[BioRuby-cvs] bioruby/lib/bio/db fantom.rb, 1.10, 1.11 fasta.rb, 1.20, 1.21 gff.rb, 1.2, 1.3 go.rb, 1.7, 1.8 nbrf.rb, 1.3, 1.4 prosite.rb, 0.10, 0.11

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/db
In directory pub.open-bio.org:/tmp/cvs-serv17319/lib/bio/db

Modified Files:
	fantom.rb fasta.rb gff.rb go.rb nbrf.rb prosite.rb 
Log Message:
* 'alias :foo :bar' is changed to 'alias foo bar'


Index: prosite.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/prosite.rb,v
retrieving revision 0.10
retrieving revision 0.11
diff -C2 -d -r0.10 -r0.11
*** prosite.rb	8 Sep 2005 01:22:11 -0000	0.10
--- prosite.rb	26 Sep 2005 13:00:06 -0000	0.11
***************
*** 455,459 ****
    begin
      require 'pp'
!     alias :p :pp
    rescue LoadError
    end
--- 455,459 ----
    begin
      require 'pp'
!     alias p pp
    rescue LoadError
    end

Index: go.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/go.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** go.rb	8 Sep 2005 01:22:11 -0000	1.7
--- go.rb	26 Sep 2005 13:00:06 -0000	1.8
***************
*** 201,205 ****
      attr_reader :date
      attr_reader :assigned_by 
!     alias :entry_id :db_object_id
  
  
--- 201,205 ----
      attr_reader :date
      attr_reader :assigned_by 
!     alias entry_id db_object_id
  
  

Index: nbrf.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/nbrf.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** nbrf.rb	8 Sep 2005 01:22:11 -0000	1.3
--- nbrf.rb	26 Sep 2005 13:00:06 -0000	1.4
***************
*** 50,59 ****
      attr_reader :entry_overrun
  
!     alias :accession :entry_id
  
      def entry
        @entry = ">#{@seq_type or 'XX'};#{@entry_id}\n#{definition}\n#{@data}*\n"
      end
!     alias :to_s :entry
  
      def seq_class
--- 50,59 ----
      attr_reader :entry_overrun
  
!     alias accession entry_id
  
      def entry
        @entry = ">#{@seq_type or 'XX'};#{@entry_id}\n#{definition}\n#{@data}*\n"
      end
!     alias to_s entry
  
      def seq_class

Index: fasta.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/fasta.rb,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** fasta.rb	8 Sep 2005 01:22:11 -0000	1.20
--- fasta.rb	26 Sep 2005 13:00:06 -0000	1.21
***************
*** 43,53 ****
        @entry = ">#{@definition}\n#{@data.strip}\n"
      end
!     alias :to_s :entry
  
      def query(factory)
        factory.query(@entry)
      end
!     alias :fasta :query
!     alias :blast :query
  
      def seq
--- 43,53 ----
        @entry = ">#{@definition}\n#{@data.strip}\n"
      end
!     alias to_s entry
  
      def query(factory)
        factory.query(@entry)
      end
!     alias fasta query
!     alias blast query
  
      def seq

Index: fantom.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/fantom.rb,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** fantom.rb	8 Sep 2005 01:22:11 -0000	1.10
--- fantom.rb	26 Sep 2005 13:00:06 -0000	1.11
***************
*** 148,152 ****
            @representative_sequence
          end
!         alias :representative_clone :representative_sequence
  
          def representative_annotations
--- 148,152 ----
            @representative_sequence
          end
!         alias representative_clone representative_sequence
  
          def representative_annotations

Index: gff.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/gff.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** gff.rb	8 Sep 2005 01:22:11 -0000	1.2
--- gff.rb	26 Sep 2005 13:00:06 -0000	1.3
***************
*** 70,74 ****
    begin
      require 'pp'
!     alias :p :pp
    rescue LoadError
    end
--- 70,74 ----
    begin
      require 'pp'
!     alias p pp
    rescue LoadError
    end