[BioRuby-cvs] bioruby/lib/bio/io ncbirest.rb,1.1,1.2

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv12443

Modified Files:
	ncbirest.rb 
Log Message:
* doc update


Index: ncbirest.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/ncbirest.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** ncbirest.rb	19 Feb 2008 03:36:52 -0000	1.1
--- ncbirest.rb	19 Feb 2008 04:49:35 -0000	1.2
***************
*** 1,4 ****
  #
! # = bio/io/ncbrest.rb - NCBI Entrez client module
  #
  # Copyright::  Copyright (C) 2008 Toshiaki Katayama <k at bioruby.org>
--- 1,4 ----
  #
! # = bio/io/ncbirest.rb - NCBI Entrez client module
  #
  # Copyright::  Copyright (C) 2008 Toshiaki Katayama <k at bioruby.org>
***************
*** 16,26 ****
  # The Bio::NCBI::REST class provides REST client for the NCBI E-Utilities
  #
! # * Entrez utilities index:
! #      http://www.ncbi.nlm.nih.gov/entrez/utils/utils_index.html
! # * How to link:
! #     http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helplinks.chapter.linkshelp
  #
  # == Usage
  #
  #  Bio::NCBI::REST.esearch("tardigrada", {"db"=>"nuccore", "rettype"=>"gb"})
  #  Bio::NCBI::REST.esearch("yeast kinase", {"db"=>"nuccore", "rettype"=>"gb", "retmode"=>"xml", "retmax"=>5})
--- 16,26 ----
  # The Bio::NCBI::REST class provides REST client for the NCBI E-Utilities
  #
! # Entrez utilities index:
! #
! # * http://www.ncbi.nlm.nih.gov/entrez/utils/utils_index.html
  #
  # == Usage
  #
+ #  Bio::NCBI::REST.esearch("tardigrada", {"db"=>"nuccore", "rettype"=>"count"})
  #  Bio::NCBI::REST.esearch("tardigrada", {"db"=>"nuccore", "rettype"=>"gb"})
  #  Bio::NCBI::REST.esearch("yeast kinase", {"db"=>"nuccore", "rettype"=>"gb", "retmode"=>"xml", "retmax"=>5})
***************
*** 64,69 ****
    # * _str_: query string (required)
    # * _hash_: hash of E-Utils option {"db" => "nuccore", "rettype" => "gb"}
!   #   * _db_: "nuccore", "pubmed", ...
!   #   * _retmode_: "xml", "html", ...
    #   * _rettype_: "gb", "medline", "count", ...
    #   * _retmax_: integer (default 100)
--- 64,69 ----
    # * _str_: query string (required)
    # * _hash_: hash of E-Utils option {"db" => "nuccore", "rettype" => "gb"}
!   #   * _db_: "nuccore", "nucleotide", "protein", "pubmed", ...
!   #   * _retmode_: "text", "xml", "html", ...
    #   * _rettype_: "gb", "medline", "count", ...
    #   * _retmax_: integer (default 100)
***************
*** 100,109 ****
    # Retrieve a database entry by given ID and using E-Utils (efetch) and
    # returns an array of entry string. Multiple IDs can be supplied.
    # ---
    # *Arguments*:
    # * _ids_: list of NCBI entry IDs (required)
    # * _hash_: hash of E-Utils option {"db" => "nuccore", "rettype" => "gb"}
!   #   * _db_: "nuccore", "pubmed", ...
!   #   * _retmode_: "xml", "html", ...
    #   * _rettype_: "gb", "medline", "count",...
    #   * _retmax_: integer (default 100)
--- 100,114 ----
    # Retrieve a database entry by given ID and using E-Utils (efetch) and
    # returns an array of entry string. Multiple IDs can be supplied.
+   #
+   # For information on the possible arguments, see
+   #
+   # * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html
+   #
    # ---
    # *Arguments*:
    # * _ids_: list of NCBI entry IDs (required)
    # * _hash_: hash of E-Utils option {"db" => "nuccore", "rettype" => "gb"}
!   #   * _db_: "nuccore", "nucleotide", "protein", "pubmed", ...
!   #   * _retmode_: "text", "xml", "html", ...
    #   * _rettype_: "gb", "medline", "count",...
    #   * _retmax_: integer (default 100)