lib/bio/io/ddbjxml.rb in bio-1.0.0 vs lib/bio/io/ddbjxml.rb in bio-1.1.0
- old
+ new
@@ -1,32 +1,14 @@
#
# = bio/io/ddbjxml.rb - DDBJ SOAP server access class
#
# Copyright:: Copyright (C) 2003, 2004
-# KATAYAMA Toshiaki <k@bioruby.org>
-# License:: LGPL
+# Toshiaki Katayama <k@bioruby.org>
+# License:: The Ruby License
#
-# $Id: ddbjxml.rb,v 1.10 2006/02/02 16:30:29 nakao Exp $
+# $Id: ddbjxml.rb,v 1.14 2007/04/05 23:35:41 trevor Exp $
#
-#--
-#
-# This library is free software; you can redistribute it and/or
-# modify it under the terms of the GNU Lesser General Public
-# License as published by the Free Software Foundation; either
-# version 2 of the License, or (at your option) any later version.
-#
-# This library is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this library; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-#
-#++
-#
require 'bio/io/soapwsdl'
require 'bio/db/genbank/ddbj'
@@ -43,10 +25,17 @@
#
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
@@ -70,29 +59,24 @@
# param = '-m 8 -e 0.001'
# puts serv.searchParam(program, database, query, param)
#
# === WSDL Methods
#
- # ==== searchSimple(program, database, query)
+ # * searchSimple(program, database, query)
#
# Returns a blast report in the default format.
#
- # ==== searchParam(program, database, query, param)
+ # * 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"
-
- # returns a Bio::DDBJ::XML::Blast object.
- def initialize(wsdl = nil)
- super(wsdl || SERVER_URI)
- end
end
# === ClustalW
#
@@ -121,24 +105,19 @@
# puts serv.analyzeSimple(query)
# puts serv.analyzeParam(query, '-align -matrix=blosum')
#
# === WSDL Methods
#
- # ==== analyzeSimple(query)
- # ==== analyzeParam(query, param)
+ # * analyzeSimple(query)
+ # * analyzeParam(query, param)
#
# === References
#
# * http://xml.nig.ac.jp/doc/ClustalW.txt
#
class ClustalW < XML
SERVER_URI = BASE_URI + "ClustalW.wsdl"
-
- # returns a Bio::DDBJ::XML::ClustalW object.
- def initialize(wsdl = nil)
- super(wsdl || SERVER_URI)
- end
end
# == DDBJ
#
@@ -156,28 +135,23 @@
# 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)
+ # * 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"
-
- # returns a Bio::DDBJ::XML::DDBJ object.
- def initialize(wsdl = nil)
- super(wsdl || SERVER_URI)
- end
end
# == Fasta
#
@@ -194,24 +168,19 @@
# query = ">Test\nAGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC"
# puts serv.searchParam('fastx34_t', 'PDB', query, '-n')
#
# === WSDL Methods
#
- # ==== searchSimple(program, database, query)
- # ==== searchParam(program, database, query, param)
+ # * 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"
-
- # returns a Bio::DDBJ::XML::Fasta object.
- def initialize(wsdl = nil)
- super(wsdl || SERVER_URI)
- end
end
# == GetEntry
#
@@ -225,51 +194,46 @@
# 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)
+ # * 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"
-
- # returns a Bio::DDBJ::XML::GetEntry object.
- def initialize(wsdl = nil)
- super(wsdl || SERVER_URI)
- end
end
# === Gib
#
@@ -292,33 +256,28 @@
# 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)
+ # * 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"
-
- # returns a Bio::DDBJ::XML::Gib object.
- def initialize(wsdl = nil)
- super(wsdl || SERVER_URI)
- end
end
# === Gtop
#
@@ -332,24 +291,19 @@
# puts serv.getOrganismList
# puts serv.getMasterInfo('thrA', 'ecol0')
#
# === WSDL Methods
#
- # ==== getOrganismList
- # ==== getMasterInfo(orfID, organism)
+ # * getOrganismList
+ # * getMasterInfo(orfID, organism)
#
# === References
#
# * http://xml.nig.ac.jp/doc/Gtop.txt
#
class Gtop < XML
SERVER_URI = BASE_URI + "Gtop.wsdl"
-
- # returns a Bio::DDBJ::XML::Gtop object.
- def initialize(wsdl = nil)
- super(wsdl || SERVER_URI)
- end
end
# === PML
#
@@ -362,28 +316,23 @@
# 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)
+ # * 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"
-
- # returns a Bio::DDBJ::XML::PML object.
- def initialize(wsdl = nil)
- super(wsdl || SERVER_URI)
- end
end
# === SRS
#
@@ -397,24 +346,19 @@
# puts serv.searchSimple('[pathway-des:sugar]')
# puts serv.searchParam('[swissprot-des:cohesin]', '-f seq -sf fasta')
#
# === WSDL Methods
#
- # ==== searchSimple(query)
- # ==== searchParam(query, param)
+ # * searchSimple(query)
+ # * searchParam(query, param)
#
# === Examples
#
# * http://xml.nig.ac.jp/doc/SRS.txt
#
class SRS < XML
SERVER_URI = BASE_URI + "SRS.wsdl"
-
- # returns a Bio::DDBJ::XML::SRS object.
- def initialize(wsdl = nil)
- super(wsdl || SERVER_URI)
- end
end
# === TxSearch
#
@@ -434,26 +378,21 @@
# 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)
+ # * 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"
-
- # returns a Bio::DDBJ::XML::TxSearch object.
- def initialize(wsdl = nil)
- super(wsdl || SERVER_URI)
- end
end
end # XML
end # DDBJ