[BioRuby-cvs] bioruby ChangeLog,1.56,1.57

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv15096

Modified Files:
	ChangeLog 
Log Message:
Changes by ngoto during Phyloinformatics Hackathon are written in the
ChangeLog and incompatible changes after 1.0.0 are written in Changes-0.7.rd.


Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.56
retrieving revision 1.57
diff -C2 -d -r1.56 -r1.57
*** ChangeLog	24 Dec 2006 18:32:55 -0000	1.56
--- ChangeLog	28 Dec 2006 15:35:50 -0000	1.57
***************
*** 30,33 ****
--- 30,78 ----
  	
  	  Bio::Iprscan::Report for InterProScan output is newly added.		
+ 2006-12-15  Naohisa Goto <ng at bioruby.org>
+ 
+ 	* lib/bio/appl/mafft/report.rb
+ 
+ 	  Bio::MAFFT::Report#initialize is changed to get a string of
+ 	  multi-fasta formmatted text instead of Array.
+ 
+ 2006-12-14  Naohisa Goto <ng at bioruby.org>
+ 
+ 	* lib/bio/appl/phylip/alignment.rb
+ 
+ 	  Phylip format multiple sequence alignment parser class
+ 	  Bio::Phylip::PhylipFormat is newly added.
+ 
+ 	* lib/bio/appl/phylip/distance_matrix.rb
+ 
+ 	  Bio::Phylip::DistanceMatrix, a parser for phylip distance matrix
+ 	  (generated by dnadist/protdist/restdist programs) is newly added.
+ 
+ 	* lib/bio/appl/gcg/msf.rb, lib/bio/appl/gcg/seq.rb
+ 
+ 	  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 are
+ 	  newly added.
+ 
+ 	* lib/bio/alignment.rb
+ 
+ 	  Output of Phylip interleaved/non-interleaved format (.phy),
+ 	  Molphy alignment format (.mol), and GCG MSF format (.msf)
+ 	  are supported. Bio::Alignment::ClustalWFormatter is removed
+ 	  and methods in the module are renamed and moved to
+ 	  Bio::Alignment::Output.
+ 
+ 	* lib/bio/appl/clustalw.rb, lib/bio/appl/mafft.rb, lib/bio/appl/sim4.rb
+ 
+ 	  Changed to use Bio::Command instead of Open3.popen3.
+ 	
+ 2006-12-13  Naohisa Goto <ng at bioruby.org>
+ 
+ 	* lib/bio/tree.rb, lib/bio/db/newick.rb
+ 
+ 	  Bio::PhylogeneticTree is renamed to Bio::Tree, and
+ 	  lib/bio/phylogenetictree.rb is renamed to lib/bio/tree.rb.
+ 	  NHX (New Hampshire eXtended) parser/writer support are added.
  
  2006-10-05  Naohisa Goto <ng at bioruby.org>