[BioRuby-cvs] bioruby/lib/bio sequence.rb,0.58.2.10,0.58.2.11

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv15857/lib/bio

Modified Files:
      Tag: BRANCH-biohackathon2008
	sequence.rb 
Log Message:
* Bio::Sequence.read is renamed to Bio::Sequence.input because this method is
  a pair of Bio::Sequence#output. Bio::Sequence.read still exists as an
  alias of Bio::Sequence.
* Added document for Bio::Sequence#accessions, and fixed not to contain nil
  in the returned array.


Index: sequence.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence.rb,v
retrieving revision 0.58.2.10
retrieving revision 0.58.2.11
diff -C2 -d -r0.58.2.10 -r0.58.2.11
*** sequence.rb	27 Mar 2008 13:38:31 -0000	0.58.2.10
--- sequence.rb	24 Apr 2008 14:28:25 -0000	0.58.2.11
***************
*** 369,373 ****
    # (GenBank, EMBL, fasta format, etc.)
    #
!   #   s = Bio::Sequence.read(str)
    # ---
    # *Arguments*:
--- 369,373 ----
    # (GenBank, EMBL, fasta format, etc.)
    #
!   #   s = Bio::Sequence.input(str)
    # ---
    # *Arguments*:
***************
*** 375,379 ****
    # * (optional) _format_: format specification (class or nil)
    # *Returns*:: Bio::Sequence object
!   def self.read(str, format = nil)
      if format then
        klass = format
--- 375,379 ----
    # * (optional) _format_: format specification (class or nil)
    # *Returns*:: Bio::Sequence object
!   def self.input(str, format = nil)
      if format then
        klass = format
***************
*** 384,391 ****
      obj.to_biosequence
    end
!   
!   
    def accessions
!     return [@primary_accession, @secondary_accessions].flatten
    end
  
--- 384,398 ----
      obj.to_biosequence
    end
! 
!   # alias of Bio::Sequence.input
!   def self.read(str, format = nil)
!     input(str, format)
!   end
! 
!   # accession numbers of the sequence
!   #
!   # *Returns*:: Array of String
    def accessions
!     [ @primary_accession, @secondary_accessions ].flatten.compact
    end