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Mar 19, 2014

  1. Naohisa Goto

    Bug fix: SEQRES serNum digits were extended in PDB v3.2 (2008)

    * Bug fix: SEQRES serNum digits were extended in PDB v3.2 (2008).
      Thanks to a researcher who reports the patch via email.
    authored March 19, 2014

Jan 17, 2014

  1. Naohisa Goto

    suppress "source :rubygems is deprecated" warning

    authored January 18, 2014
  2. Naohisa Goto

    gemfiles/Gemfile.travis-rbx: Gemfile for rbx (Rubinius) on Travis-ci

     * gemfiles/Gemfile.travis-rbx: Gemfile for rbx (Rubinius) on Travis-ci
     * .travis.yml is modified to use gemfile/Gemfile.travis-rbx for rbx.
    authored January 18, 2014
  3. Naohisa Goto

    .travis.yml: fix mistakes

    authored January 18, 2014
  4. Naohisa Goto

    Ruby 2.1 workaround: Array#uniq does not always choose the first item

     * Ruby 2.1 workaround: Array#uniq does not always choose the first item.
       Thanks to Andrew Grimm who reported the issue.
       (#92 )
       Note that the behavior change is also regarded as a bug in Ruby and
       is fixed. (https://bugs.ruby-lang.org/issues/9340 )
    authored January 18, 2014
  5. Naohisa Goto

    .travis.yml: workaround to avoid error in Ruby 1.8.7 and jruby-18mode

     * workaround to avoid error in Ruby 1.8.7 and jruby-18mode
       (reference: rubygems/rubygems#763 )
    authored January 18, 2014
  6. Naohisa Goto

    .travis.yml: rbx version is changed to 2.2.3

     * rbx version is changed to 2.2.3
     * add dependent gems for rbx platforms, described in
       http://docs.travis-ci.com/user/languages/ruby/
    authored January 18, 2014

Jan 10, 2014

  1. Naohisa Goto

    .travis.yml: change ruby versions for tar and gem integration tests

     * In tar and gem integration tests, Ruby versions are changed to
       MRI 2.0.0 and jruby-19mode.
     * Add jruby-18mode
     * Add rbx-2.1.1
    authored January 11, 2014

Jan 08, 2014

  1. Naohisa Goto

    .travis.yml: Add 2.1.0 and 2.0.0, remove rbx-XXmode

     * Add 2.1.0 and 2.0.0
     * Remove rbx-18mode and rbx-19mode
     * 1.9.2 is moved from "include" to "rvm".
     * 1.8.7 is moved from "rvm" to "include", and remove
       "gemfiles/Gemfile.travis-ruby1.8" line from "gemfile".
     * Remove "exclude" and simplify build matrix.
     * Suggested by agrimm in #91
    authored January 09, 2014

Dec 10, 2013

  1. Brynjar Smári Bjarnason

    Bug fix: Only do gsub on bio_ref.reference.authors if it exists.

     * Bug fix: Only do gsub on bio_ref.reference.authors if it exists.
       Fix #89
    authored December 09, 2013 ngoto committed December 10, 2013
  2. Brynjar Smári Bjarnason

    Bug fix: Missing require when generating genbank output for BioSQL se…

    …quence
    
     * Bug fix: Missing require when generating genbank output for BioSQL
       sequence. Partly fix #89
    authored December 09, 2013 ngoto committed December 10, 2013

Nov 23, 2013

  1. Naohisa Goto

    Benchmark example1-seqnos.aln in addition to example1.aln

     * sample/benchmark_clustalw_report.rb: Benchmark parsing speed of
       example1-seqnos.aln in addition to example1.aln.
    authored November 23, 2013
  2. Andrew Grimm

    Add benchmark script for Bio::ClustalW::Report.

    authored September 17, 2013 ngoto committed November 23, 2013
  3. Naohisa Goto

    Bio::ClustalW::Report#do_parse speed optimization

     * Bio::ClustalW::Report#do_parse speed optimization. Thanks to
       Andrew Grimm who indicates the optimization point.
       (#86 )
     * "$" in the regular expression is changed to "\z". In this context,
       the "$" was intended to be matched with only the end of the string.
    authored November 23, 2013
  4. Naohisa Goto

    New test data: ClustalW with -SEQNOS=ON option

     * test/data/clustalw/example1-seqnos.aln: New test data: ClustalW
       running with -SEQNOS=ON option.
     * Bio::TestClustalWReport::TestClustalWReportSeqnos: new test class
       that parses the above data.
    authored November 23, 2013
  5. Naohisa Goto

    Simplify test data path in setup

     * Bio::TestClustalWReport::TestClustalWReport#setup: simplify test data
       filename path.
     * Modify indentes and void lines.
    authored November 23, 2013
  6. Naohisa Goto

    Common test methods are moved to a module

     * New namespace module Bio::TestClustalWReport.
     * Common test methods are moved to CommonTestMethods,
       and test classes using the methods include it.
     * The test_sequences method is split into two methods
       CommonTestMethods#test_sequence0 and test_sequence1.
    authored November 23, 2013

Aug 23, 2013

  1. Naohisa Goto

    Test bug fix: Read test file with binary mode to avoid encoding error

     * Test bug fix: Read test file with binary mode to avoid string encoding
       error. Thanks to nieder (github.com/nieder) who reports the bug.
       (#84)
    authored August 23, 2013
  2. Yuki Naito

    Modified siRNA design rules by Ui-Tei and Reynolds

     * Ui-Tei rule: Avoided contiguous GCs 10 nt or more.
     * Reynolds rule: Total score of eight criteria is calculated.
       * Returns numerical score for functional siRNA instead of returning 'true'.
       * Returns 'false' for non-functional siRNA, as usual.
     * Unit tests are modified to reflect these changes.
    authored April 05, 2013 ngoto committed August 23, 2013

Jun 28, 2013

  1. Naohisa Goto

    Use Bio::UniProtKB instead of Bio::UniProt

     * Use Bio::UniProtKB instead of Bio::UniProt.
     * Test class names are also changed from UniProt to UniProtKB.
    authored June 28, 2013
  2. Naohisa Goto

    rename test/unit/bio/db/embl/test_uniprot_new_part.rb to test_uniprot…

    …kb_new_part.rb
    authored June 28, 2013
  3. Naohisa Goto

    Reflect the rename of Bio::UniProtKB from SPTR to UniProtKB.

     * Reflect the rename of Bio::UniProtKB from SPTR to UniProtKB.
     * Test class names are also changed.
    authored June 28, 2013
  4. Naohisa Goto

    test_sptr.rb is renamed to test_uniprotkb.rb

    authored June 28, 2013
  5. Naohisa Goto

    Add autoload of Bio::UniProtKB, and modify comments of deprecated cla…

    …sses.
    authored June 28, 2013
  6. Naohisa Goto

    Bio::SwissProt and Bio::TrEMBL are deprecated

     * Bio::SwissProt and Bio::TrEMBL are deprecated.
     * Show warning messages when using these classes.
    authored June 28, 2013
  7. Naohisa Goto

    Bio::UniProt is changed to be an alias of Bio::UniProtKB.

    authored June 28, 2013
  8. Naohisa Goto

    Bio::SPTR is renamed as Bio::UniProtKB and changed to an alias

     * Bio::SPTR is renamed to Bio::UniProtKB.
     * For older programs which use Bio::SPTR, set Bio::SPTR as an alias of
       Bio::UniProtKB.
    authored June 28, 2013

Jun 27, 2013

  1. Naohisa Goto

    Rename lib/bio/db/embl/sptr.rb to uniprotkb.rb

    authored June 27, 2013
  2. Naohisa Goto

    Bio::RefSeq and Bio::DDBJ are deprecated. Show warnings.

     * Bio::RefSeq and Bio::DDBJ are deprecated because they were only
       an alias of Bio::GenBank. Please use Bio::GenBank instead.
     * Show warning message when loading the classes and initializing
       a new instance.
     * Changed to require genbank.rb only when GenBank is not defined.
       This might reduce the possibility of circular require.
    authored June 27, 2013
  3. Naohisa Goto

    Remove descriptions about DDBJ Web API (WABI)

    authored June 27, 2013
  4. Naohisa Goto

    Remove ddbjsoap method that uses Bio::DDBJ::XML

    authored June 27, 2013
  5. Naohisa Goto

    Remove Bio::Blast::Remote::DDBJ from the comment line

    authored June 27, 2013

Jun 25, 2013

  1. Naohisa Goto

    Delete sample/demo_ddbjxml.rb which uses Bio::DDBJ::XML

    authored June 25, 2013
  2. Naohisa Goto

    Remove Bio::Blast::Remote::DDBJ, Bio::Blast.ddbj and related components

     * Remove Bio::Blast::Remote::DDBJ, Bio::Blast.ddbj and related components
       which use Bio::DDBJ::XML or Bio::DDBJ::REST.
    authored June 25, 2013
  3. Naohisa Goto

    Remove Bio::DDBJ::XML and REST due to suspension of DDBJ Web API (WABI)

     * Remove Bio::DDBJ::XML and Bio::DDBJ::REST due to suspension of
       DDBJ Web API (WABI). DDBJ says that it is now under reconstruction
       and the API will be completely changed. Thus, I've decided to throw
       away current API client in Ruby and to implement new one with the new
       API.
     * Autoload lines in lib/bio/db/genbank/ddbj.rb are removed.
     * Tests are also removed.
    authored June 25, 2013
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