[BioRuby-cvs] bioruby/doc Changes-0.7.rd,1.17,1.18

[Naohisa Goto]

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

Modified Files:
	Changes-0.7.rd 
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: Changes-0.7.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Changes-0.7.rd,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** Changes-0.7.rd	22 Mar 2006 10:19:22 -0000	1.17
--- Changes-0.7.rd	28 Dec 2006 15:35:50 -0000	1.18
***************
*** 184,187 ****
--- 184,189 ----
  --- Bio::Alignment
  
+ In 0.7.0:
+ 
  * Old Bio::Alignment class is renamed to Bio::Alignment::OriginalAlignment.
    Now, new Bio::Alignment is a module. However, you don't mind so much
***************
*** 200,203 ****
--- 202,210 ----
  * There are more and more changes to be written...
  
+ In 1.1.0:
+ 
+ * Bio::Alignment::ClustalWFormatter is removed and methods in this module
+   are renemed and moved to Bio::Alignment::Output.
+ 
  --- Bio::PDB
  
***************
*** 240,243 ****
--- 247,260 ----
  * There are more and more changes to be written...
  
+ In 1.1.0:
+ 
+ * In Bio::PDB::ATOM#name, #resName, #iCode, and #charge, whitespaces are
+   stripped during initializing.
+ * In Bio::PDB::ATOM#segID, whitespaces are right-stripped during initializing.
+ * In Bio::PDB::ATOM#element, whitespaces are left-stripped during initializing.
+ * Bio::PDB::HETATM#name, #resName, #iCode, #charge, #segID, and #element
+   are also subject to the above changes, because Bio::PDB::HETATM inherits
+   Bio::PDB::ATOM.
+ 
  --- Bio::FlatFile
  
***************
*** 262,270 ****
    structure (which is not recommended) would not work.
  
! In 1.0.1:
  
  * Bio::FlatFile#entry_start_pos and #entry_ended_pos are enabled
    only when Bio::FlatFile#entry_pos_flag is true.
  
  === Deleted files
  
--- 279,302 ----
    structure (which is not recommended) would not work.
  
! In 1.1.0:
  
  * Bio::FlatFile#entry_start_pos and #entry_ended_pos are enabled
    only when Bio::FlatFile#entry_pos_flag is true.
  
+ --- Bio::ClustalW, Bio::MAFFT, Bio::Sim4
+ 
+ In 1.1.0:
+ 
+ * Bio::(ClustalW|MAFFT|Sim4)#option is changed to #options.
+ * Bio::ClustalW::errorlog and Bio::(MAFFT|Sim4)#log are removed.
+   No replacements/alternatives are available.
+ 
+ --- Bio::MAFFT::Report
+ 
+ In 1.1.0:
+ 
+ * Bio::MAFFT::Report#initialize is changed to get a string of multi-fasta
+   formmatted text instead of Array.
+ 
  === Deleted files