[BioRuby-cvs] bioruby/lib/bio/db/embl common.rb, 1.7, 1.8 embl.rb, 1.24, 1.25 sptr.rb, 1.28, 1.29

[Mitsuteru C. Nakao]

Update of /home/repository/bioruby/bioruby/lib/bio/db/embl
In directory pub.open-bio.org:/tmp/cvs-serv12425/lib/bio/db/embl

Modified Files:
	common.rb embl.rb sptr.rb 
Log Message:
* Removed TAB.


Index: sptr.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/sptr.rb,v
retrieving revision 1.28
retrieving revision 1.29
diff -C2 -d -r1.28 -r1.29
*** sptr.rb	1 Nov 2005 02:16:06 -0000	1.28
--- sptr.rb	2 Nov 2005 07:30:14 -0000	1.29
***************
*** 69,75 ****
  
      if key
!       @data['ID'][key]	# String/Int
      else
!       @data['ID']		# Hash
      end
    end
--- 69,75 ----
  
      if key
!       @data['ID'][key] # String/Int
      else
!       @data['ID']      # Hash
      end
    end
***************
*** 517,521 ****
  
      when nil
!       return @data['CC']	
  
      else
--- 517,521 ----
  
      when nil
!       return @data['CC']
  
      else

Index: embl.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/embl.rb,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** embl.rb	1 Nov 2005 02:16:06 -0000	1.24
--- embl.rb	2 Nov 2005 07:30:14 -0000	1.25
***************
*** 242,251 ****
          next if line =~ /^FEATURES/
  
!         head = line[0,20].strip	# feature key (source, CDS, ...)
!         body = line[20,60].chomp	# feature value (position, /qualifier=)
          if line =~ /^FT {3}(\S+)/
!           ary.push([ $1, body ])	# [ feature, position, /q="data", ... ]
          elsif body =~ /^ \// and not in_quote
!           ary.last.push(body)		# /q="data..., /q=data, /q
  
            if body =~ /=" / and body !~ /"$/
--- 242,251 ----
          next if line =~ /^FEATURES/
  
!         head = line[0,20].strip  # feature key (source, CDS, ...)
!         body = line[20,60].chomp # feature value (position, /qualifier=)
          if line =~ /^FT {3}(\S+)/
!           ary.push([ $1, body ]) # [ feature, position, /q="data", ... ]
          elsif body =~ /^ \// and not in_quote
!           ary.last.push(body)    # /q="data..., /q=data, /q
  
            if body =~ /=" / and body !~ /"$/
***************
*** 254,258 ****
  
          else
!           ary.last.last << body	# ...data..., ...data..."
  
            if body =~ /"$/
--- 254,258 ----
  
          else
!           ary.last.last << body # ...data..., ...data..."
  
            if body =~ /"$/

Index: common.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/common.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** common.rb	1 Nov 2005 02:16:06 -0000	1.7
--- common.rb	2 Nov 2005 07:30:14 -0000	1.8
***************
*** 75,80 ****
  module Common
  
!   DELIMITER	= RS = "\n//\n"
!   TAGSIZE	= 5
  
    def initialize(entry)
--- 75,81 ----
  module Common
  
!   DELIMITER = "\n//\n"
!   RS = DELIMITER
!   TAGSIZE = 5
  
    def initialize(entry)
***************
*** 119,123 ****
      @data['DE']
    end
!   alias description de	
    alias definition de   # API
    
--- 120,124 ----
      @data['DE']
    end
!   alias description de
    alias definition de   # API
    
***************
*** 216,220 ****
        if get('KW').size > 0
          tmp = fetch('KW').sub(/.$/,'')
!         @data['KW'] = tmp.split(/;/).map {|e| e.strip }	
        else
          @data['KW'] = []
--- 217,221 ----
        if get('KW').size > 0
          tmp = fetch('KW').sub(/.$/,'')
!         @data['KW'] = tmp.split(/;/).map {|e| e.strip }
        else
          @data['KW'] = []