[BioRuby-cvs] bioruby/lib/bio sequence.rb,0.58.2.10,0.58.2.11
Naohisa Goto
ngoto at dev.open-bio.org
Thu Apr 24 14:28:27 UTC 2008
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
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