[BioRuby-cvs] bioruby/lib/bio/io flatfile.rb,1.51,1.52

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv15819/lib/bio/io

Modified Files:
	flatfile.rb 
Log Message:
New files/classes: Bio::GCG::Msf in lib/bio/appl/gcg/msf.rb for GCG msf 
multiple sequence alignment format parser, and Bio::GCG::Seq in 
lib/bio/appl/gcg/seq.rb for GCG sequence format parser.

Autoload of the classes (in bio.rb) and file format autodetection
(in flatfile.rb) are also supported.

Bio::Alignment::Output#output_msf, #output(:msf, ...) are added
to generate msf formatted string from multiple alignment object.


Index: flatfile.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/flatfile.rb,v
retrieving revision 1.51
retrieving revision 1.52
diff -C2 -d -r1.51 -r1.52
*** flatfile.rb	22 Jun 2006 14:32:47 -0000	1.51
--- flatfile.rb	14 Dec 2006 19:52:53 -0000	1.52
***************
*** 1184,1187 ****
--- 1184,1193 ----
            /^CLUSTAL .*\(.*\).*sequence +alignment/ ],
  
+           gcg_msf = RuleRegexp[ 'Bio::GCG::Msf',
+           /^!!(N|A)A_MULTIPLE_ALIGNMENT .+/ ],
+ 
+           gcg_seq = RuleRegexp[ 'Bio::GCG::Seq',
+           /^!!(N|A)A_SEQUENCE .+/ ],
+ 
            blastxml = RuleRegexp[ 'Bio::Blast::Report',
              /\<\!DOCTYPE BlastOutput PUBLIC / ],