bioinform 0.3.0 → 0.3.1

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 954a02afb784d086d006e59e97f57400a10f7858
+  metadata.gz: 14f2fb7993dff9e7a405856ff0e44989e1fd4d1a
+  data.tar.gz: 268ceea6bb9741c463e30923c4a26b8a9a8092a3
 SHA512:
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-  data.tar.gz: 81e3dba3f91e3f4acc6838efe5e197da2712f070a4962e3d29bd0df81a0834eb513542ecfcbaca62802cd32fdaa90e883c356d1a008abde9715e5183e52501ee
+  metadata.gz: aa01a07bcf91915f1e562bd7a16a2d74f74334215ee9cdf7e9cbb0516fcf589e8c28731de319f5c8fb1b412e39a111aabc6b689a791257d35fe008ea1e54b777
+  data.tar.gz: 63c27498b5b1c8ca1954c2b950cf202480516e5b5aa534ca1c02f00e4e7e310d16db4ac4d2934e462c071b29be939b40a292fbd97ad7b57321d44933f7f87523

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    bioinform (0.3.0)
+    bioinform (0.3.1)
 
 GEM
   remote: https://rubygems.org/

data/lib/bioinform/data_models/pcm.rb

@@ -29,7 +29,12 @@ module Bioinform
       VALIDATOR = PM::VALIDATOR * PCM.count_validator(eps: 1.0e-4).make_strict
       DIFFERENT_COUNTS_VALIDATOR = PM::VALIDATOR * PCM.count_validator(eps: nil).make_strict
 
-      def initialize(matrix, alphabet: NucleotideAlphabet, validator: PCM::VALIDATOR)
+
+      def self.default_validator
+        PCM::VALIDATOR
+      end
+
+      def initialize(matrix, alphabet: NucleotideAlphabet, validator: default_validator)
         super
         # validator already checked count discrepancy. We store median count.
         @count = matrix.map{|pos| pos.inject(0.0, &:+) }.sort[matrix.length / 2]

data/lib/bioinform/data_models/pm.rb

@@ -20,7 +20,7 @@ module Bioinform
       }
 
       attr_reader :matrix, :alphabet
-      def initialize(matrix, alphabet: NucleotideAlphabet, validator: PM::VALIDATOR)
+      def initialize(matrix, alphabet: NucleotideAlphabet, validator: default_validator)
         validation_results = validator.validate_params(matrix, alphabet)
         unless validation_results.valid?
           raise ValidationError.new('Invalid matrix.', validation_errors: validation_results)
@@ -29,15 +29,23 @@ module Bioinform
         @alphabet = alphabet
       end
 
-      def self.from_string(input, alphabet: NucleotideAlphabet, parser: DEFAULT_PARSER)
+      def self.default_validator
+        PM::VALIDATOR
+      end
+
+      def default_validator
+        self.class.default_validator
+      end
+
+      def self.from_string(input, alphabet: NucleotideAlphabet, parser: DEFAULT_PARSER, validator: default_validator)
         info = parser.parse!(input)
-        self.new(info[:matrix], alphabet: alphabet).named( info[:name] )
+        self.new(info[:matrix], alphabet: alphabet, validator: validator).named( info[:name] )
       end
 
-      def self.from_file(filename, alphabet: NucleotideAlphabet, parser: DEFAULT_PARSER)
+      def self.from_file(filename, alphabet: NucleotideAlphabet, parser: DEFAULT_PARSER, validator: default_validator)
         info = parser.parse!(File.read(filename))
         name = (info[:name] && !info[:name].strip.empty?) ? info[:name] : File.basename(filename, File.extname(filename))
-        self.new(info[:matrix], alphabet: alphabet).named( name )
+        self.new(info[:matrix], alphabet: alphabet, validator: validator).named( name )
       end
 
       def length

data/lib/bioinform/data_models/ppm.rb

@@ -7,6 +7,10 @@ module Bioinform
     end
 
     class PPM < PM
+      def self.default_validator
+        PPM::VALIDATOR
+      end
+
       def self.probability_validator(eps: 1.0e-4)
         Validator.new{|matrix, alphabet|
           errors = []
@@ -26,10 +30,6 @@ module Bioinform
       end
 
       VALIDATOR = PM::VALIDATOR * PPM.probability_validator(eps: 1.0e-4).make_strict
-
-      def initialize(matrix, alphabet: NucleotideAlphabet, validator: PPM::VALIDATOR)
-        super  # default validator redefined
-      end
     end
   end
 end

data/lib/bioinform/data_models/pwm.rb

@@ -8,8 +8,9 @@ module Bioinform
 
     class PWM < PM
       VALIDATOR = PM::VALIDATOR
-      def initialize(matrix, alphabet: NucleotideAlphabet, validator: PWM::VALIDATOR)
-        super  # default validator redefined
+
+      def self.default_validator
+        PWM::VALIDATOR
       end
 
       def score(word)

data/lib/bioinform/version.rb

@@ -1,3 +1,3 @@
 module Bioinform
-  VERSION = "0.3.0"
+  VERSION = "0.3.1"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bioinform
 version: !ruby/object:Gem::Version
-  version: 0.3.0
+  version: 0.3.1
 platform: ruby
 authors:
 - Ilya Vorontsov
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-04-19 00:00:00.000000000 Z
+date: 2016-04-22 00:00:00.000000000 Z
 dependencies: []
 description: A bunch of useful classes for bioinformatics
 email: