scaffolder 0.4.1 → 0.4.2

data/Rakefile

@@ -18,6 +18,7 @@ Jeweler::Tasks.new do |gem|
   gem.description = %Q{Organise sequence contigs into genome scaffolds using simple human-readable YAML files.}
   gem.email = "mail@michaelbarton.me.uk"
   gem.authors = ["Michael Barton"]
+  gem.test_files = Dir['test/**/*.rb']
 end
 Jeweler::RubygemsDotOrgTasks.new
 

data/VERSION

@@ -1 +1 @@
-0.4.1
+0.4.2

data/lib/scaffolder.rb

@@ -140,8 +140,8 @@ require 'bio'
 #     that the insert sequence fills. For example if a 5 base pair insert fills
 #     a 4 base region, the host sequence stop position is increased by the
 #     difference: 1.
-#   * The region is subsequenced if specified.
-#   * The region is reverse complemented if specified.
+# * The region is subsequenced if specified.
+# * The region is reverse complemented if specified.
 #
 # === WARNING
 #

data/lib/scaffolder/region/sequence.rb

@@ -42,8 +42,6 @@ class Scaffolder::Region::Sequence < Scaffolder::Region
     end
   end
 
-#  attribute :inserts, :default => Array.new
-
   # Adds each of the sequence inserts to the raw sequence. Updates the sequence
   # length each time an insert is added to reflect the change.
   #
@@ -54,6 +52,12 @@ class Scaffolder::Region::Sequence < Scaffolder::Region
   # @raise [CoordinateError] if any insert open position is greater than the
   #   close position
   def sequence_hook
+    @updated_sequence ||= update_sequence_with_inserts
+  end
+
+  private
+
+  def update_sequence_with_inserts
     # Set the sequence stop positon if not defined as the stop
     # position is updated as each insert is added
     @stop ||= raw_sequence.length

data/scaffolder.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{scaffolder}
-  s.version = "0.4.1"
+  s.version = "0.4.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Michael Barton"]
-  s.date = %q{2011-01-04}
+  s.date = %q{2011-06-03}
   s.description = %q{Organise sequence contigs into genome scaffolds using simple human-readable YAML files.}
   s.email = %q{mail@michaelbarton.me.uk}
   s.extra_rdoc_files = [
@@ -48,14 +48,7 @@ Gem::Specification.new do |s|
   s.require_paths = ["lib"]
   s.rubygems_version = %q{1.3.7}
   s.summary = %q{Genome scaffolding for human beings.}
-  s.test_files = [
-    "test/helper.rb",
-    "test/test_insert.rb",
-    "test/test_region.rb",
-    "test/test_scaffolder.rb",
-    "test/test_sequence.rb",
-    "test/test_unresolved.rb"
-  ]
+  s.test_files = ["test/helper.rb", "test/test_insert.rb", "test/test_region.rb", "test/test_scaffolder.rb", "test/test_sequence.rb", "test/test_unresolved.rb"]
 
   if s.respond_to? :specification_version then
     current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION

data/test/test_sequence.rb

@@ -83,6 +83,12 @@ class TestSequence < Test::Unit::TestCase
         assert_equal(@sequence.sequence,'ATGCGGTAGTAACTGACTAGCATG')
       end
 
+      should "update the sequence with a simple insert with repeated method calls" do
+        @sequence.inserts [@insert]
+        assert_equal(@sequence.sequence,'ATGCGGTAGTAACTGACTAGCATG')
+        assert_equal(@sequence.sequence,'ATGCGGTAGTAACTGACTAGCATG')
+      end
+
       should "update the sequence stop position after adding a simple insert" do
         @sequence.inserts [@insert]
         assert_equal(@sequence.stop,24)

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: scaffolder
 version: !ruby/object:Gem::Version 
-  hash: 13
+  hash: 11
   prerelease: false
   segments: 
   - 0
   - 4
-  - 1
-  version: 0.4.1
+  - 2
+  version: 0.4.2
 platform: ruby
 authors: 
 - Michael Barton
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-01-04 00:00:00 -05:00
+date: 2011-06-03 00:00:00 -04:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency