diff --git a/RELEASE_NOTES.rdoc b/RELEASE_NOTES.rdoc index 71efb1dda..ac1da5b31 100644 --- a/RELEASE_NOTES.rdoc +++ b/RELEASE_NOTES.rdoc @@ -1,6 +1,6 @@ = BioRuby 1.5.0 RELEASE NOTES -A lot of changes have been made to the BioRuby 1.5.0 after the version 1.4.2 +A lot of changes have been made to the BioRuby 1.4.3 after the version 1.4.2 is released. This document describes important and/or incompatible changes since the BioRuby 1.4.2 release. @@ -8,9 +8,16 @@ For known problems, see KNOWN_ISSUES.rdoc. == New features -=== (tbd) +=== Bio::KEGG::KGML -(paragraph) +* New class Bio::KEGG::KGML::Graphics for storing a graphics element. + In the instance of the class, "coords" attribute is now available. +* New class Bio::KEGG::KGML::Substrate for storing a substrate element. +* New class Bio::KEGG::KGML::Product for storing a product element. +* New method Bio::KEGG::KGML::Reaction#id. +* Improve RDoc documentation. +* Unit tests are added. +* There are incompatible changes. See Incompatible changes below. === Other new features @@ -37,6 +44,37 @@ by default when opening a file, unless text mode is explicitly specified with open mode string or with options. Due to the change, files using CR+LF line separator might not be read correctly. +=== Bio::KEGG::KGML + +* Bio::KEGG::KGML::Reaction#substrates and Bio::KEGG::KGML::Reaction#products + are changed to return an array containing Bio::KEGG::KGML::Substrate and + Bio::KEGG::KGML::Product objects, respectively. The changes enables us to + get ID of substrates and products that were thrown away in the previous + versions. +* Most attribute methods that were different from the KGML attribute names + are renamed to the names compatible with the KGML attribute names. Old + method names are changed to aliases of them and marked as deprecated. + The old names will be removed in the future. + * Bio::KEGG::KGML::Entry#id (old name: entry_id) + * Bio::KEGG::KGML::Entry#type (old name: category) + * Bio::KEGG::KGML::Entry#entry1 (old name: node1) + * Bio::KEGG::KGML::Entry#entry2 (old name: node2) + * Bio::KEGG::KGML::Entry#type (old name: rel) + * Bio::KEGG::KGML::Reaction#name (old name: entry_id) + * Bio::KEGG::KGML::Reaction#type (old name: direction) +* Following attribute methods are deprecated because two or more graphics + elements may exist in an entry element. They will be removed in the future. + Instead, please use instance methods of Bio::KEGG::KGML::Graphics, which + can be obtained from Bio::KEGG::KGML::Entry#graphics attribute. + * Bio::KEGG::KGML::Entry#label + * Bio::KEGG::KGML::Entry#shape + * Bio::KEGG::KGML::Entry#x + * Bio::KEGG::KGML::Entry#y + * Bio::KEGG::KGML::Entry#width + * Bio::KEGG::KGML::Entry#height + * Bio::KEGG::KGML::Entry#fgcolor + * Bio::KEGG::KGML::Entry#bgcolor + === BioRuby development * rdoc.zsh is removed because it have not been used for a long time.