  #
-  # === WSDL Methods
-  #
-  # * getAsyncResult( requestId )
-  # * getAsyncResultMime( requestId )
-  #
-  # === Examples
-  #
-  # * http://xml.nig.ac.jp/doc/RequestManager.txt
-  #
-  class RequestManager < XML
-    SERVER_URI = BASE_URI + "RequestManager.wsdl"
-
-    # RequestManager using DDBJ REST interface
-    class REST
-      require 'bio/command'
-
-      Uri = 'http://xml.nig.ac.jp/rest/Invoke'
-      Service = 'RequestManager'
-
-      def getAsyncResult(requestId)
-        params = {
-          'service'   => Service,
-          'method'    => 'getAsyncResult',
-          'requestId' => requestId.to_s
-        }
-        r = Bio::Command.post_form(Uri, params)
-        r.body
-      end
-    end #class REST
-
-    unless defined? new_orig then
-      class << RequestManager
-        alias new_orig new
-        private :new_orig
-      end
-    end
-
-    # creates a new driver
-    def self.new(wsdl = nil)
-      begin
-        new_orig(wsdl)
-      rescue RuntimeError
-        REST.new
-      end
-    end
-  end #class RequestManager
-
-  # === SRS
-  #
-  # Sequence Retrieving System
-  # 
-  # * http://xml.nig.ac.jp/doc/SRS.txt
-  # 
-  # === Examples
-  #
-  #   serv = Bio::DDBJ::XML::SRS.new
-  #   puts serv.searchSimple('[pathway-des:sugar]')
-  #   puts serv.searchParam('[swissprot-des:cohesin]', '-f seq -sf fasta')
-  #
-  # === WSDL Methods
-  #
-  # * searchSimple(query)
-  # * searchParam(query, param)
-  #
-  # === Examples
-  #
-  # * http://xml.nig.ac.jp/doc/SRS.txt
-  #
-  class SRS < XML
-    SERVER_URI = BASE_URI + "SRS.wsdl"
-  end
-  
-
-  # === TxSearch
-  #
-  # Searching taxonomy information.
-  # 
-  # * http://xml.nig.ac.jp/doc/TxSearch.txt
-  #
-  # === Examples
-  #
-  #   serv = Bio::DDBJ::XML::TxSearch.new
-  #   puts serv.searchSimple('*coli')
-  #   puts serv.searchSimple('*tardigrada*')
-  #   puts serv.getTxId('Escherichia coli')
-  #   puts serv.getTxName('562')
-  #
-  #   query = ["Campylobacter coli", "Escherichia coli"].join("\n")
-  #   rank = ["family", "genus"].join("\n")
-  #   puts serv.searchLineage(query, rank, 'Bacteria')
-  #
-  # === WSDL Methdos
-  #
-  # * searchSimple(tx_Name)
-  # * searchParam(tx_Name, tx_Clas, tx_Rank, tx_Rmax, tx_Dcls)
-  # * getTxId(tx_Name)
-  # * getTxName(tx_Id)
-  # * searchLineage(query, ranks, superkingdom)
-  # 
-  # === References
-  #
-  # * http://xml.nig.ac.jp/doc/TxSearch.txt
-  #
-  class TxSearch < XML
-    SERVER_URI = BASE_URI + "TxSearch.wsdl"
-  end
-
-end # XML
-
-end # DDBJ
-end # Bio
-