bioinform 0.3.0 → 0.3.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA1:
-  metadata.gz: 64c5e6fe652d85bd538d08020e5d06779e676fa7
-  data.tar.gz: 954a02afb784d086d006e59e97f57400a10f7858
+SHA256:
+  metadata.gz: 815bb48e1022dbcf03e50fd8fe9ea2aebde5af49982a6dd724dd8076b6f8feb2
+  data.tar.gz: 2763d993767d26629452e4b1249005ac9a1fd2a2e7ea2144bad6fb64c1f4db01
 SHA512:
-  metadata.gz: f3e549ad3b7b20a45ba37dc90c25660af7f1a455cf358aced90991570b76070da5688872141a32e54590a6cd0e65622fe2010b9b27b34466886b15f5a6b7856e
-  data.tar.gz: 81e3dba3f91e3f4acc6838efe5e197da2712f070a4962e3d29bd0df81a0834eb513542ecfcbaca62802cd32fdaa90e883c356d1a008abde9715e5183e52501ee
+  metadata.gz: f2c27432312380b2595e42560e9edcf37d78790a06f8f4ebd4524e464fc2a2a50856b1c81935d921b8e240d1c914d737acb3baabdbf24f37cb84c77e991c2084
+  data.tar.gz: c6d1a75d09883d8cef6c1cec3a1aa2df635b02bcc86b7dea3d633e32f69649e3a0a324e0edde779c0dd30e541a4ea7017d74b30e16491e0b0d1c437c77adfd7f

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    bioinform (0.3.0)
+    bioinform (0.3.2)
 
 GEM
   remote: https://rubygems.org/
@@ -81,4 +81,4 @@ DEPENDENCIES
   wdm
 
 BUNDLED WITH
-   1.11.2
+   2.2.33

data/lib/bioinform/data_models/named_model.rb

@@ -16,8 +16,8 @@ module Bioinform
 
       private :motif_klasses, :motif?
 
-      def method_missing(meth, *args, &block)
-        result = model.public_send(meth, *args, &block)
+      def method_missing(meth, *args, **kwargs, &block)
+        result = model.public_send(meth, *args, **kwargs, &block)
         if motif?(result) && ! result.is_a?(self.class)
           self.class.new(result, name)
         else

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 = "0.3.2"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bioinform
 version: !ruby/object:Gem::Version
-  version: 0.3.0
+  version: 0.3.2
 platform: ruby
 authors:
 - Ilya Vorontsov
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2016-04-19 00:00:00.000000000 Z
+date: 2026-01-02 00:00:00.000000000 Z
 dependencies: []
 description: A bunch of useful classes for bioinformatics
 email:
@@ -106,7 +106,7 @@ files:
 homepage: ''
 licenses: []
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -121,9 +121,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.5.1
-signing_key: 
+rubygems_version: 3.2.33
+signing_key:
 specification_version: 4
 summary: Classes for work with different input formats of positional matrices and
   IUPAC-words and making simple transform and statistics with them. Also module includes