[BioRuby-cvs] bioruby/lib/bio/io ddbjxml.rb,1.11,1.12
Katayama Toshiaki
k at dev.open-bio.org
Tue Sep 19 05:44:43 UTC 2006
Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv31340/lib/bio/io
Modified Files:
ddbjxml.rb
Log Message:
* initialize methods are unified in the super class
Index: ddbjxml.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/ddbjxml.rb,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** ddbjxml.rb 8 May 2006 14:29:58 -0000 1.11
--- ddbjxml.rb 19 Sep 2006 05:44:41 -0000 1.12
***************
*** 3,7 ****
#
# Copyright:: Copyright (C) 2003, 2004
! # KATAYAMA Toshiaki <k at bioruby.org>
# License:: Ruby's
#
--- 3,7 ----
#
# Copyright:: Copyright (C) 2003, 2004
! # Toshiaki Katayama <k at bioruby.org>
# License:: Ruby's
#
***************
*** 28,31 ****
--- 28,35 ----
BASE_URI = "http://xml.nig.ac.jp/wsdl/"
+ def initialize(wsdl = nil)
+ super(wsdl || self.class::SERVER_URI)
+ end
+
# === Description
#
***************
*** 55,63 ****
# === 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.
--- 59,67 ----
# === 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.
***************
*** 69,77 ****
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
--- 73,76 ----
***************
*** 106,111 ****
# === WSDL Methods
#
! # ==== analyzeSimple(query)
! # ==== analyzeParam(query, param)
#
# === References
--- 105,110 ----
# === WSDL Methods
#
! # * analyzeSimple(query)
! # * analyzeParam(query, param)
#
# === References
***************
*** 115,123 ****
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
--- 114,117 ----
***************
*** 141,150 ****
# === WSDL Methods
#
! # ==== getFFEntry(accession)
! # ==== getXMLEntry(accession)
! # ==== getFeatureInfo(accession, feature)
! # ==== getAllFeatures(accession)
! # ==== getRelatedFeatures(accession, start, stop)
! # ==== getRelatedFeaturesSeq(accession, start, stop)
#
# === References
--- 135,144 ----
# === WSDL Methods
#
! # * getFFEntry(accession)
! # * getXMLEntry(accession)
! # * getFeatureInfo(accession, feature)
! # * getAllFeatures(accession)
! # * getRelatedFeatures(accession, start, stop)
! # * getRelatedFeaturesSeq(accession, start, stop)
#
# === References
***************
*** 154,162 ****
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
--- 148,151 ----
***************
*** 179,184 ****
# === WSDL Methods
#
! # ==== searchSimple(program, database, query)
! # ==== searchParam(program, database, query, param)
#
# === References
--- 168,173 ----
# === WSDL Methods
#
! # * searchSimple(program, database, query)
! # * searchParam(program, database, query, param)
#
# === References
***************
*** 188,196 ****
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
--- 177,180 ----
***************
*** 210,242 ****
# === 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
--- 194,226 ----
# === 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
***************
*** 246,254 ****
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
--- 230,233 ----
***************
*** 277,291 ****
# === WSDL Methods
#
! # ==== getOrganismList
! # ==== getChIDList
! # ==== getOrganismNameFromChid(chid)
! # ==== getChIDFromOrganismName(orgName)
! # ==== getAccession(chid)
! # ==== getPieceNumber(chid)
! # ==== getDivision(chid)
! # ==== getType(chid)
! # ==== getFlatFile(chid)
! # ==== getFastaFile(chid, type)
! # ==== getCDS(chid)
#
# === References
--- 256,270 ----
# === WSDL Methods
#
! # * getOrganismList
! # * getChIDList
! # * getOrganismNameFromChid(chid)
! # * getChIDFromOrganismName(orgName)
! # * getAccession(chid)
! # * getPieceNumber(chid)
! # * getDivision(chid)
! # * getType(chid)
! # * getFlatFile(chid)
! # * getFastaFile(chid, type)
! # * getCDS(chid)
#
# === References
***************
*** 295,303 ****
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
--- 274,277 ----
***************
*** 317,322 ****
# === WSDL Methods
#
! # ==== getOrganismList
! # ==== getMasterInfo(orfID, organism)
#
# === References
--- 291,296 ----
# === WSDL Methods
#
! # * getOrganismList
! # * getMasterInfo(orfID, organism)
#
# === References
***************
*** 326,334 ****
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
--- 300,303 ----
***************
*** 347,356 ****
# === 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
--- 316,325 ----
# === 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
***************
*** 360,368 ****
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
--- 329,332 ----
***************
*** 382,387 ****
# === WSDL Methods
#
! # ==== searchSimple(query)
! # ==== searchParam(query, param)
#
# === Examples
--- 346,351 ----
# === WSDL Methods
#
! # * searchSimple(query)
! # * searchParam(query, param)
#
# === Examples
***************
*** 391,399 ****
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
--- 355,358 ----
***************
*** 419,427 ****
# === 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
--- 378,386 ----
# === 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
***************
*** 431,439 ****
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
--- 390,393 ----
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