bio 1.4.1 → 1.4.2

data/KNOWN_ISSUES.rdoc

@@ -23,19 +23,24 @@ Currently, BioRuby do not care string encodings. In some cases,
 Encoding::CompatibilityError or "ArgumentError: invalid byte sequence in
 (encoding name)" may be raised.
 
-=== Ruby 1.9.0
+=== End-of-life Ruby versions
+
+==== Ruby 1.9.0
 
 (WONT_FIX) Ruby 1.9.0 is NOT supported because it isn't a stable release.
 Use Ruby 1.9.1 or later.
 
-=== Ruby 1.8.2 or earlier
+==== Ruby 1.8.5 or earlier
+
+(WONT_FIX) Problems observed only with Ruby 1.8.5 or earlier will not be
+fixed. Note that Ruby 1.8.5 or earlier is no longer supported, as described
+in README.rdoc.
+
+==== Ruby 1.8.2 or earlier
 
 (WONT_FIX) In some cases, temporary files and directories may not be
 removed because of the lack of FileUtils.remove_entry_secure.
 
-(WONT_FIX) We will soon end support for Ruby 1.8.2. Note that Ruby
-1.8.1 or earlier is no longer supported, as described in README.rdoc.
-
 === Issues about SOAP/WSDL
 
 SOAP4R (SOAP and WSDL implementation) is no longer bundled with Ruby 1.9.
@@ -52,6 +57,15 @@ fixed and new patch is available on the above URL. Note that some Linux
 distributions would have incorporated the patch in their manners, and may
 have the same problem.
 
+=== RubyGems 0.8.11 or earlier
+
+(WONT_FIX) With very old version of RubyGems, use 'require_gem' which was
+deprecated in RubyGems 0.9.0 and removed in RubyGems 1.0.1.
+
+  #!/usr/bin/env ruby
+  require 'rubygems'
+  require_gem 'bio'
+
 == 2. OS and/or architecture-dependent issues
 
 === Microsoft Windows
@@ -116,6 +130,11 @@ correctly, even running on Ruby 1.8.x. Instead, use Bio::NCBI::REST.
 Bio::KEGG::Taxonomy fails to parse current KEGG taxonomy data file probably
 because of the growth of the data size.
 
+=== Bio::SPTR
+
+Bio::SPTR should be updated to follow UniProtKB format changes described
+in http://www.uniprot.org/docs/sp_news.htm .
+
 == 4. Compatibility issues with other libraries/extensions
 
 === ActiveRecord
@@ -128,3 +147,19 @@ know which version is suitable.
 BioRuby Shell on Web uses Ruby on Rails, but the author of the document does
 not know which version is suitable.
 
+== 5. Historical descriptions
+
+=== CVS
+
+For historical purposes: the anonymous CVS was provided at 
+
+* http://cvs.bioruby.org/
+
+and could be obtained by the following procedure.
+
+  % cvs -d :pserver:cvs@code.open-bio.org:/home/repository/bioruby login
+  CVS password: cvs (login with a password 'cvs' for the first time)
+  % cvs -d :pserver:cvs@code.open-bio.org:/home/repository/bioruby co bioruby
+
+These may be closed without any prior notice.
+

data/README.rdoc

@@ -9,7 +9,7 @@ License::   The Ruby License
 
 = BioRuby
 
-Copyright (C) 2001-2010 Toshiaki Katayama <k@bioruby.org>
+Copyright (C) 2001-2011 Toshiaki Katayama <k@bioruby.org>
 
 BioRuby is an open source Ruby library for developing bioinformatics
 software.  Object oriented scripting language Ruby has many features
@@ -42,6 +42,7 @@ services including KEGG API can be easily utilized by BioRuby.
 README.rdoc:: This file. General information and installation procedure.
 RELEASE_NOTES.rdoc:: News and important changes in this release.
 KNOWN_ISSUES.rdoc:: Known issues and bugs in BioRuby.
+doc/RELEASE_NOTES-1.4.1.rdoc:: News and incompatible changes from 1.4.0 to 1.4.1.
 doc/RELEASE_NOTES-1.4.0.rdoc:: News and incompatible changes from 1.3.1 to 1.4.0.
 doc/Changes-1.3.rdoc:: News and incompatible changes from 1.2.1 to 1.3.0.
 doc/Changes-0.7.rd:: News and incompatible changes from 0.6.4 to 1.2.1.
@@ -55,6 +56,7 @@ doc/KEGG_API.rd:: Documents about KEGG API, including usage of Bio::KEGG::API.
 ==== BioRuby development
 
 ChangeLog:: History of changes.
+doc/ChangeLog-before-1.3.1:: changes before 1.3.1.
 README_DEV.rdoc:: Describes ways to contribute to the BioRuby project, including coding styles and documentation guidelines.
 
 ==== Documents written in Japanese
@@ -72,6 +74,9 @@ mailing lists, Wiki documentation etc. in the top page.
 
 * http://bioruby.org/
 
+Mirror site is available, hosted on Open Bioinformatics Foundation (OBF).
+
+* http://bioruby.open-bio.org/
 
 == WHERE TO OBTAIN
 
@@ -83,7 +88,7 @@ The stable release is freely available from the BioRuby website.
 
 === RubyGems
 
-RubyGems[URL:http://rubyforge.org/projects/rubygems/] version of
+{RubyGems (packaging system for Ruby)}[http://rubygems.org/] version of
 the BioRuby package is also available for easy installation.
 
 * http://rubyforge.org/projects/bioruby/
@@ -98,27 +103,15 @@ and can be obtained by the following procedure:
 
   % git clone git://github.com/bioruby/bioruby.git
 
-==== CVS
-
-CVS is now deprecated as source control has moved to github. Please use git 
-instead of CVS. For historical purposes: the anonymous CVS was provided at 
-
-* http://cvs.bioruby.org/
-
-and could be obtained by the following procedure.
-
-  % cvs -d :pserver:cvs@code.open-bio.org:/home/repository/bioruby login
-  CVS password: cvs (login with a password 'cvs' for the first time)
-  % cvs -d :pserver:cvs@code.open-bio.org:/home/repository/bioruby co bioruby
-
 
 == REQUIREMENTS
 
-* Ruby 1.8.2 or later (except Ruby 1.9.0) -- http://www.ruby-lang.org/
-  * Ruby 1.8.7-p174 or later, or Ruby 1.8.6-p383 or later is recommended.
+* Ruby 1.8.6 or later (except Ruby 1.9.0) -- http://www.ruby-lang.org/
+  * Ruby 1.8.7-p352 or later is recommended.
   * Not yet fully ready with Ruby 1.9, although many components can now work
     in Ruby 1.9.1 and Ruby 1.9.2.
 
+
 == OPTIONAL REQUIREMENTS
 
 Some optional libraries can be utilized to extend BioRuby's functionality.
@@ -141,11 +134,6 @@ Accessing BioSQL database created by other Open Bio* libraries:
   {RubyForge:MySQL/Ruby}[http://rubyforge.org/projects/mysql-ruby/],
   {RubyForge:postgres-pr}[http://rubyforge.org/projects/postgres-pr], or
   {RubyForge:ActiveRecord Oracle enhanced adapter}[http://rubyforge.org/projects/oracle-enhanced/].
-* For BioRuby 1.2.1 or older version,
-  {RubyForge:Ruby/DBI}[http://rubyforge.org/projects/ruby-dbi] and
-  at least one driver from MySQL/Ruby, postgres-pr, or
-  {RubyForge:ruby-oci8}[http://ruby-oci8.rubyforge.org/]
-  (note that ruby-oci8 can only work with ruby-dbi 0.2.2).
 
 For parsing PhyloXML format files:
 
@@ -155,6 +143,20 @@ For parsing PhyloXML format files:
 
 == INSTALL
 
+=== INSTALL by using RubyGems (recommended)
+
+If you are using RubyGems, just type
+
+  % gems install bio
+
+Alternatively, manually download bio-X.X.X.gem from 
+http://rubyforge.org/projects/bioruby/ and install it by using gems command.
+
+RubyGems is bundled with Ruby 1.9.1 or later. For Ruby 1.8.7 or earlier,
+download and install RubyGems from http://rubygems.org/ .
+
+=== INSTALL without RubyGems
+
 In the bioruby source directory (such as bioruby-x.x.x/), run setup.rb
 as follows:
 
@@ -188,12 +190,6 @@ and run
 
 for more details.
 
-=== RubyGems
-
-If you are using RubyGems, just type
-
-  % gems install bio
-
 
 == SETUP
 
@@ -227,21 +223,26 @@ You can also read other documentation in the 'doc' directory.
 
   bioruby-x.x.x/doc/
 
-=== RubyGems
+=== RubyGems on Ruby 1.8.x
 
-With RubyGems, you need to load 'rubygems' library before using 'bio'.
+With RubyGems on Ruby 1.8.x, you may need to load 'rubygems' library before
+using 'bio'. This may not be needed, depending on settings of Ruby.
 
   #!/usr/bin/env ruby
   require 'rubygems'
   require 'bio'
 
-With old version of RubyGems, use 'require_gem' which was deprecated in
-RubyGems 0.9.0 and removed in RubyGems 1.0.1.
 
-  #!/usr/bin/env ruby
-  require 'rubygems'
-  require_gem 'bio'
+== PLUGIN (Biogem)
+
+Many plugins (called Biogem) are now available. See http://biogems.info/
+for list of plugins and related software utilizing BioRuby.
+
+* http://biogems.info/
+
+To develop your own plugin, see "Plugins" pages of BioRuby Wiki.
 
+* http://bioruby.open-bio.org/wiki/Plugins
 
 == LICENSE
 

data/RELEASE_NOTES.rdoc

@@ -1,104 +1,132 @@
-= BioRuby 1.4.1 RELEASE NOTES
+= BioRuby 1.4.2 RELEASE NOTES
 
-A lot of changes have been made to the BioRuby 1.4.1 after the version 1.4.0
+A lot of changes have been made to the BioRuby 1.4.2 after the version 1.4.1
 is released. This document describes important and/or incompatible changes
-since the BioRuby 1.4.0 release.
+since the BioRuby 1.4.1 release.
 
 For known problems, see KNOWN_ISSUES.rdoc.
 
 == New features
 
-=== PAML Codeml support is significantly improved
+=== Speed-up of Bio::RestrictionEnzyme::Analysis.cut
 
-PAML Codeml result parser is completely rewritten and is significantly
-improved. The code is developed by Pjotr Prins.
+The running speed of Bio::RestrictionEnzyme::Analysis.cut is significantly
+increased. The new code is 50 to 80 fold faster than the previous code
+when cutting 1Mbp sequence running on Ruby 1.9.2p180. The code is written
+by Tomoaki NISHIYAMA and Naohisa Goto.
 
-=== KEGG PATHWAY and KEGG MODULE parser
+=== New classes Bio::DDBJ::REST, REST interface for DDBJ web service
 
-Parsers for KEGG PATHWAY and KEGG MODULE data are added. The code is developed
-by Kozo Nishida and Toshiaki Katayama.
+For DDBJ Web API for Biology (WABI) web service, in additon to SOAP, REST
+(REpresentational State Transfer) interface is added as Bio::DDBJ::REST.
+Currently, only selected APIs are implemented.
 
-=== Bio::KEGG improvements
+=== Bio::Blast with remote DDBJ server uses REST instead of SOAP
 
-Following new methods are added.
+Bio::Blast with remote DDBJ server uses REST instead of SOAP, because
+Soap4r (SOAP library for Ruby) does not work well with Ruby 1.9.
+We can now use remote DDBJ BLAST server with Ruby 1.9.
 
-* Bio::KEGG::GENES#keggclass, keggclasses, names_as_array, names,
-  motifs_as_strings, motifs_as_hash, motifs
-* Bio::KEGG::GENOME#original_databases
+=== Tutorial is updated
 
-=== Test codes are added and improved.
+The Tutorial.rd is updated by Pjotr Prins and Michael O'Keefe.
 
-Test codes are added and improved. Tney are developed by Kazuhiro Hayashi,
-Kozo Nishida, John Prince, and Naohisa Goto.
+=== Many unit tests are added
 
-=== Other new methods
+Added many unit tests for Bio::GenBank, Bio::GenPept, Bio::NBRF, Bio::PDB
+and so on. Most of them are developed by Kazuhiro Hayashi during the
+Google Summer of Code 2010.
 
-* Bio::Fastq#mask
-* Bio::Sequence#output_fasta
-* Bio::ClustalW::Report#get_sequence
-* Bio::Reference#==
-* Bio::Location#==
-* Bio::Locations#==
-* Bio::FastaNumericFormat#to_biosequence
+=== Other new features
 
-== Bug fixes
+* New method Bio::Fastq#to_s for convenience. Note that the use of the method
+  may cause loss of performance. To get each input sequence entry as-is,
+  consider using Bio::FlatFile#entry_raw. To output fastq format data,
+  consider using Bio::Sequence#output(:fastq).
+* New methods Bio::NCBI::REST::EFetch.nucleotide and protein,
+  to get data from "nucleotide" and "protein" database respectively.
+  Because NCBI changed not to accept "gb" format for the database
+  "sequence", the two new methods are added for convenience.
+* In BioRuby Shell, efetch method uses the above new methods.
+* In GenomeNet remote BLAST execution, database "mine-aa" and "mine-nt"
+  with KEGG organism codes are now supported.
+* Support for Ruby 1.9.2 / 1.9.3 is improved.
 
-=== Bio::Tree
+== Bug fixes
 
-Following methods did not work correctly.
+=== Bio::Blast
 
-* Bio::Tree#collect_edge!
-* Bio::Tree#remove_edge_if
+* Failure of remote BLAST execution is fixed, due to the changes in GenomeNet
+  and DDBJ.
+* When executing remote BLAST with "genomenet" server, options "-b" and "-v"
+  are now correctly used to limit the number of hits to be reported.
 
-=== Bio::KEGG::GENES and Bio::KEGG::GENOME
+=== Bio::SPTR (Bio::UniProt)
 
-* Fixed bugs in Bio::KEGG::GENES#pathway.
-* Fixed parser errors due to the format changes of KEGG GENES and KEGG GENOME.
+* Due to the UniProtKB format changes, ID, DE, and WEB RESOURCE of CC lines
+  were not correctly parsed. See also below about incompatible change of
+  the fix.
 
 === 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.
+* Bio::Reference#pubmed_url is updated to follow recent NCBI changes.
+* Fixed: Bio::Newick#reparse failure.
+* Fixed: In Bio::MEDLINE#reference, doi field should be filled.
+* Fixed: Bio::Reference#endnote fails when url is not set.
+* Fixed: Bio::FastaFormat#query passes nil to the given factory object.
+* Fixed: In BioRuby Shell, efetch() with no additional arguments fails
+  because of the NCBI site changes.
+* Fixed: In BioRuby Shell, getent() fails when EMBOSS seqret is not found.
+* Fixed: In BioRuby Shell, demo() fails due to the above two issues.
 
 == Incompatible changes
 
-=== Bio::PAML::Codeml::Report
+=== Bio::Sequence#output(:fastq)
+
+In Fastq output formatter, default width value is changed from 70 to nil.
+The nil means "without wrapping". The new default behavior without wrapping
+is generally good with many recent applications that read fastq.
+
+=== Bio::SPTR CC line topic "WEB RESOURCE"
 
-The code is completely rewritten. See the RDoc for details.
+In the return value of Bio::SPTR#cc('WEB RESOURCE'), "NAME" and "NOTE"
+are now renamed to "Name" and "Note", respectively. The change is due to
+the UniProt format change since UniProtKB release 12.2 of 11-Sep-2007.
+(See http://www.uniprot.org/docs/sp_news.htm#rel12.2 for details.)
+Note that "Name" and "Note" are used even when parsing older format.
+The change would also affect Marshal.dump (and YAML.dump) data.
 
-=== Bio::KEGG::ORTHOLOGY
+=== Bio::Blast with the remote GenomeNet server
 
-Bio::KEGG::ORTHOLOGY#pathways is changed to return a hash. The old pathway
-method is renamed to pathways_in_keggclass for compatibility.
+When executing remote BLAST with "genomenet" server, options "-b" and "-v"
+are now correctly used to limit the number of hits to be reported.
+In 1.4.1 and before, "-B" and "-V" were mistakenly used for the purpose.
 
-=== Bio::AAindex2
+=== Bio::Blast with the remote DDBJ server
 
-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::Blast with remote DDBJ server uses REST instead of SOAP.
 
-=== Bio::MEDLINE
+=== Bio::RestrictionEnzyme internal data structure change
 
-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.
+Due to the speedup, internal data structure of the following classes
+are changed: Bio::RestrictionEnzyme::Range::SequenceRange,
+Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts,
+Bio::RestrictionEnzyme::Range::SequenceRange::Fragment.
+This indicates that Marshal.dump (and YAML.dump) data generated by older
+versions cannot be loaded by the new version, and vice versa, although
+public APIs of the classes keep compatibility.
 
 == 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
+* Bio::SPTR should be updated to follow UniProtKB format changes.
+* Problems observed only with Ruby 1.8.5 or earlier will not be fixed.
+* Descriptions about very old RubyGems 0.8.11 or earlier and about CVS
+  repository are moved from README.rdoc.
 
-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.
+== Other important news
 
-Curreltly, due to the change, test/functional/bio/test_command.rb may fail
-on Windows with Ruby 1.9.X.
+* Required ruby version is now Ruby 1.8.6 or later (except 1.9.0).
 

data/bioruby.gemspec

@@ -3,7 +3,7 @@
 # 
 Gem::Specification.new do |s|
   s.name = 'bio'
-  s.version = "1.4.1"
+  s.version = "1.4.2"
 
   s.author = "BioRuby project"
   s.email = "staff@bioruby.org"
@@ -38,6 +38,7 @@ Gem::Specification.new do |s|
     "doc/KEGG_API.rd",
     "doc/KEGG_API.rd.ja",
     "doc/RELEASE_NOTES-1.4.0.rdoc",
+    "doc/RELEASE_NOTES-1.4.1.rdoc",
     "doc/Tutorial.rd",
     "doc/Tutorial.rd.html",
     "doc/Tutorial.rd.ja",
@@ -186,6 +187,7 @@ Gem::Specification.new do |s|
     "lib/bio/io/biosql/config/database.yml",
     "lib/bio/io/das.rb",
     "lib/bio/io/dbget.rb",
+    "lib/bio/io/ddbjrest.rb",
     "lib/bio/io/ddbjxml.rb",
     "lib/bio/io/ebisoap.rb",
     "lib/bio/io/ensembl.rb",
@@ -279,6 +281,7 @@ Gem::Specification.new do |s|
     "lib/bio/util/restriction_enzyme/analysis.rb",
     "lib/bio/util/restriction_enzyme/analysis_basic.rb",
     "lib/bio/util/restriction_enzyme/cut_symbol.rb",
+    "lib/bio/util/restriction_enzyme/dense_int_array.rb",
     "lib/bio/util/restriction_enzyme/double_stranded.rb",
     "lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb",
     "lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb",
@@ -297,6 +300,7 @@ Gem::Specification.new do |s|
     "lib/bio/util/restriction_enzyme/single_strand.rb",
     "lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb",
     "lib/bio/util/restriction_enzyme/single_strand_complement.rb",
+    "lib/bio/util/restriction_enzyme/sorted_num_array.rb",
     "lib/bio/util/restriction_enzyme/string_formatting.rb",
     "lib/bio/util/sirna.rb",
     "lib/bio/version.rb",
@@ -363,6 +367,7 @@ Gem::Specification.new do |s|
     "sample/ssearch2tab.rb",
     "sample/tdiary.rb",
     "sample/test_phyloxml_big.rb",
+    "sample/test_restriction_enzyme_long.rb",
     "sample/tfastx2tab.rb",
     "sample/vs-genes.rb",
     "setup.rb",
@@ -402,6 +407,7 @@ Gem::Specification.new do |s|
     "test/data/command/echoarg2.bat",
     "test/data/embl/AB090716.embl",
     "test/data/embl/AB090716.embl.rel89",
+    "test/data/fasta/EFTU_BACSU.fasta",
     "test/data/fasta/example1.txt",
     "test/data/fasta/example2.txt",
     "test/data/fastq/README.txt",
@@ -456,12 +462,15 @@ Gem::Specification.new do |s|
     "test/data/fastq/wrapping_as_solexa.fastq",
     "test/data/fastq/wrapping_original_sanger.fastq",
     "test/data/gcg/pileup-aa.msf",
+    "test/data/genbank/CAA35997.gp",
+    "test/data/genbank/SCU49845.gb",
     "test/data/genscan/sample.report",
     "test/data/go/selected_component.ontology",
     "test/data/go/selected_gene_association.sgd",
     "test/data/go/selected_wikipedia2go",
     "test/data/iprscan/merged.raw",
     "test/data/iprscan/merged.txt",
+    "test/data/litdb/1717226.litdb",
     "test/data/medline/20146148_modified.medline",
     "test/data/meme/db",
     "test/data/meme/mast",
@@ -481,6 +490,7 @@ Gem::Specification.new do |s|
     "test/data/phyloxml/made_up.xml",
     "test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml",
     "test/data/phyloxml/phyloxml_examples.xml",
+    "test/data/pir/CRAB_ANAPL.pir",
     "test/data/prosite/prosite.dat",
     "test/data/refseq/nm_126355.entret",
     "test/data/rpsblast/misc.rpsblast",
@@ -493,7 +503,10 @@ Gem::Specification.new do |s|
     "test/data/soft/GDS100_partial.soft",
     "test/data/soft/GSE3457_family_partial.soft",
     "test/data/uniprot/p53_human.uniprot",
+    "test/functional/bio/appl/blast/test_remote.rb",
+    "test/functional/bio/appl/test_blast.rb",
     "test/functional/bio/appl/test_pts1.rb",
+    "test/functional/bio/io/test_ddbjrest.rb",
     "test/functional/bio/io/test_ensembl.rb",
     "test/functional/bio/io/test_pubmed.rb",
     "test/functional/bio/io/test_soapwsdl.rb",
@@ -536,9 +549,13 @@ Gem::Specification.new do |s|
     "test/unit/bio/db/embl/test_embl_to_bioseq.rb",
     "test/unit/bio/db/embl/test_sptr.rb",
     "test/unit/bio/db/embl/test_uniprot.rb",
+    "test/unit/bio/db/embl/test_uniprot_new_part.rb",
     "test/unit/bio/db/fasta/test_defline.rb",
     "test/unit/bio/db/fasta/test_defline_misc.rb",
     "test/unit/bio/db/fasta/test_format_qual.rb",
+    "test/unit/bio/db/genbank/test_common.rb",
+    "test/unit/bio/db/genbank/test_genbank.rb",
+    "test/unit/bio/db/genbank/test_genpept.rb",
     "test/unit/bio/db/kegg/test_compound.rb",
     "test/unit/bio/db/kegg/test_drug.rb",
     "test/unit/bio/db/kegg/test_enzyme.rb",
@@ -558,7 +575,9 @@ Gem::Specification.new do |s|
     "test/unit/bio/db/test_gff.rb",
     "test/unit/bio/db/test_go.rb",
     "test/unit/bio/db/test_lasergene.rb",
+    "test/unit/bio/db/test_litdb.rb",
     "test/unit/bio/db/test_medline.rb",
+    "test/unit/bio/db/test_nbrf.rb",
     "test/unit/bio/db/test_newick.rb",
     "test/unit/bio/db/test_nexus.rb",
     "test/unit/bio/db/test_phyloxml.rb",
@@ -606,9 +625,11 @@ Gem::Specification.new do |s|
     "test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb",
     "test/unit/bio/util/restriction_enzyme/test_analysis.rb",
     "test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb",
+    "test/unit/bio/util/restriction_enzyme/test_dense_int_array.rb",
     "test/unit/bio/util/restriction_enzyme/test_double_stranded.rb",
     "test/unit/bio/util/restriction_enzyme/test_single_strand.rb",
     "test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb",
+    "test/unit/bio/util/restriction_enzyme/test_sorted_num_array.rb",
     "test/unit/bio/util/restriction_enzyme/test_string_formatting.rb",
     "test/unit/bio/util/test_color_scheme.rb",
     "test/unit/bio/util/test_contingency_table.rb",
@@ -624,7 +645,8 @@ Gem::Specification.new do |s|
     "README_DEV.rdoc",
     "RELEASE_NOTES.rdoc",
     "doc/Changes-1.3.rdoc",
-    "doc/RELEASE_NOTES-1.4.0.rdoc"
+    "doc/RELEASE_NOTES-1.4.0.rdoc",
+    "doc/RELEASE_NOTES-1.4.1.rdoc"
   ]
   s.rdoc_options << '--main' << 'README.rdoc'
   s.rdoc_options << '--title' << 'BioRuby API documentation'