[BioRuby-cvs] bioruby/doc Changes-0.7.rd,1.14,1.15

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/doc
In directory pub.open-bio.org:/tmp/cvs-serv1785/doc

Modified Files:
	Changes-0.7.rd 
Log Message:
added Bio::FlatFile incompatible changes.


Index: Changes-0.7.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Changes-0.7.rd,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** Changes-0.7.rd	16 Jan 2006 15:25:43 -0000	1.14
--- Changes-0.7.rd	22 Feb 2006 15:09:45 -0000	1.15
***************
*** 227,230 ****
--- 227,252 ----
  * There are more and more changes to be written...
  
+ --- Bio::FlatFile
+ 
+ In 0.7.2:
+ 
+ * Bio::FlatFile.open, Bio::FlatFile.auto and Bio::FlatFile.new are changed
+   not to accept the last argument to specify raw mode, e.g. :raw => true,
+   :raw => false, true or false. Instead, please use Bio::FlatFile#raw=
+   method after creating a new object.
+ * Now, first argument of Bio::FlatFile.open, which shall be a database
+   class or nil, can be omitted, and you can do
+   Bio::FlatFile.open(filename, ...). Note that 
+   Bio::FlatFile.open(dbclass, filaname, ...) is still available.
+ * Bio::FlatFile#io is obsoleted. Please use Bio::FlatFile#to_io instead.
+ * When reading GenBank or GenPept files, comments at the  head of the file
+   before the first "LOCUS" lines are now skipped by default.
+   When reading other file formats, white space characters are skipped.
+ * File format autodetection routine is completely rewritten.
+   If it fails to determine data format which was previously determined,
+   please report us with the data.
+ * Internal structure is now completely changed. Codes depend on the internal
+   structure (which is not recommended) would not work.
+ 
  === Deleted files