bio-gff3.gemspec in bio-gff3-0.8.4 vs bio-gff3.gemspec in bio-gff3-0.8.5

@@ -3,15 +3,15 @@
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
 
 Gem::Specification.new do |s|
   s.name = %q{bio-gff3}
-  s.version = "0.8.4"
+  s.version = "0.8.5"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Pjotr Prins"]
-  s.date = %q{2011-01-03}
+  s.date = %q{2011-01-13}
   s.default_executable = %q{gff3-fetch}
   s.description = %q{GFF3 (genome browser) information and digest mRNA and CDS sequences.
 Options for low memory use and caching of records.
 Support for external FASTA files.
 }
@@ -29,34 +29,48 @@
     "Rakefile",
     "VERSION",
     "bin/gff3-fetch",
     "bio-gff3.gemspec",
     "lib/bio-gff3.rb",
-    "lib/bio/db/gff/gffassemble.rb",
-    "lib/bio/db/gff/gffdb.rb",
-    "lib/bio/db/gff/gfffasta.rb",
-    "lib/bio/db/gff/gfffileiterator.rb",
-    "lib/bio/db/gff/gffinmemory.rb",
-    "lib/bio/db/gff/gffnocache.rb",
-    "lib/bio/db/gff/gffparser.rb",
+    "lib/bio/db/gff/digest/gffinmemory.rb",
+    "lib/bio/db/gff/digest/gffnocache.rb",
+    "lib/bio/db/gff/digest/gffparser.rb",
+    "lib/bio/db/gff/file/gfffasta.rb",
+    "lib/bio/db/gff/file/gfffileiterator.rb",
+    "lib/bio/db/gff/gff3.rb",
+    "lib/bio/db/gff/gff3fasta.rb",
+    "lib/bio/db/gff/gff3parsefile.rb",
+    "lib/bio/db/gff/gff3parserec.rb",
+    "lib/bio/db/gff/gffcomponent.rb",
+    "lib/bio/db/gff/gffrecord.rb",
+    "lib/bio/db/gff/gffsection.rb",
+    "lib/bio/db/gff/gffsequence.rb",
+    "lib/bio/db/gff/gffvalidate.rb",
     "lib/bio/output/gfffastawriter.rb",
+    "lib/bio/output/gfflogger.rb",
     "lib/bio/system/lruhash.rb",
     "spec/gff3_assemble2_spec.rb",
     "spec/gff3_assemble3_spec.rb",
     "spec/gff3_assemble_spec.rb",
     "spec/gff3_fileiterator_spec.rb",
     "spec/gffdb_spec.rb",
+    "spec/gffparserec.rb",
     "test/data/gff/MhA1_Contig1133.fa",
     "test/data/gff/MhA1_Contig1133.gff3",
     "test/data/gff/MhA1_Contig125.fa",
     "test/data/gff/MhA1_Contig125.gff3",
     "test/data/gff/standard.gff3",
     "test/data/gff/test-cds.gff3",
     "test/data/gff/test-ext-fasta.fa",
     "test/data/gff/test-ext-fasta.gff3",
     "test/data/gff/test.gff3",
+    "test/data/regression/test_ext_gff3.rtest",
+    "test/data/regression/test_gff3.rtest",
+    "test/data/regression/test_nocache_ext_gff3.rtest",
+    "test/data/regression/test_nocache_gff3.rtest",
     "test/helper.rb",
+    "test/regressiontest.rb",
     "test/test_bio-gff3.rb"
   ]
   s.homepage = %q{http://github.com/pjotrp/bioruby-gff3}
   s.licenses = ["MIT"]
   s.require_paths = ["lib"]
@@ -66,41 +80,55 @@
     "spec/gff3_assemble2_spec.rb",
     "spec/gff3_assemble3_spec.rb",
     "spec/gff3_assemble_spec.rb",
     "spec/gff3_fileiterator_spec.rb",
     "spec/gffdb_spec.rb",
+    "spec/gffparserec.rb",
     "test/helper.rb",
+    "test/regressiontest.rb",
     "test/test_bio-gff3.rb"
   ]
 
   if s.respond_to? :specification_version then
     current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
     s.specification_version = 3
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<bio>, [">= 1.3.1"])
+      s.add_runtime_dependency(%q<bio-logger>, ["> 0.5.0"])
       s.add_development_dependency(%q<shoulda>, [">= 0"])
       s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
       s.add_development_dependency(%q<jeweler>, ["~> 1.5.2"])
       s.add_development_dependency(%q<rcov>, [">= 0"])
-      s.add_development_dependency(%q<bio>, [">= 1.3.1"])
       s.add_development_dependency(%q<rspec>, [">= 2.0.0"])
+      s.add_runtime_dependency(%q<bio>, [">= 1.4.1"])
+      s.add_runtime_dependency(%q<log4r>, ["> 1.1.6"])
+      s.add_runtime_dependency(%q<bio-logger>, [">= 0.6.1"])
+      s.add_development_dependency(%q<rspec>, ["> 2.0"])
     else
       s.add_dependency(%q<bio>, [">= 1.3.1"])
+      s.add_dependency(%q<bio-logger>, ["> 0.5.0"])
       s.add_dependency(%q<shoulda>, [">= 0"])
       s.add_dependency(%q<bundler>, ["~> 1.0.0"])
       s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
       s.add_dependency(%q<rcov>, [">= 0"])
-      s.add_dependency(%q<bio>, [">= 1.3.1"])
       s.add_dependency(%q<rspec>, [">= 2.0.0"])
+      s.add_dependency(%q<bio>, [">= 1.4.1"])
+      s.add_dependency(%q<log4r>, ["> 1.1.6"])
+      s.add_dependency(%q<bio-logger>, [">= 0.6.1"])
+      s.add_dependency(%q<rspec>, ["> 2.0"])
     end
   else
     s.add_dependency(%q<bio>, [">= 1.3.1"])
+    s.add_dependency(%q<bio-logger>, ["> 0.5.0"])
     s.add_dependency(%q<shoulda>, [">= 0"])
     s.add_dependency(%q<bundler>, ["~> 1.0.0"])
     s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
     s.add_dependency(%q<rcov>, [">= 0"])
-    s.add_dependency(%q<bio>, [">= 1.3.1"])
     s.add_dependency(%q<rspec>, [">= 2.0.0"])
+    s.add_dependency(%q<bio>, [">= 1.4.1"])
+    s.add_dependency(%q<log4r>, ["> 1.1.6"])
+    s.add_dependency(%q<bio-logger>, [">= 0.6.1"])
+    s.add_dependency(%q<rspec>, ["> 2.0"])
   end
 end