[DRE-commits] [ruby-bio] 01/11: Merge tag 'upstream/1.4.3.0001'
Cédric Boutillier
boutil at alioth.debian.org
Tue Aug 6 22:19:01 UTC 2013
This is an automated email from the git hooks/post-receive script.
boutil pushed a commit to branch master
in repository ruby-bio.
commit e4f32fe15961b1533cb4816f24b97fe3cc1a6a15
Merge: 7126978 9e15cc5
Author: Cédric Boutillier <boutil at debian.org>
Date: Tue Aug 6 08:03:23 2013 +0200
Merge tag 'upstream/1.4.3.0001'
Upstream version 1.4.3.0001
# gpg: Signature faite le mar. 06 août 2013 08:03:05 CEST avec la clef RSA d'identifiant 8F9F8F09
# gpg: Bonne signature de « Cédric Boutillier <boutil at debian.org> »
# gpg: alias « Cédric Boutillier <cedric.boutillier at upmc.fr> »
# gpg: alias « Cédric Boutillier <cedric.boutillier at polytechnique.org> »
# gpg: alias « Cédric Boutillier <cedric.boutillier at gmail.com> »
.travis.yml | 66 +
ChangeLog | 5496 ++++----------------
KNOWN_ISSUES.rdoc | 69 +-
README.rdoc | 112 +-
README_DEV.rdoc | 95 +-
RELEASE_NOTES.rdoc | 274 +-
Rakefile | 206 +-
bioruby.gemspec | 39 +-
bioruby.gemspec.erb | 9 +-
ChangeLog => doc/ChangeLog-before-1.4.2 | 9 +
RELEASE_NOTES.rdoc => doc/RELEASE_NOTES-1.4.2.rdoc | 0
doc/Tutorial.rd | 24 +-
doc/Tutorial.rd.html | 32 +-
etc/bioinformatics/seqdatabase.ini | 209 +-
gemfiles/Gemfile.travis-jruby1.8 | 7 +
gemfiles/Gemfile.travis-jruby1.9 | 10 +
gemfiles/Gemfile.travis-ruby1.8 | 7 +
gemfiles/Gemfile.travis-ruby1.9 | 10 +
gemfiles/modify-Gemfile.rb | 28 +
gemfiles/prepare-gemspec.rb | 25 +
lib/bio/alignment.rb | 2 +-
lib/bio/appl/bl2seq/report.rb | 6 +-
lib/bio/appl/blast/ddbj.rb | 3 -
lib/bio/appl/blast/format0.rb | 64 +-
lib/bio/appl/blast/genomenet.rb | 49 +-
lib/bio/appl/blast/ncbioptions.rb | 11 +-
lib/bio/appl/blast/remote.rb | 11 +-
lib/bio/appl/blast/report.rb | 16 +-
lib/bio/appl/blast/rpsblast.rb | 5 +-
lib/bio/appl/blast/wublast.rb | 6 +-
lib/bio/command.rb | 154 +-
lib/bio/data/na.rb | 2 +-
lib/bio/db/embl/embl.rb | 74 +
lib/bio/db/embl/format_embl.rb | 4 -
lib/bio/db/fasta.rb | 102 +-
lib/bio/db/fasta/defline.rb | 2 +-
lib/bio/db/fasta/format_fasta.rb | 4 -
lib/bio/db/fasta/format_qual.rb | 5 -
lib/bio/db/fastq/format_fastq.rb | 1 -
lib/bio/db/genbank/format_genbank.rb | 4 -
lib/bio/db/gff.rb | 54 +-
lib/bio/db/kegg/genes.rb | 6 +-
lib/bio/db/kegg/kgml.rb | 529 +-
lib/bio/db/newick.rb | 244 -
lib/bio/db/pdb.rb | 5 +-
lib/bio/db/pdb/atom.rb | 5 +-
lib/bio/db/pdb/chain.rb | 5 +-
lib/bio/db/pdb/chemicalcomponent.rb | 5 +-
lib/bio/db/pdb/model.rb | 4 +-
lib/bio/db/pdb/pdb.rb | 3 +-
lib/bio/db/pdb/residue.rb | 4 +-
lib/bio/db/pdb/utils.rb | 11 +-
lib/bio/db/phyloxml/phyloxml_parser.rb | 57 +-
lib/bio/feature.rb | 5 +-
lib/bio/io/flatfile/autodetection.rb | 2 +-
lib/bio/io/flatfile/buffer.rb | 84 +
lib/bio/sequence.rb | 10 +-
lib/bio/sequence/aa.rb | 8 +-
lib/bio/sequence/adapter.rb | 12 +-
lib/bio/sequence/common.rb | 6 +-
lib/bio/sequence/compat.rb | 9 +-
lib/bio/sequence/dblink.rb | 11 +-
lib/bio/sequence/format.rb | 6 -
lib/bio/sequence/format_raw.rb | 4 -
lib/bio/sequence/generic.rb | 7 +-
lib/bio/sequence/na.rb | 10 +-
lib/bio/sequence/quality_score.rb | 2 +
lib/bio/sequence/sequence_masker.rb | 3 +
lib/bio/shell/core.rb | 1 +
lib/bio/tree.rb | 3 +-
lib/bio/tree/output.rb | 264 +
lib/bio/util/restriction_enzyme.rb | 4 +-
lib/bio/util/restriction_enzyme/analysis.rb | 13 +-
lib/bio/util/restriction_enzyme/analysis_basic.rb | 7 +-
lib/bio/util/restriction_enzyme/cut_symbol.rb | 5 +-
lib/bio/util/restriction_enzyme/dense_int_array.rb | 3 +
lib/bio/util/restriction_enzyme/double_stranded.rb | 7 +-
.../double_stranded/aligned_strands.rb | 7 +-
.../double_stranded/cut_location_pair.rb | 7 +-
.../cut_location_pair_in_enzyme_notation.rb | 7 +-
.../double_stranded/cut_locations.rb | 7 +-
.../cut_locations_in_enzyme_notation.rb | 7 +-
lib/bio/util/restriction_enzyme/range/cut_range.rb | 7 +-
.../util/restriction_enzyme/range/cut_ranges.rb | 7 +-
.../range/horizontal_cut_range.rb | 7 +-
.../restriction_enzyme/range/sequence_range.rb | 7 +-
.../range/sequence_range/calculated_cuts.rb | 7 +-
.../range/sequence_range/fragment.rb | 7 +-
.../range/sequence_range/fragments.rb | 7 +-
.../restriction_enzyme/range/vertical_cut_range.rb | 7 +-
lib/bio/util/restriction_enzyme/single_strand.rb | 6 +-
.../cut_locations_in_enzyme_notation.rb | 7 +-
.../restriction_enzyme/single_strand_complement.rb | 7 +-
.../util/restriction_enzyme/sorted_num_array.rb | 3 +
.../util/restriction_enzyme/string_formatting.rb | 7 +-
lib/bio/version.rb | 15 +-
metadata.yml | 2079 +++++---
rdoc.zsh | 8 -
{etc/bioinformatics => sample}/seqdatabase.ini | 0
test/bioruby_test_helper.rb | 49 +-
test/data/KEGG/test.kgml | 37 +
test/data/command/echoarg2.sh | 4 +
test/functional/bio/test_command.rb | 86 +-
.../bio/appl/blast/test_remote.rb | 0
.../{functional => network}/bio/appl/test_blast.rb | 0
test/{functional => network}/bio/appl/test_pts1.rb | 0
.../bio/io/test_ddbjrest.rb | 0
.../{functional => network}/bio/io/test_ensembl.rb | 0
test/{functional => network}/bio/io/test_pubmed.rb | 0
.../bio/io/test_soapwsdl.rb | 0
test/{functional => network}/bio/io/test_togows.rb | 0
test/network/bio/test_command.rb | 35 +
test/runner.rb | 22 +-
test/unit/bio/appl/blast/test_report.rb | 119 +
test/unit/bio/appl/blast/test_rpsblast.rb | 1 +
test/unit/bio/data/test_na.rb | 2 +-
test/unit/bio/db/embl/test_embl.rb | 9 +-
test/unit/bio/db/embl/test_embl_rel89.rb | 9 +-
test/unit/bio/db/fasta/test_defline.rb | 2 +-
test/unit/bio/db/genbank/test_genpept.rb | 2 +-
test/unit/bio/db/kegg/test_drug.rb | 2 +-
test/unit/bio/db/kegg/test_genome.rb | 2 +-
test/unit/bio/db/kegg/test_glycan.rb | 2 +-
test/unit/bio/db/kegg/test_kgml.rb | 1022 ++++
test/unit/bio/db/sanger_chromatogram/test_abif.rb | 3 +-
test/unit/bio/db/sanger_chromatogram/test_scf.rb | 6 +-
test/unit/bio/db/test_newick.rb | 2 +
test/unit/bio/db/test_phyloxml.rb | 56 +-
test/unit/bio/db/test_phyloxml_writer.rb | 24 +-
test/unit/bio/db/test_soft.rb | 2 +-
test/unit/bio/io/flatfile/test_autodetection.rb | 6 +
test/unit/bio/io/flatfile/test_buffer.rb | 141 +
test/unit/bio/sequence/test_common.rb | 40 +-
test/unit/bio/sequence/test_na.rb | 2 +-
test/unit/bio/test_command.rb | 13 +-
test/unit/bio/test_sequence.rb | 4 +-
test/unit/bio/test_tree.rb | 22 +-
test/unit/bio/util/test_restriction_enzyme.rb | 2 +-
138 files changed, 6346 insertions(+), 6275 deletions(-)
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