Added news and incompatible changes.

doc/Changes-1.4.rdoc

@@ -5,10 +5,105 @@ is released.
 
 == New features
 
-== Deprecated classes
+=== PhyloXML support
+
+Support for reading and writing PhyloXML file format is added. New classes
+Bio::PhyloXML::Parser and Bio::PhyloXML::Writer are used to read and write
+a PhyloXML file, respectively.
+
+The code is developed by Diana Jaunzeikare, mentored by Christian M Zmasek
+and co-mentors, supported by Google Summer of Code 2009 in collaboration
+with the National Evolutionary Synthesis Center (NESCent).
+
+=== FASTQ file format support
+
+Support for reading and writing FASTQ file format is added. All of the
+three FASTQ format variants are supported.
+
+To read a FASTQ file, Bio::FlatFile can be used. File format auto-detection
+of the FASTQ format is supported (although the three format variants should
+be specified later by users if quality scores are needed).
+
+New class Bio::Fastq is the parser class for the FASTQ format. An object
+of the Bio::Fastq class can be converted to a Bio::Sequence object with the
+"to_biosequnece" method. Bio::Sequence#output now supports output of the
+FASTQ format.
+
+The code is written by Naohisa Goto, with the help of discussions in the
+open-bio-l mailing list. The prototype of Bio::Fastq class was first
+developed during the BioHackathon 2009 held in Okinawa.
+
+=== DNA chromatogram support
+
+Support for reading DNA chromatogram files are added. SCF and and ABIF file
+formats are supported. The code is developed by Anthony Underwood.
+
+=== MEME (motif-based sequence analysis tools) support
+
+Support for running MAST (Motif Aliginment & Search Tool, part of the MEME
+Suite, motif-based sequence analysis tools) and parsing its results are
+added. The code is developed by Adam Kraut.
+
+=== Improvement of KEGG parser classes
+
+Some new methods are added to parse new fields added to some KEGG file
+formats. Unit tests for KEGG parsers are also added and improved. In
+addition, return value types of some methods are also changed for unifying
+APIs among KEGG parser classes. See incompatible changes below for details.
+
+=== Many sample scripts are added
+
+Many sample scripts showing demonstrations of usages of classes are added.
+They are moved from primitive test codes for the classes described in the
+"if __FILE__ == $0" convention in the library files.
+
+=== Unit tests can test installed BioRuby
+
+Mechanism to load library and to find test data in the unit tests are changed,
+and the library path and test data path can be specified with environment
+variables. BIORUBY_TEST_LIB is the path to be added to the Ruby's $LOAD_PATH.
+For example, to test BioRuby installed in
+/usr/local/lib/site_ruby/1.8, run
+  env BIORUBY_TEST_LIB=/usr/local/lib/site_ruby/1.8 ruby test/runner.rb
+
+BIORUBY_TEST_DATA is the path of the test data, and BIORUBY_TEST_DEBUG is a
+flag to turn on debug of the tests.
+
+== Deprecated features
+
+=== "if __FILE__ == $0" convention
+
+Primitive test codes in the "if __FILE__ == $0" convention are removed and
+their contents are moved to the sample scripts named sample/demo_*.rb
+(except some older files).
+
+== Known problems
+
+See KNOWN_ISSUES.rdoc for details.
 
 == Incompatible changes
 
+=== Bio::NCBI::REST
+
+NCBI announces that all Entrez E-utility requests must contain email and
+tool parameters, and requests without them will return error after June
+2010.
+
+To set default email address and tool name, following methods are added.
+* Bio::NCBI.default_email=(email)
+* Bio::NCBI.default_tool=(tool_name)
+
+For every query, Bio::NCBI::REST checks the email and tool parameters and
+raises error if they are empty.
+
+IMPORTANT NOTE: No default email address is preset in BioRuby. Programmers
+using BioRuby must set their own email address or implement to get user's
+email address in some way (from input form, configuration file, etc).
+
+Default tool name is set as "#{$0} (bioruby/#{Bio::BIORUBY_VERSION_ID})".
+For example, if you run "ruby my_script.rb" with BioRuby 1.4.0, the value is
+"my_script.rb (bioruby/1.4.0)".
+
 === Bio::KEGG
 
 ==== #dblinks
@@ -55,12 +150,11 @@ Bio::KEGG::REACTION#rpairs is changed to return a Hash. Each key of the
 hash is a KEGG Rpair ID and its value is an array containing name and type.
 If old behavior (returns as tokens) is needed, use rpairs_as_tokens.
 
-=== Bio::KEGG::ORTHOLOGY
+==== Bio::KEGG::ORTHOLOGY
 
 Bio::KEGG:ORTHOLOGY#dblinks_as_hash does not lower-case database names.
 
 === Bio::RestrictionEnzyme
 
-Format validation when creating a object is turned off because of
-efficiency.
+Format validation when creating an object is turned off because of efficiency.