[BioRuby-cvs] bioruby/lib/bio/db/kegg genome.rb,0.15,0.16

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/db/kegg
In directory dev.open-bio.org:/tmp/cvs-serv28666/lib/bio/db/kegg

Modified Files:
	genome.rb 
Log Message:
* disease, data_source, original_db methods are added
* scaffolds, gc, genomemap methods are obsoleted


Index: genome.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/genome.rb,v
retrieving revision 0.15
retrieving revision 0.16
diff -C2 -d -r0.15 -r0.16
*** genome.rb	19 Sep 2006 05:52:45 -0000	0.15
--- genome.rb	15 Jan 2007 04:37:29 -0000	0.16
***************
*** 2,6 ****
  # = bio/db/kegg/genome.rb - KEGG/GENOME database class
  #
! # Copyright::  Copyright (C) 2001, 2002 Toshiaki Katayama <k at bioruby.org>
  # License::    Ruby's
  #
--- 2,6 ----
  # = bio/db/kegg/genome.rb - KEGG/GENOME database class
  #
! # Copyright::  Copyright (C) 2001, 2002, 2007 Toshiaki Katayama <k at bioruby.org>
  # License::    Ruby's
  #
***************
*** 72,75 ****
--- 72,90 ----
    end
  
+   # DATA_SOURCE -- Returns contents of the DATA_SOURCE record as a String.
+   def data_source
+     field_fetch('DATA_SOURCE')
+   end
+ 
+   # ORIGINAL_DB -- Returns contents of the ORIGINAL_DB record as a String.
+   def original_db
+     field_fetch('ORIGINAL_DB')
+   end
+ 
+   # DISEASE -- Returns contents of the COMMENT record as a String.
+   def disease
+     field_fetch('DISEASE')
+   end
+ 
    # COMMENT -- Returns contents of the COMMENT record as a String.
    def comment
***************
*** 99,104 ****
                hash['journal']	= $1
                hash['volume']	= $2
!               hash['pages']		= $3
!               hash['year']		= $5
                hash['medline']	= $6
              else
--- 114,119 ----
                hash['journal']	= $1
                hash['volume']	= $2
!               hash['pages']	= $3
!               hash['year']	= $5
                hash['medline']	= $6
              else
***************
*** 145,163 ****
    end
  
-   # SCAFFOLD -- Returns contents of the SCAFFOLD records as an Array of Hash.
-   def scaffolds
-     unless @data['SCAFFOLD']
-       @data['SCAFFOLD'] = []
-       toptag2array(get('SCAFFOLD')).each do |chr|
-         hash = Hash.new('')
-         subtag2array(chr).each do |field|
-           hash[tag_get(field)] = truncate(tag_cut(field))
-         end
-         @data['SCAFFOLD'].push(hash)
-       end
-     end
-     @data['SCAFFOLD']
-   end
- 
    # STATISTICS -- Returns contents of the STATISTICS record as a Hash.
    def statistics
--- 160,163 ----
***************
*** 167,177 ****
          case line
          when /nucleotides:\s+(\d+)/
!           hash['nalen'] = $1.to_i
          when /protein genes:\s+(\d+)/
            hash['num_gene'] = $1.to_i
          when /RNA genes:\s+(\d+)/
            hash['num_rna'] = $1.to_i
-         when /G\+C content:\s+(\d+.\d+)/
-           hash['gc'] = $1.to_f
          end
        end
--- 167,175 ----
          case line
          when /nucleotides:\s+(\d+)/
!           hash['num_nuc'] = $1.to_i
          when /protein genes:\s+(\d+)/
            hash['num_gene'] = $1.to_i
          when /RNA genes:\s+(\d+)/
            hash['num_rna'] = $1.to_i
          end
        end
***************
*** 183,187 ****
    # Returns number of nucleotides from the STATISTICS record as a Fixnum.
    def nalen
!     statistics['nalen']
    end
    alias length nalen
--- 181,185 ----
    # Returns number of nucleotides from the STATISTICS record as a Fixnum.
    def nalen
!     statistics['num_nuc']
    end
    alias length nalen
***************
*** 197,210 ****
    end
  
-   # Returns G+C content from the STATISTICS record as a Float.
-   def gc
-     statistics['gc']
-   end
- 
-   # GENOMEMAP -- Returns contents of the GENOMEMAP record as a String.
-   def genomemap
-     field_fetch('GENOMEMAP')
-   end
- 
  end # GENOME
      
--- 195,198 ----
***************
*** 239,245 ****
        %w( CHROMOSOME chromosomes ),
        %w( PLASMID plasmids ),
!       %w( SCAFFOLD plasmids ),
!       %w( STATISTICS statistics nalen num_gene num_rna gc ),
!       %w( GENOMEMAP genomemap ),
      ].each do |x|
        puts "### " + x.shift
--- 227,231 ----
        %w( CHROMOSOME chromosomes ),
        %w( PLASMID plasmids ),
!       %w( STATISTICS statistics nalen num_gene num_rna ),
      ].each do |x|
        puts "### " + x.shift