[BioRuby-cvs] bioruby/lib/bio sequence.rb,0.37,0.38

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio
In directory pub.open-bio.org:/tmp/cvs-serv27061/lib/bio

Modified Files:
	sequence.rb 
Log Message:
* fixed Bio::Sequence::AA#molecular_weight to use AminoAcid#weight also


Index: sequence.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence.rb,v
retrieving revision 0.37
retrieving revision 0.38
diff -C2 -d -r0.37 -r0.38
*** sequence.rb	7 Aug 2005 08:19:28 -0000	0.37
--- sequence.rb	7 Aug 2005 09:58:22 -0000	0.38
***************
*** 2,6 ****
  # bio/sequence.rb - biological sequence class
  #
! #   Copyright (C) 2000-2004 KATAYAMA Toshiaki <k at bioruby.org>
  #   Copyright (C) 2001 Yoshinori K. Okuji <o at bioruby.org>
  #   Copyright (C) 2003 GOTO Naohisa <ng at bioruby.org>
--- 2,6 ----
  # bio/sequence.rb - biological sequence class
  #
! #   Copyright (C) 2000-2005 KATAYAMA Toshiaki <k at bioruby.org>
  #   Copyright (C) 2001 Yoshinori K. Okuji <o at bioruby.org>
  #   Copyright (C) 2003 GOTO Naohisa <ng at bioruby.org>
***************
*** 322,328 ****
  
        # AminoAcid is defined in bio/data/aa.rb
!       def molecular_weight(hash = nil)
! 	hash = AminoAcid.weight unless hash
! 	total(hash) - NucleicAcid.weight[:water] * (self.length - 1)
        end
  
--- 322,327 ----
  
        # AminoAcid is defined in bio/data/aa.rb
!       def molecular_weight
!         AminoAcid.weight(self)
        end
  
***************
*** 593,597 ****
        Show abnormal bases other than 'atgcu'.
  
! --- Bio::Sequence::NA#molecular_weight(hash)
  
        Estimate the weight of this biological string molecule.
--- 592,596 ----
        Show abnormal bases other than 'atgcu'.
  
! --- Bio::Sequence::NA#molecular_weight
  
        Estimate the weight of this biological string molecule.
***************
*** 631,635 ****
        Similar to codes but returns long names.
  
! --- Bio::Sequence::AA#molecular_weight(hash)
  
        Estimate the weight of this protein.
--- 630,634 ----
        Similar to codes but returns long names.
  
! --- Bio::Sequence::AA#molecular_weight
  
        Estimate the weight of this protein.