[BioRuby-cvs] bioruby/lib/bio/db rebase.rb,1.5,1.6

[Trevor Wennblom]

Update of /home/repository/bioruby/bioruby/lib/bio/db
In directory dev.open-bio.org:/tmp/cvs-serv32678

Modified Files:
	rebase.rb 
Log Message:
Updated REBASE to conform to README.DEV

Index: rebase.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/rebase.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** rebase.rb	31 Dec 2006 20:44:21 -0000	1.5
--- rebase.rb	31 Dec 2006 23:22:03 -0000	1.6
***************
*** 142,148 ****
    end
  
!   # Iterate over each entry
    def each
!     @data.each { |v| yield v }
    end
  
--- 142,153 ----
    end
  
!   # Calls _block_ once for each element in <tt>@data</tt> hash, passing that element as a parameter.
!   #
!   # ---
!   # *Arguments*
!   # * Accepts a block
!   # *Returns*:: results of _block_ operations
    def each
!     @data.each { |item| yield item }
    end
  
***************
*** 158,165 ****
    end
  
!   # [+enzyme_lines+] contents of EMBOSS formatted enzymes file (_required_)
!   # [+reference_lines+] contents of EMBOSS formatted references file (_optional_)
!   # [+supplier_lines+] contents of EMBOSS formatted suppliers files (_optional_)
!   # [+yaml+] enzyme_lines, reference_lines, and supplier_lines are read as YAML if set to true (_default_ +false+)
    def initialize( enzyme_lines, reference_lines = nil, supplier_lines = nil, yaml = false )
      # All your REBASE are belong to us.
--- 163,175 ----
    end
  
!   # Constructor
!   #
!   # ---
!   # *Arguments*
!   # * +enzyme_lines+: (_required_) contents of EMBOSS formatted enzymes file 
!   # * +reference_lines+: (_optional_) contents of EMBOSS formatted references file 
!   # * +supplier_lines+: (_optional_) contents of EMBOSS formatted suppliers files 
!   # * +yaml+: (_optional_, _default_ +false+) enzyme_lines, reference_lines, and supplier_lines are read as YAML if set to true 
!   # *Returns*:: Bio::REBASE
    def initialize( enzyme_lines, reference_lines = nil, supplier_lines = nil, yaml = false )
      # All your REBASE are belong to us.
***************
*** 180,183 ****
--- 190,198 ----
  
    # List the enzymes available
+   #
+   # ---
+   # *Arguments*
+   # * _none_
+   # *Returns*:: +Array+ sorted enzyme names
    def enzymes
      @data.keys.sort
***************
*** 188,195 ****
--- 203,218 ----
    #  rebase.save_yaml( 'enz.yaml', 'ref.yaml' )
    #  rebase.save_yaml( 'enz.yaml', 'ref.yaml', 'sup.yaml' )
+   #
+   # ---
+   # *Arguments*
+   # * +f_enzyme+: (_required_) Filename to save YAML formatted output of enzyme data
+   # * +f_reference+: (_optional_) Filename to save YAML formatted output of reference data
+   # * +f_supplier+: (_optional_) Filename to save YAML formatted output of supplier data  
+   # *Returns*:: nothing
    def save_yaml( f_enzyme, f_reference=nil, f_supplier=nil )
      File.open(f_enzyme, 'w') { |f| f.puts YAML.dump(@enzyme_data) }
      File.open(f_reference, 'w') { |f| f.puts YAML.dump(@reference_data) } if f_reference
      File.open(f_supplier, 'w') { |f| f.puts YAML.dump(@supplier_data) } if f_supplier
+     return
    end
  
***************
*** 198,201 ****
--- 221,231 ----
    #  rebase = Bio::REBASE.read( 'emboss_e', 'emboss_r' )
    #  rebase = Bio::REBASE.read( 'emboss_e', 'emboss_r', 'emboss_s' )
+   #
+   # ---
+   # *Arguments*
+   # * +f_enzyme+: (_required_) Filename to read enzyme data
+   # * +f_reference+: (_optional_) Filename to read reference data
+   # * +f_supplier+: (_optional_) Filename to read supplier data  
+   # *Returns*:: Bio::REBASE object
    def self.read( f_enzyme, f_reference=nil, f_supplier=nil )
      e = IO.readlines(f_enzyme)
***************
*** 209,212 ****
--- 239,249 ----
    #  rebase = Bio::REBASE.load_yaml( 'enz.yaml', 'ref.yaml' )
    #  rebase = Bio::REBASE.load_yaml( 'enz.yaml', 'ref.yaml', 'sup.yaml' )
+   #
+   # ---
+   # *Arguments*
+   # * +f_enzyme+: (_required_) Filename to read YAML-formatted enzyme data
+   # * +f_reference+: (_optional_) Filename to read YAML-formatted reference data
+   # * +f_supplier+: (_optional_) Filename to read YAML-formatted supplier data  
+   # *Returns*:: Bio::REBASE object
    def self.load_yaml( f_enzyme, f_reference=nil, f_supplier=nil )
      e = YAML.load_file(f_enzyme)