[BioRuby-cvs] bioruby/lib/bio/shell/plugin seq.rb,1.1,1.2

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/shell/plugin
In directory pub.open-bio.org:/tmp/cvs-serv23142/shell/plugin

Modified Files:
	seq.rb 
Log Message:
* Bio::Sequence::NA#gc_percent is changed returns integer instead of float
* Bio::Sequence::NA#gc method is removed
* added Bio::Sequence#guess and Bio::Sequence.guess
* plugin - modified to use new guess method


Index: seq.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/seq.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** seq.rb	23 Sep 2005 13:57:08 -0000	1.1
--- seq.rb	23 Sep 2005 14:27:59 -0000	1.2
***************
*** 58,65 ****
        end
      else
!       case Bio::Seq.guess(str)
!       when :NA
          display na_report(str)
!       when :AA
          display aa_report(str)
        end
--- 58,65 ----
        end
      else
!       moltype = Bio::Seq.guess(str)
!       if moltype == Bio::Sequence::NA
          display na_report(str)
!       elsif moltype == Bio::Sequence::AA
          display aa_report(str)
        end
***************
*** 79,83 ****
      str << "translation -2     : #{seq.translate(-2)}\n"
      str << "translation -3     : #{seq.translate(-3)}\n"
!     str << "gc percent         : #{seq.gc} %\n"
      str << "composition        : #{seq.composition.inspect}\n"
      str << "molecular weight   : #{seq.molecular_weight}\n"
--- 79,83 ----
      str << "translation -2     : #{seq.translate(-2)}\n"
      str << "translation -3     : #{seq.translate(-3)}\n"
!     str << "gc percent         : #{seq.gc_percent} %\n"
      str << "composition        : #{seq.composition.inspect}\n"
      str << "molecular weight   : #{seq.molecular_weight}\n"