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base fork: syncrou/bioruby
base: ce9e53f3c2
...
head fork: syncrou/bioruby
compare: 2680cc181d
Checking mergeability… Don't worry, you can still create the pull request.
  • 2 commits
  • 3 files changed
  • 0 commit comments
  • 1 contributor
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16 bioruby.gemspec
@@ -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",
@@ -402,6 +403,7 @@ 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 +458,15 @@ 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 +486,7 @@ 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",
@@ -493,6 +499,8 @@ 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_ensembl.rb",
"test/functional/bio/io/test_pubmed.rb",
@@ -539,6 +547,9 @@ Gem::Specification.new do |s|
"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 +569,9 @@ 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",
@@ -624,7 +637,8 @@ 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'
View
9 lib/bio/io/biosql/ar-biosql.rb
@@ -231,6 +231,14 @@ class Taxon < DummyBase
has_one :taxon_genbank_common_name, :class_name => "TaxonName", :conditions=>"name_class = 'genbank common name'"
has_one :bioentry, :class_name => "Bioentry"
+ def ancestors
+ if(self.left_value && self.right_value)
+ Taxon.find(:all, :conditions => "#{self.left_value} BETWEEN left_value AND right_value", :order => :left_value)
+ else
+ return []
+ end
+ end
+
def species
return self if node_rank =='species'
ancestors.each do |t|
@@ -240,6 +248,7 @@ def species
end
return nil
end
+
end
class TermDbxref < DummyBase
set_table_name "term_dbxref"
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