= BioRuby 1.4.1 RELEASE NOTES

A lot of changes have been made to the BioRuby 1.4.1 after the version 1.4.0
is released. This document describes important and/or incompatible changes
since the BioRuby 1.4.0 release.

For known problems, see KNOWN_ISSUES.rdoc.

== New features

=== PAML Codeml support is significantly improved

PAML Codeml result parser is completely rewritten and is significantly
improved. The code is developed by Pjotr Prins.

=== KEGG PATHWAY and KEGG MODULE parser

Parsers for KEGG PATHWAY and KEGG MODULE data are added. The code is developed
by Kozo Nishida and Toshiaki Katayama.

=== Bio::KEGG improvements

Following new methods are added.

* Bio::KEGG::GENES#keggclass, keggclasses, names_as_array, names,
  motifs_as_strings, motifs_as_hash, motifs
* Bio::KEGG::GENOME#original_databases

=== Test codes are added and improved.

Test codes are added and improved. Tney are developed by Kazuhiro Hayashi,
Kozo Nishida, John Prince, and Naohisa Goto.

=== Other new methods

* Bio::Fastq#mask
* Bio::Sequence#output_fasta
* Bio::ClustalW::Report#get_sequence
* Bio::Reference#==
* Bio::Location#==
* Bio::Locations#==
* Bio::FastaNumericFormat#to_biosequence

== Bug fixes

=== Bio::Tree

Following methods did not work correctly.

* Bio::Tree#collect_edge!
* Bio::Tree#remove_edge_if

=== Bio::KEGG::GENES and Bio::KEGG::GENOME

* Fixed bugs in Bio::KEGG::GENES#pathway.
* Fixed parser errors due to the format changes of KEGG GENES and KEGG GENOME.

=== Other bug fixes

* In Bio::Command, changed not to call fork(2) on platforms that do not
  support it.
* Bio::MEDLINE#initialize should handle continuation of lines.
* Typo and a missing field in Bio::GO::GeneAssociation#to_str.
* Bug fix of Bio::FastaNumericFormat#to_biosequence.
* Fixed UniProt GN parsing issue in Bio::SPTR.

== Incompatible changes

=== Bio::PAML::Codeml::Report

The code is completely rewritten. See the RDoc for details.

=== Bio::KEGG::ORTHOLOGY

Bio::KEGG::ORTHOLOGY#pathways is changed to return a hash. The old pathway
method is renamed to pathways_in_keggclass for compatibility.

=== Bio::AAindex2

Bio::AAindex2 now copies each symmetric element for lower triangular matrix
to the upper right part, because the Matrix class in Ruby 1.9.2 no longer
accepts any dimension mismatches. We think the previous behavior is a bug.

=== Bio::MEDLINE

Bio::MEDLINE#reference no longer puts empty values in the returned
Bio::Reference object. We think the previous behavior is a bug.
We also think the effect is very small.

== Known issues

The following issues are added or updated. See KNOWN_ISSUES.rdoc for other
already known issues.

=== String escaping of command-line arguments in Ruby 1.9.X on Windows

After BioRuby 1.4.1, in Ruby 1.9.X running on Windows, escaping of
command-line arguments are processed by the Ruby interpreter. Before BioRuby
1.4.0, the escaping is executed in Bio::Command#escape_shell_windows, and
the behavior is different from the Ruby interpreter's one.

Curreltly, due to the change, test/functional/bio/test_command.rb may fail
on Windows with Ruby 1.9.X.

