bio-ucsc-api 0.5.3 → 0.6.0

data/ChangeLog.md

@@ -1,4 +1,6 @@
 #Change Log
+ * **NEW** (v0.6.0): Support ActiveRecord v4.0 (a part of Ruby on Ralils v4.0). Other related library dependencies are also updated. To Supress deprecation warnings for using dynamic finders such as 'find_by_name_and_chrom', use `ActiveSupport::Deprecation.silenced = true`. Because ActiveRecord v4.0 does not support Ruby v1.8.7 and earlier, Ruby UCSC API no longer supports these older Rubies.
+ * **UPDATE** (v0.6.0): Ruby UCSC API is now licensed under the MIT License. See also the LICENSE.txt file.
  * **BUG-FIX** (v 0.5.3): Support ActiveRecord/ActiveSupport version 3 only.
  * **UPDATE** (v 0.5.3): The Rat Rn5 database is supported.
  * **UPDATE** (v 0.5.3): Bug-fix and update to pass all specs on Ruby 2.0.0-p0.

data/Gemfile

@@ -1,21 +1,22 @@
 source "http://rubygems.org"
 # Add dependencies required to use your gem here.
-# Example:
-#   gem "activesupport", ">= 2.3.5"
-gem "activerecord",         "~> 3.0.7"
-gem "activesupport",        "~> 3.0.7"
-gem "mysql",                "~> 2.8.1"
-gem "bio-genomic-interval", ">= 0.1.2"
-gem "safe_attributes",      ">= 1.0.8"
+
+gem "activerecord",                    "~> 4.0.2"
+gem "activesupport",                   "~> 4.0.2"
+gem "mysql",                           "~> 2.9.1"
+gem "safe_attributes",                 "~> 1.0.10"
+gem "activerecord-deprecated_finders", "~> 1.0.3"
+gem "bio-genomic-interval",            ">= 0.1.2"
+
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
 group :development do
-  gem "rake", "~> 10.1.0" # was "~> 0.9.2.2"
-  gem "rspec", "~> 2.9.0" # was ~> 2.5.0
-  gem "bundler", "~> 1.3.5" # was ~>1.1.0 was ~> 1.0.0
-  gem "jeweler", "~> 1.8.3" # was ~> 1.5.2
-  gem "bio", ">= 1.4.1"
-  gem "rdoc", ">= 3.9.1"
+  gem "rake",    "~> 10.1.0" 
+  gem "rspec",   "~> 2.14.1"
+  gem "bundler", "~> 1.3.5"
+  gem "jeweler", "~> 1.8.8"
+  gem "bio",     ">= 1.4.3"
+  gem "rdoc",    ">= 4.0.1"
   # gem "simplecov", :require => false, :group => :test
 end  

data/Gemfile.lock

@@ -1,22 +1,29 @@
 GEM
   remote: http://rubygems.org/
   specs:
-    activemodel (3.0.20)
-      activesupport (= 3.0.20)
-      builder (~> 2.1.2)
-      i18n (~> 0.5.0)
-    activerecord (3.0.20)
-      activemodel (= 3.0.20)
-      activesupport (= 3.0.20)
-      arel (~> 2.0.10)
-      tzinfo (~> 0.3.23)
-    activesupport (3.0.20)
+    activemodel (4.0.2)
+      activesupport (= 4.0.2)
+      builder (~> 3.1.0)
+    activerecord (4.0.2)
+      activemodel (= 4.0.2)
+      activerecord-deprecated_finders (~> 1.0.2)
+      activesupport (= 4.0.2)
+      arel (~> 4.0.0)
+    activerecord-deprecated_finders (1.0.3)
+    activesupport (4.0.2)
+      i18n (~> 0.6, >= 0.6.4)
+      minitest (~> 4.2)
+      multi_json (~> 1.3)
+      thread_safe (~> 0.1)
+      tzinfo (~> 0.3.37)
     addressable (2.3.5)
-    arel (2.0.10)
+    arel (4.0.1)
+    atomic (1.1.14)
+    atomic (1.1.14-java)
     bio (1.4.3.0001)
     bio-genomic-interval (0.1.2)
-    builder (2.1.2)
-    diff-lcs (1.1.3)
+    builder (3.1.4)
+    diff-lcs (1.2.5)
     faraday (0.8.8)
       multipart-post (~> 1.2.0)
     git (1.2.6)
@@ -28,10 +35,10 @@ GEM
       nokogiri (~> 1.5.2)
       oauth2
     hashie (2.0.5)
-    highline (1.6.19)
+    highline (1.6.20)
     httpauth (0.2.0)
-    i18n (0.5.0)
-    jeweler (1.8.7)
+    i18n (0.6.9)
+    jeweler (1.8.8)
       builder
       bundler (~> 1.0)
       git (>= 1.2.5)
@@ -40,14 +47,15 @@ GEM
       nokogiri (= 1.5.10)
       rake
       rdoc
-    json (1.8.0)
-    json (1.8.0-java)
+    json (1.8.1)
+    json (1.8.1-java)
     jwt (0.1.8)
       multi_json (>= 1.5)
-    multi_json (1.7.9)
+    minitest (4.7.5)
+    multi_json (1.8.2)
     multi_xml (0.5.5)
     multipart-post (1.2.0)
-    mysql (2.8.1)
+    mysql (2.9.1)
     nokogiri (1.5.10)
     nokogiri (1.5.10-java)
     oauth2 (0.9.2)
@@ -61,31 +69,36 @@ GEM
     rake (10.1.0)
     rdoc (4.0.1)
       json (~> 1.4)
-    rspec (2.9.0)
-      rspec-core (~> 2.9.0)
-      rspec-expectations (~> 2.9.0)
-      rspec-mocks (~> 2.9.0)
-    rspec-core (2.9.0)
-    rspec-expectations (2.9.1)
-      diff-lcs (~> 1.1.3)
-    rspec-mocks (2.9.0)
+    rspec (2.14.1)
+      rspec-core (~> 2.14.0)
+      rspec-expectations (~> 2.14.0)
+      rspec-mocks (~> 2.14.0)
+    rspec-core (2.14.7)
+    rspec-expectations (2.14.4)
+      diff-lcs (>= 1.1.3, < 2.0)
+    rspec-mocks (2.14.4)
     safe_attributes (1.0.10)
       activerecord (>= 3.0.0)
-    tzinfo (0.3.37)
+    thread_safe (0.1.3)
+      atomic
+    thread_safe (0.1.3-java)
+      atomic
+    tzinfo (0.3.38)
 
 PLATFORMS
   java
   ruby
 
 DEPENDENCIES
-  activerecord (~> 3.0.7)
-  activesupport (~> 3.0.7)
-  bio (>= 1.4.1)
+  activerecord (~> 4.0.2)
+  activerecord-deprecated_finders (~> 1.0.3)
+  activesupport (~> 4.0.2)
+  bio (>= 1.4.3)
   bio-genomic-interval (>= 0.1.2)
   bundler (~> 1.3.5)
-  jeweler (~> 1.8.3)
-  mysql (~> 2.8.1)
+  jeweler (~> 1.8.8)
+  mysql (~> 2.9.1)
   rake (~> 10.1.0)
-  rdoc (>= 3.9.1)
-  rspec (~> 2.9.0)
-  safe_attributes (>= 1.0.8)
+  rdoc (>= 4.0.1)
+  rspec (~> 2.14.1)
+  safe_attributes (~> 1.0.10)

data/LICENSE.txt

@@ -0,0 +1,20 @@
+Copyright (c) 2011-2013 MISHIMA, Hiroyuki
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

@@ -1,4 +1,4 @@
-# bio-ucsc-api version 0.5.3
+# bio-ucsc-api version 0.6.0
 
 **The Ruby UCSC API**: accessing the UCSC Genome Database using Ruby.
 
@@ -27,7 +27,7 @@ $ gem install bio-ucsc-api
 * Automatic conversion of "1-based full-closed intervals" to internal "0-based left-closed right-open intervals" (see also bioruby-genomic-interval)
 * Supporting non-official full/partial mirror MySql hosts (e.g. local servers)
 * Using Rspec for the testing framework
-* Written in pure Ruby and supporting multiple Ruby interpreter implementations including Ruby1.8, Ruby1.9, and JRuby1.6
+* Written in pure Ruby and supporting multiple Ruby interpreter implementations including Ruby1.9, Ruby2.0and JRuby1.6
 * Designed as a BioRuby plugin
 * Current version does not support table-linked bigWIG/bigBED/BAM files.
 
@@ -54,13 +54,15 @@ Supported Ruby interpreter implementations:
 
 * Ruby Version 2.0.0 or later
 * Ruby version 1.9.2 or later
-* Ruby version 1.8.7 or later
 * JRuby version 1.6.3 or later - Appropiate Java heap size may have to be specified to invoke JRuby, especially when you use Bio::Ucsc::File::Twobit. Try "jruby -J-Xmx3g your_script.rb" to keep 3G byte heap.
 
-Major dependent gems:
+* Ruby version 1.8.7 or earlier are no longer supported by UCSC API v0.6.0 and later because Ruby on Rails and ActiveRecord version 4.0 do not support these old Rubies. 
 
-* active_record version 3 - http://api.rubyonrails.org/classes/ActiveRecord/Base.html
+Major rubygem dependencies:
+
+* active_record version **4.0** - http://api.rubyonrails.org/classes/ActiveRecord/Base.html
 * safe_attributes - https://github.com/bjones/safe_attributes
+* activerecord-deprecated_finders - http://github.com/rails/activerecord-deprecated_finders -- supporting AR4.0 deprecated dynamic finders shch as 'find_all_by_name'. To suppress deprecation warnings, you have to add `ActiveSupport::Deprecation.silenced = true`.
 * bioruby-genomic-interval - https://github.com/misshie/bioruby-genomic-interval
 * mysql (MySQL/Ruby MySQL API module) - http://www.tmtm.org/mysql/ruby/README.html
 
@@ -70,14 +72,17 @@ See also:
 * UCSCBin library - https://github.com/misshie/UCSCBin
  
 # Change Log
-See 'ChangeLog.md'.
+ * **NEW** (v0.6.0): Support ActiveRecord v4.0 (a part of Ruby on Ralils v4.0). Other related library dependencies are also updated. To Supress deprecation warnings for using dynamic finders such as 'find_by_name_and_chrom', use `ActiveSupport::Deprecation.silenced = true`. Because ActiveRecord v4.0 does not support Ruby v1.8.7 and earlier, Ruby UCSC API no longer supports these older Rubies. 
+ * **UPDATE** (v0.6.0): Ruby UCSC API is now licensed under the MIT License. See also the LICENSE.txt file.
+ 
+See 'ChangeLog.md' for older changes.
 
 # How to Use
 ## Basics
-* A database of a genome assembly is represented as a module in the `Bio::Ucsc module`. For example, human hg19 database is referred by `Bio::Ucsc::Hg19`.
-* Before using a database, establish a connection to the database. For example, `Bio::Ucsc::Hg19::DBConnection.connect`. 
-* A table in a database is represented as a class in the database module. For example, the snp132 table in the hg19 database is referred by `Bio::Ucsc::Hg19::Snp132`.
-* Queries to a field (column) in a table are represented by class methods of the table class. For example, finding the first record (row) of the snp132 table in the hg19 database is `Bio::Ucsc::Hg19::Snp132.first`. 
+* A database of a genome assembly is represented as a module in the `Bio::Ucsc` module. For example, the human hg19 database is referred by `Bio::Ucsc::Hg19`.
+* Before using a database, establish a connection to the database. For example, `Bio::Ucsc::Hg19.connect`. 
+* A table in a database is represented as a class in the database module. For example, the snp138 table in the hg19 database is referred by `Bio::Ucsc::Hg19::Snp138`.
+* Queries to a field (column) in a table are represented by class methods of the table class. For example, finding the first record (row) of the snp138 table in the hg19 database is `Bio::Ucsc::Hg19::Snp138.first`. 
 * Queries using genomic intervals are supported by the named scope ".with_intervals" and ".with_intervals_excl (omitting pertially included annotations)" method of the table class. These methods accept a genomic interval string like `chr1:1233-5678`. If a table to query has the "bin" column, the bin index system is automatically used to speed-up the query.
 * Fields in a retrieved record can be acccessed by using instance methods of a record object. For example, the name field of a table record stored in the result" variable is `result.name`.  
 
@@ -87,49 +92,66 @@ At first, you have to declare the API and establish the connection to a database
 ```ruby
  require 'bio-ucsc'
 
- include Bio # shorthand for ommitting the "Bio::" prefix
- Ucsc::Hg19.connect
+ DB = Bio::Ucsc::Hg19
+ DB.connect
+ 
+ # Suppressing deprecation warnings for using dynamic finders such as 'find_by_name_and_chrom'.
+ # These syles are deprecated in ActiveRecord 4.0. 
+ ActiveSupport::Deprecation.silenced = true
 ```
 
 Table search using genomic intervals:
 
 ```ruby
- Ucsc::Hg19::Snp131.with_interval("chr1:1-11,000").find(:all).each do |e|
+ DB = Bio::Ucsc::Hg19
+ DB.connect
+ 
+ DB::Snp138.with_interval("chr1:1-11,000").find(:all).each do |e|
    i = GenomicInterval.zero_based(e.chrom, e.chromStart, e.chromEnd)
    puts "#{i.chrom}\t#{i.chr_start}\t#{e.name}\t#{e[:class]}" # "e.class" does not work
  end
 
  gi = "chr17:7,579,614-7,579,700"
- puts Ucsc::Hg19::Snp131.with_interval(gi).find(:all)
+ puts DB::Snp138.with_interval(gi).find(:all)
 
- puts Ucsc::Hg19::Snp131.with_interval_excl(gi).find(:all)
+ puts DB::Snp138.with_interval_excl(gi).find(:all)
 
- relation = Ucsc::Hg19::Snp131.with_interval(gi).select(:name)
+ relation = DB::Snp138.with_interval(gi).select(:name)
  puts relation.to_sql 
-  # => SELECT name FROM `snp131`
-        WHERE (chrom = 'chr17' AND bin in (642,80,9,1,0)
-        AND ((chromStart BETWEEN 7579613 AND 7579700) AND
-             (chromEnd   BETWEEN 7579613 AND 7579700)))"
+  # => SELECT name FROM `snp138`
+  #      WHERE (chrom = 'chr17' AND bin in (642,80,9,1,0)
+  #      AND ((chromStart BETWEEN 7579613 AND 7579700) AND
+  #           (chromEnd   BETWEEN 7579613 AND 7579700)))
  puts relation.find_all_by_class_and_strand("in-del", "+").size # => 1
 
- puts Ucsc::Hg19::Snp131.find_by_name("rs56289060")
+ # Rails4 style
+ puts DB::Snp138.where(name: "rs56289060").first
+
+ # Old style 
+ ActiveSupport::Deprecation.silenced = true # Suppress warnings
+ puts DB::Snp138.find_all_by_name("rs56289060").first
 ```
 
 Sometimes, queries using raw SQLs provide elegant solutions.
 
 ```ruby
+ DB = Bio::Ucsc::Hg19
+ DB.connect
+ 
  sql << 'SQL'
  SELECT name,chrom,chromStart,chromEnd,observed
- FROM snp131 
+ FROM snp138 
  WHERE name="rs56289060"
  SQL
- puts Ucsc::Hg19::Snp131.find_by_sql(sql)
+ puts DB::Snp138.find_by_sql(sql)
 ```
 For gene prediction (genePred) tables, such as RefSeq, EndGene, and WgEncodeGencodeBasicV12, Ruby UCSC API automatically implements `#exon`, `#introns`, `#cdss` (or an alias `#cdses`) methods. Exons, introns, and CDSes are accessible as Array objects of `Bio::GenomicInterval`.
 
 ```ruby
- Bio::Ucsc::Hg19.connect
- r = Bio::Ucsc::Hg19::RefGene.with_interval("chr1:1,000,000-1,100,000").first
+ DB = Bio::Ucsc::Hg19
+ DB.connect
+ 
+ r = DB::RefGene.with_interval("chr1:1,000,000-1,100,000").first
  puts "gene strand = #{r.strand}"
  r.exons.each{|x|puts "[#{x.chr_start}, #{x.chr_end}]"}
  r.cdss.each{|x|puts "[#{x.chr_start}, #{x.chr_end}]"}
@@ -139,22 +161,22 @@ For gene prediction (genePred) tables, such as RefSeq, EndGene, and WgEncodeGenc
 retrieve reference sequence from a locally-stored 2bit file. The "hg19.2bit" file can be downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit
 
 ```ruby
- hg19ref = Ucsc::File::Twobit.load("hg19.2bit")
+ hg19ref = Bio::Ucsc::File::Twobit.load("hg19.2bit")
  puts hg19ref.find_by_interval("chr1:9,500-10,999")
 
  # another way to access a twobit file
- puts Ucsc::File::Twobit.open("hg19.2bit"){|tb|tb.find_by_interval("chr1:9,500-10,999")}
+ puts Bio::Ucsc::File::Twobit.open("hg19.2bit"){|tb|tb.find_by_interval("chr1:9,500-10,999")}
 ```
 
 Connetcting to non-official or local full/partial mirror MySQL servers
 
 ```ruby
- Ucsc::Hg18.connect( :db_host => 'localhost',
-                     :db_username => 'genome',
-                     :db_password => '' )
+ Bio::Ucsc::Hg18.connect( :db_host => 'localhost',
+                          :db_username => 'genome',
+                         :db_password => '' )
 
- Ucsc::Hg18.default # reset to connect UCSC's public MySQL sever
- Ucsc::Hg18.connect
+ Bio::Ucsc::Hg18.default # reset to connect UCSC's public MySQL sever
+ Bio::Ucsc::Hg18.connect
 ```
 
 And see also sample scripts in the samples directory.
@@ -226,13 +248,12 @@ Bio::Ucsc::Hg19.connect
 Bio::Ucsc::Hg18.connect
 joiner = Bio::Ucsc::Schema::Joiner.load
 joiner.variables["gbd"] = ["hg19", "hg18"]
-joiner.define_association(Bio::Ucsc::Hg19::Snp131)
-# "first" is required because the snp131Seq method always returns an array.
-puts Bio::Ucsc::Hg19::Snp131.find_by_name("rs242").snp131Seq.first.file_offset
+joiner.define_association(Bio::Ucsc::Hg19::Snp138)
+# "first" is required because the snp138Seq method always returns an array.
+puts Bio::Ucsc::Hg19::Snp138.find_by_name("rs242").snp138Seq.first.file_offset
 ```
 
 # Copyright
 **Copyright**: (c) 2011-2013 MISHIMA, Hiroyuki (hmishima at nagasaki-u.ac.jp / Twitter: @mishima_eng (in English) and @mishimahryk (in Japanese)  
 **Copyright**: (c) 2010 Jan Aerts  
-**License**: Ruby license (Ruby's / GPLv2 dual). See COPYING and COPYING.ja for further details..
-
+**License**: The MIT license. See LICENSE.txt for further details..

data/Rakefile

@@ -17,7 +17,7 @@ Jeweler::Tasks.new do |gem|
   # see http://docs.rubygems.org/read/chapter/20 for more options
   gem.name = "bio-ucsc-api"
   gem.homepage = "http://github.com/misshie/bioruby-ucsc-api"
-  gem.license = "Ruby (Ruby's/GPLv2 dual)"
+  gem.license = "The MIT License"
   gem.summary = %Q{The Ruby UCSC API: accessing the UCSC Genome Database using Ruby}
   gem.description = %Q{Ruby UCSC API: accessing the UCSC Genome Database using Ruby}
   gem.email = "missy@be.to"

data/VERSION

@@ -1 +1 @@
-0.5.3
+0.6.0

data/bio-ucsc-api.gemspec

@@ -5,27 +5,28 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-ucsc-api"
-  s.version = "0.5.3"
+  s.version = "0.6.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Hiroyuki Mishima", "Jan Aerts"]
-  s.date = "2013-08-27"
+  s.date = "2013-12-11"
   s.description = "Ruby UCSC API: accessing the UCSC Genome Database using Ruby"
   s.email = "missy@be.to"
   s.extra_rdoc_files = [
     "ChangeLog.md",
+    "LICENSE.txt",
     "README.md"
   ]
   s.files = [
-    "COPYING",
-    "COPYING.ja",
     "ChangeLog.md",
     "Gemfile",
     "Gemfile.lock",
+    "LICENSE.txt",
     "README.md",
     "Rakefile",
     "VERSION",
     "bio-ucsc-api.gemspec",
+    "lib/#bio-ucsc.rb#",
     "lib/bio-ucsc-api.rb",
     "lib/bio-ucsc.rb",
     "lib/bio-ucsc/ailmel1.rb",
@@ -433,7 +434,7 @@ Gem::Specification.new do |s|
     "samples/symbol2summary.rb"
   ]
   s.homepage = "http://github.com/misshie/bioruby-ucsc-api"
-  s.licenses = ["Ruby (Ruby's/GPLv2 dual)"]
+  s.licenses = ["The MIT License"]
   s.require_paths = ["lib"]
   s.rubygems_version = "1.8.11"
   s.summary = "The Ruby UCSC API: accessing the UCSC Genome Database using Ruby"
@@ -442,42 +443,45 @@ Gem::Specification.new do |s|
     s.specification_version = 3
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<activerecord>, ["~> 3.0.7"])
-      s.add_runtime_dependency(%q<activesupport>, ["~> 3.0.7"])
-      s.add_runtime_dependency(%q<mysql>, ["~> 2.8.1"])
+      s.add_runtime_dependency(%q<activerecord>, ["~> 4.0.2"])
+      s.add_runtime_dependency(%q<activesupport>, ["~> 4.0.2"])
+      s.add_runtime_dependency(%q<mysql>, ["~> 2.9.1"])
+      s.add_runtime_dependency(%q<safe_attributes>, ["~> 1.0.10"])
+      s.add_runtime_dependency(%q<activerecord-deprecated_finders>, ["~> 1.0.3"])
       s.add_runtime_dependency(%q<bio-genomic-interval>, [">= 0.1.2"])
-      s.add_runtime_dependency(%q<safe_attributes>, [">= 1.0.8"])
       s.add_development_dependency(%q<rake>, ["~> 10.1.0"])
-      s.add_development_dependency(%q<rspec>, ["~> 2.9.0"])
+      s.add_development_dependency(%q<rspec>, ["~> 2.14.1"])
       s.add_development_dependency(%q<bundler>, ["~> 1.3.5"])
-      s.add_development_dependency(%q<jeweler>, ["~> 1.8.3"])
-      s.add_development_dependency(%q<bio>, [">= 1.4.1"])
-      s.add_development_dependency(%q<rdoc>, [">= 3.9.1"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.8.8"])
+      s.add_development_dependency(%q<bio>, [">= 1.4.3"])
+      s.add_development_dependency(%q<rdoc>, [">= 4.0.1"])
     else
-      s.add_dependency(%q<activerecord>, ["~> 3.0.7"])
-      s.add_dependency(%q<activesupport>, ["~> 3.0.7"])
-      s.add_dependency(%q<mysql>, ["~> 2.8.1"])
+      s.add_dependency(%q<activerecord>, ["~> 4.0.2"])
+      s.add_dependency(%q<activesupport>, ["~> 4.0.2"])
+      s.add_dependency(%q<mysql>, ["~> 2.9.1"])
+      s.add_dependency(%q<safe_attributes>, ["~> 1.0.10"])
+      s.add_dependency(%q<activerecord-deprecated_finders>, ["~> 1.0.3"])
       s.add_dependency(%q<bio-genomic-interval>, [">= 0.1.2"])
-      s.add_dependency(%q<safe_attributes>, [">= 1.0.8"])
       s.add_dependency(%q<rake>, ["~> 10.1.0"])
-      s.add_dependency(%q<rspec>, ["~> 2.9.0"])
+      s.add_dependency(%q<rspec>, ["~> 2.14.1"])
       s.add_dependency(%q<bundler>, ["~> 1.3.5"])
-      s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
-      s.add_dependency(%q<bio>, [">= 1.4.1"])
-      s.add_dependency(%q<rdoc>, [">= 3.9.1"])
+      s.add_dependency(%q<jeweler>, ["~> 1.8.8"])
+      s.add_dependency(%q<bio>, [">= 1.4.3"])
+      s.add_dependency(%q<rdoc>, [">= 4.0.1"])
     end
   else
-    s.add_dependency(%q<activerecord>, ["~> 3.0.7"])
-    s.add_dependency(%q<activesupport>, ["~> 3.0.7"])
-    s.add_dependency(%q<mysql>, ["~> 2.8.1"])
+    s.add_dependency(%q<activerecord>, ["~> 4.0.2"])
+    s.add_dependency(%q<activesupport>, ["~> 4.0.2"])
+    s.add_dependency(%q<mysql>, ["~> 2.9.1"])
+    s.add_dependency(%q<safe_attributes>, ["~> 1.0.10"])
+    s.add_dependency(%q<activerecord-deprecated_finders>, ["~> 1.0.3"])
     s.add_dependency(%q<bio-genomic-interval>, [">= 0.1.2"])
-    s.add_dependency(%q<safe_attributes>, [">= 1.0.8"])
     s.add_dependency(%q<rake>, ["~> 10.1.0"])
-    s.add_dependency(%q<rspec>, ["~> 2.9.0"])
+    s.add_dependency(%q<rspec>, ["~> 2.14.1"])
     s.add_dependency(%q<bundler>, ["~> 1.3.5"])
-    s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
-    s.add_dependency(%q<bio>, [">= 1.4.1"])
-    s.add_dependency(%q<rdoc>, [">= 3.9.1"])
+    s.add_dependency(%q<jeweler>, ["~> 1.8.8"])
+    s.add_dependency(%q<bio>, [">= 1.4.3"])
+    s.add_dependency(%q<rdoc>, [">= 4.0.1"])
   end
 end
 

data/lib/#bio-ucsc.rb#

@@ -0,0 +1,209 @@
+#
+# = bio-ucsc.rb
+# Copyright::   Copyright (C) 2011-2013
+#               MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     Ruby licence (Ryby's / GPLv2 dual)
+
+base = "#{::File.dirname(__FILE__)}/bio-ucsc"
+
+require 'rubygems'
+gem 'activerecord', "~> 4.0.2"
+require "active_record"
+gem "safe_attributes"
+require "safe_attributes"
+gem "activerecord-deprecated_finders"
+require "active_record/deprecated_finders"
+#ActiveSupport::Deprecation.silenced = true
+
+require "#{base}/ucsc_bin"
+require "#{base}/genomic-interval-bin"
+require "#{base}/gi.rb"
+
+module Bio
+  module Ucsc
+    VERSION = "0.6.0"
+    base = "#{::File.dirname(__FILE__)}/bio-ucsc"
+    
+    # mammmals #####################################
+    # human genome assemblies
+    autoload :Hg19, "#{base}/hg19"
+    autoload :Hg18, "#{base}/hg18"
+
+    # chimp genome assemblies
+    autoload :PanTro3, "#{base}/pantro3"
+
+    # orangutan genome assemblies
+    autoload :PonAbe2, "#{base}/ponabe2"
+
+    # rhesus macaque genome assemblies
+    autoload :RheMac2, "#{base}/rhemac2"
+
+    # marmoset genome assemblies
+    autoload :CalJac3, "#{base}/caljac3"
+
+    # mouse genome assemblies
+    autoload :Mm9,  "#{base}/mm9"
+    autoload :Mm10, "#{base}/mm10"
+
+    # rat genome assemblies
+    autoload :Rn5, "#{base}/rn5"
+    autoload :Rn4, "#{base}/rn4"
+
+    # guinea pig genome assemblies
+    autoload :CavPor3, "#{base}/cavpor3"
+
+    # rabbit genome assemblies
+    autoload :OryCun2, "#{base}/orycun2"
+
+    # cat genome assemblies
+    autoload :FelCat4, "#{base}/felcat4"
+
+    # panda genome assemblies
+    autoload :AilMel1, "#{base}/ailmel1"
+    
+    # dog genome assemblies
+    autoload :CanFam2, "#{base}/canfam2"
+
+    # horse genome assemblies
+    autoload :EquCab2, "#{base}/equcab2"
+
+    # pig genome assemblies
+    autoload :SusScr2, "#{base}/susscr2"
+
+    # sheep genome assemblies
+    autoload :OviAri1, "#{base}/oviari1"
+
+    # cow genome assemblies
+    autoload :BosTau4, "#{base}/bostau4"
+
+    # elephant genome assemblies
+    autoload :LoxAfr3, "#{base}/loxafr3"
+
+    # opossum genome assemblies
+    autoload :MonDom5, "#{base}/mondom5"
+
+    # platypus genome assemblies
+    autoload :OrnAna1, "#{base}/ornana1"
+
+    # vertebrates #################################
+    # chiken genome assemblies
+    autoload :GalGal4, "#{base}/galgal4"
+
+    # zebra finch genome assemblies
+    autoload :TaeGut1, "#{base}/taegut1"
+
+    # lizard genome assemblies
+    autoload :AnoCar2, "#{base}/anocar2"
+
+    # X. tropicalis genome assemblies
+    autoload :XenTro2, "#{base}/xentro2"
+
+    # zebrafish genome assemblies
+    autoload :DanRer7, "#{base}/danrer7"
+
+    # tetraodon genome assemblies
+    autoload :TetNig2, "#{base}/tetnig2"
+
+    # fugu genome assemblies
+    autoload :Fr2, "#{base}/fr2"
+
+    # stickleback genome assemblies
+    autoload :GasAcu1, "#{base}/gasacu1"
+
+    # medaka genome assemblies
+    autoload :OryLat2, "#{base}/orylat2"
+
+    # lamprey genome assemblies
+    autoload :PetMar1, "#{base}/petmar1"
+
+    # deuterostomes ###############################
+    # lancelet genome assemblies
+    autoload :BraFlo1, "#{base}/braflo1.rb"
+
+    # sea squirt genome assemblies
+    autoload :Ci2, "#{base}/ci2"
+
+    # sea urchin genome assemblies
+    autoload :StrPur2, "#{base}/strpur2"
+
+    # insects  ####################################
+    # D. melanogaster genome assemblies
+    autoload :Dm3, "#{base}/dm3" 
+
+    # D. silulans genome assemblies
+    autoload :DroSim1, "#{base}/drosim1"
+
+    # D. sechellia genome assemblies
+    autoload :DroSec1, "#{base}/drosec1"
+
+    # D. yakuba genome assemblies
+    autoload :DroYak2, "#{base}/droyak2"
+
+    # D. erecta genome assemblies
+    autoload :DroEre1, "#{base}/droere1"
+
+    # D. ananassae genome assemblies
+    autoload :DroAna2, "#{base}/droana2"
+
+    # D. pseudoobscura genome assemblies
+    autoload :Dp3, "#{base}/dp3"
+
+    # D. persimilis genome assemblies
+    autoload :DroPer1, "#{base}/droper1"
+
+    # D. virilis genome assemblies
+    autoload :DroVir2, "#{base}/drovir2"
+
+    # D. mojavensis genome assemblies
+    autoload :DroMoj2, "#{base}/dromoj2"
+
+    # D. grimshawi genome assemblies
+    autoload :DroGri1, "#{base}/drogri1"
+
+    # Anopheles mosquito genome assemblies
+    autoload :AnoGam1, "#{base}/anogam1"
+
+    # honey bee genome assemblies
+    autoload :ApiMel2, "#{base}/apimel2"
+
+    # nematodes ###################################
+    # C. elegans genome assemblies
+    autoload :Ce6, "#{base}/ce6"
+
+    # C. brenneri genome assemblies
+    autoload :CaePb2, "#{base}/caepb2"
+
+    # C. briggsae genome assemblies
+    autoload :Cb3, "#{base}/cb3"
+
+    # C. remanei genome assemblies
+    autoload :CaeRem3, "#{base}/caerem3"
+
+    # C. japonica genome assemblies
+    autoload :CaeJap1, "#{base}/caejap1"
+
+    # P. pacificus genome assemblies
+    autoload :PriPac1, "#{base}/pripac1"
+
+    # others  #####################################
+    # sea hare genome assemblies
+    autoload :AplCal1, "#{base}/aplcal1"
+
+    # yeast genome assemblies
+    autoload :SacCer2, "#{base}/saccer2"
+
+    # genome assembly independent dababases #######
+    autoload :UniProt, "#{base}/uniprot"
+    autoload :Proteome,  "#{base}/proteome"
+    autoload :Go, "#{base}/go"
+    autoload :HgFixed, "#{base}/hgfixed"
+    autoload :VisiGene, "#{base}/visigene"
+
+    # utility classes #############################
+    # accessing genome sequences in the 2bit format 
+    # after version 0.4.0, UCSC::Reference is moved to UCSC::File::Twobit
+    autoload :File, "#{base}/file"
+    autoload :Reference, "#{base}/reference"
+    autoload :Schema, "#{base}/schema"
+  end
+end

data/lib/bio-ucsc.rb

@@ -7,17 +7,21 @@
 base = "#{::File.dirname(__FILE__)}/bio-ucsc"
 
 require 'rubygems'
-gem 'activerecord', ">=3.0.7"
+gem 'activerecord', "~> 4.0.2"
 require "active_record"
 gem "safe_attributes"
 require "safe_attributes"
+gem "activerecord-deprecated_finders"
+require "active_record/deprecated_finders"
+#ActiveSupport::Deprecation.silenced = true
+
 require "#{base}/ucsc_bin"
 require "#{base}/genomic-interval-bin"
 require "#{base}/gi.rb"
 
 module Bio
   module Ucsc
-    VERSION = "0.5.3"
+    VERSION = "0.6.0"
     base = "#{::File.dirname(__FILE__)}/bio-ucsc"
     
     # mammmals #####################################

data/samples/bed2refseq.rb

@@ -1,11 +1,10 @@
-#!/usr/local/bin/ruby-1.9
+#!/usr/bin/env ruby
 
 #require 'bio-ucsc'
 require '../lib/bio-ucsc'
 
-include Bio
-
-Ucsc::Hg19::DBConnection.connect
+DB = Bio::Ucsc::Hg19
+DB.connect
 
 genes = Array.new
 ARGF.each_line do |row|
@@ -16,7 +15,7 @@ ARGF.each_line do |row|
                                   Integer(chr_start),
                                   Integer(chr_end),)
 
-  results = Ucsc::Hg19::RefGene.with_interval(gi).select(:name2).find(:all)
+  results = DB.with_interval(gi).select(:name2).find(:all)
   genes.concat(results.map{|e|e.name2})
 end
 

data/samples/hg19-2bit-retrieve.rb

@@ -16,12 +16,11 @@ HG19_2BIT_FILE = "hg19.2bit"
 require File.dirname(__FILE__) + '/../lib/bio-ucsc'
 
 class Hg19Ref
-  include Bio::Ucsc::Hg19
+  DB = Bio::Ucsc::Hg19
 
   def run(interval)
-    DBConnection.connect
+    DB.connect
     ref = Bio::Ucsc::Reference.load(HG19_2BIT_FILE) # v0.2 and later
-
     itv = Bio::GenomicInterval.parse(interval)
 
     puts itv.to_s

data/samples/num-gene-exon.rb

@@ -13,9 +13,10 @@ require 'bio-ucsc'
 
 interval = Bio::GenomicInterval.parse(ARGV[0])
 
-Bio::Ucsc::Hg18::DBConnection.connect
+DB = Bio::Ucsc::Hg18
+DB.connect
 
-genes = Bio::Ucsc::Hg18::RefGene.with_interval(interval).find(:all).map{|e|e.name2}.uniq
+genes = DB::RefGene.with_interval(interval).find(:all).map{|e|e.name2}.uniq
 puts "Included  genes:"
 puts genes
 puts "Number of genes:"
@@ -24,7 +25,7 @@ puts genes.size
 total_exons = 0
 genes.each do |gene|
   total_exons +=
-    Bio::Ucsc::Hg18::RefGene.
+    DB::RefGene.
     with_interval(interval).
     find_all_by_name2(gene).
     map{|e|e.exonCount}.

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-ucsc-api
 version: !ruby/object:Gem::Version
-  version: 0.5.3
+  version: 0.6.0
   prerelease: 
 platform: ruby
 authors:
@@ -10,66 +10,77 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-08-27 00:00:00.000000000 Z
+date: 2013-12-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activerecord
-  requirement: &258436740 !ruby/object:Gem::Requirement
+  requirement: &160170600 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 3.0.7
+        version: 4.0.2
   type: :runtime
   prerelease: false
-  version_requirements: *258436740
+  version_requirements: *160170600
 - !ruby/object:Gem::Dependency
   name: activesupport
-  requirement: &258436120 !ruby/object:Gem::Requirement
+  requirement: &160169480 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 3.0.7
+        version: 4.0.2
   type: :runtime
   prerelease: false
-  version_requirements: *258436120
+  version_requirements: *160169480
 - !ruby/object:Gem::Dependency
   name: mysql
-  requirement: &258435560 !ruby/object:Gem::Requirement
+  requirement: &160168120 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 2.8.1
+        version: 2.9.1
   type: :runtime
   prerelease: false
-  version_requirements: *258435560
+  version_requirements: *160168120
 - !ruby/object:Gem::Dependency
-  name: bio-genomic-interval
-  requirement: &258451220 !ruby/object:Gem::Requirement
+  name: safe_attributes
+  requirement: &160166800 !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: 0.1.2
+        version: 1.0.10
   type: :runtime
   prerelease: false
-  version_requirements: *258451220
+  version_requirements: *160166800
 - !ruby/object:Gem::Dependency
-  name: safe_attributes
-  requirement: &258450100 !ruby/object:Gem::Requirement
+  name: activerecord-deprecated_finders
+  requirement: &160165900 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.3
+  type: :runtime
+  prerelease: false
+  version_requirements: *160165900
+- !ruby/object:Gem::Dependency
+  name: bio-genomic-interval
+  requirement: &160181120 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 1.0.8
+        version: 0.1.2
   type: :runtime
   prerelease: false
-  version_requirements: *258450100
+  version_requirements: *160181120
 - !ruby/object:Gem::Dependency
   name: rake
-  requirement: &258449180 !ruby/object:Gem::Requirement
+  requirement: &160180180 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -77,21 +88,21 @@ dependencies:
         version: 10.1.0
   type: :development
   prerelease: false
-  version_requirements: *258449180
+  version_requirements: *160180180
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &258448320 !ruby/object:Gem::Requirement
+  requirement: &160179160 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 2.9.0
+        version: 2.14.1
   type: :development
   prerelease: false
-  version_requirements: *258448320
+  version_requirements: *160179160
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &258447480 !ruby/object:Gem::Requirement
+  requirement: &160178180 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -99,57 +110,58 @@ dependencies:
         version: 1.3.5
   type: :development
   prerelease: false
-  version_requirements: *258447480
+  version_requirements: *160178180
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &258446680 !ruby/object:Gem::Requirement
+  requirement: &160177160 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.8.3
+        version: 1.8.8
   type: :development
   prerelease: false
-  version_requirements: *258446680
+  version_requirements: *160177160
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &258445800 !ruby/object:Gem::Requirement
+  requirement: &160176000 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 1.4.1
+        version: 1.4.3
   type: :development
   prerelease: false
-  version_requirements: *258445800
+  version_requirements: *160176000
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &258444980 !ruby/object:Gem::Requirement
+  requirement: &160175260 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 3.9.1
+        version: 4.0.1
   type: :development
   prerelease: false
-  version_requirements: *258444980
+  version_requirements: *160175260
 description: ! 'Ruby UCSC API: accessing the UCSC Genome Database using Ruby'
 email: missy@be.to
 executables: []
 extensions: []
 extra_rdoc_files:
 - ChangeLog.md
+- LICENSE.txt
 - README.md
 files:
-- COPYING
-- COPYING.ja
 - ChangeLog.md
 - Gemfile
 - Gemfile.lock
+- LICENSE.txt
 - README.md
 - Rakefile
 - VERSION
 - bio-ucsc-api.gemspec
+- lib/#bio-ucsc.rb#
 - lib/bio-ucsc-api.rb
 - lib/bio-ucsc.rb
 - lib/bio-ucsc/ailmel1.rb
@@ -557,7 +569,7 @@ files:
 - samples/symbol2summary.rb
 homepage: http://github.com/misshie/bioruby-ucsc-api
 licenses:
-- Ruby (Ruby's/GPLv2 dual)
+- The MIT License
 post_install_message: 
 rdoc_options: []
 require_paths:
@@ -570,7 +582,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 4260927560665571568
+      hash: -3654614311172701481
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:

data/COPYING

@@ -1,58 +0,0 @@
-BioRuby is copyrighted free software by
-  Hiroyuki Mishima <missy at be.to> / <hmishima at nagasaki-u.ac.jp>, and
-  Jan Aerts <jan.aerts@gmail.com>.
-You can redistribute it and/or modify it under either the terms of the GPL
-version 2 (see the file GPL), or the conditions below:
-
-  1. You may make and give away verbatim copies of the source form of the
-     software without restriction, provided that you duplicate all of the
-     original copyright notices and associated disclaimers.
-
-  2. You may modify your copy of the software in any way, provided that
-     you do at least ONE of the following:
-
-       a) place your modifications in the Public Domain or otherwise
-          make them Freely Available, such as by posting said
-	  modifications to Usenet or an equivalent medium, or by allowing
-	  the author to include your modifications in the software.
-
-       b) use the modified software only within your corporation or
-          organization.
-
-       c) give non-standard binaries non-standard names, with
-          instructions on where to get the original software distribution.
-
-       d) make other distribution arrangements with the author.
-
-  3. You may distribute the software in object code or binary form,
-     provided that you do at least ONE of the following:
-
-       a) distribute the binaries and library files of the software,
-	  together with instructions (in the manual page or equivalent)
-	  on where to get the original distribution.
-
-       b) accompany the distribution with the machine-readable source of
-	  the software.
-
-       c) give non-standard binaries non-standard names, with
-          instructions on where to get the original software distribution.
-
-       d) make other distribution arrangements with the author.
-
-  4. You may modify and include the part of the software into any other
-     software (possibly commercial).  But some files in the distribution
-     are not written by the author, so that they are not under these terms.
-
-     For the list of those files and their copying conditions, see the
-     file LEGAL.
-
-  5. The scripts and library files supplied as input to or produced as 
-     output from the software do not automatically fall under the
-     copyright of the software, but belong to whomever generated them, 
-     and may be sold commercially, and may be aggregated with this
-     software.
-
-  6. THIS SOFTWARE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR
-     IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
-     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-     PURPOSE.

data/COPYING.ja

@@ -1,53 +0,0 @@
-# -*- coding: iso-2022-jp -*-
-
-$BK\%W%m%0%i%`$O%U%j!<%=%U%H%&%'%"$G$9!%(BGPL (the GNU General
-Public License)$B%P!<%8%g%s(B2$B$^$?$O0J2<$K<($9>r7o$GK\%W%m%0%i%`(B
-$B$r:FG[I[$G$-$^$9!%(BGPL$B$K$D$$$F$O(BGPL$B%U%!%$%k$r;2>H$7$F2<$5$$!%(B
-
-  1. $BJ#@=$O@)8B$J$/<+M3$G$9!%(B
-
-  2. $B0J2<$N>r7o$N$$$:$l$+$rK~$?$9;~$KK\%W%m%0%i%`$N%=!<%9$r(B
-     $B<+M3$KJQ99$G$-$^$9!%(B
-
-     (a) $B%M%C%H%K%e!<%:$K%]%9%H$7$?$j!$:n<T$KJQ99$rAwIU$9$k(B
-         $B$J$I$NJ}K!$G!$JQ99$r8x3+$9$k!%(B
-
-     (b) $BJQ99$7$?K\%W%m%0%i%`$r<+J,$N=jB0$9$kAH?%FbIt$@$1$G(B
-         $B;H$&!%(B
-
-     (c) $BJQ99E@$rL@<($7$?$&$(!$%=%U%H%&%'%"$NL>A0$rJQ99$9$k!%(B
-         $B$=$N%=%U%H%&%'%"$rG[I[$9$k;~$K$OJQ99A0$NK\%W%m%0%i(B
-         $B%`$bF1;~$KG[I[$9$k!%$^$?$OJQ99A0$NK\%W%m%0%i%`$N%=!<(B
-         $B%9$NF~<jK!$rL@<($9$k!%(B
-
-     (d) $B$=$NB>$NJQ99>r7o$r:n<T$H9g0U$9$k!%(B
-
-  3. $B0J2<$N>r7o$N$$$:$l$+$rK~$?$9;~$KK\%W%m%0%i%`$r%3%s%Q%$(B
-     $B%k$7$?%*%V%8%'%/%H%3!<%I$d<B9T7A<0$G$bG[I[$G$-$^$9!%(B
-
-     (a) $B%P%$%J%j$r<u$1<h$C$??M$,%=!<%9$rF~<j$G$-$k$h$&$K!$(B
-         $B%=!<%9$NF~<jK!$rL@<($9$k!%(B
-
-     (b) $B5!3#2DFI$J%=!<%9%3!<%I$rE:IU$9$k!%(B
-
-     (c) $BJQ99$r9T$C$?%P%$%J%j$OL>A0$rJQ99$7$?$&$(!$%*%j%8%J(B
-         $B%k$N%=!<%9%3!<%I$NF~<jK!$rL@<($9$k!%(B
-
-     (d) $B$=$NB>$NG[I[>r7o$r:n<T$H9g0U$9$k!%(B
-
-  4. $BB>$N%W%m%0%i%`$X$N0zMQ$O$$$+$J$kL\E*$G$"$l<+M3$G$9!%$?(B
-     $B$@$7!$K\%W%m%0%i%`$K4^$^$l$kB>$N:n<T$K$h$k%3!<%I$O!$$=(B
-     $B$l$>$l$N:n<T$N0U8~$K$h$k@)8B$,2C$($i$l$k>l9g$,$"$j$^$9!%(B
-
-     $B$=$l$i%U%!%$%k$N0lMw$H$=$l$>$l$NG[I[>r7o$J$I$KIU$$$F$O(B
-     LEGAL$B%U%!%$%k$r;2>H$7$F$/$@$5$$!%(B
-
-  5. $BK\%W%m%0%i%`$X$NF~NO$H$J$k%9%/%j%W%H$*$h$S!$K\%W%m%0%i(B
-     $B%`$+$i$N=PNO$N8"Mx$OK\%W%m%0%i%`$N:n<T$G$O$J$/!$$=$l$>(B
-     $B$l$NF~=PNO$r@8@.$7$??M$KB0$7$^$9!%$^$?!$K\%W%m%0%i%`$K(B
-     $BAH$_9~$^$l$k$?$a$N3HD%%i%$%V%i%j$K$D$$$F$bF1MM$G$9!%(B
-
-  6. $BK\%W%m%0%i%`$OL5J]>Z$G$9!%:n<T$OK\%W%m%0%i%`$r%5%]!<%H(B
-     $B$9$k0U;V$O$"$j$^$9$,!$%W%m%0%i%`<+?H$N%P%0$"$k$$$OK\%W(B
-     $B%m%0%i%`$N<B9T$J$I$+$iH/@8$9$k$$$+$J$kB;32$KBP$7$F$b@U(B
-     $BG$$r;}$A$^$;$s!%(B