bioinform 0.1.14 → 0.1.15

checksums.yaml

@@ -1,7 +1,7 @@
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data/LICENSE

@@ -1,4 +1,5 @@
-Copyright (c) 2012 Ilya Vorontsov
+Copyright (c) 2012-2014 Ilya Vorontsov
+bioinform utilizes several methods from the `activesupport` gem.
 
 MIT License
 
@@ -19,4 +20,4 @@ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
 NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
 LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
 OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/lib/bioinform/data_models/pcm.rb

@@ -20,5 +20,15 @@ module Bioinform
     def to_ppm
       ConversionAlgorithms::PCM2PPMConverter.convert(self)
     end
+
+    def self.valid_matrix?(matrix, options = {})
+      super && matrix.all?{|pos| pos.all?{|el| el >=0 } }
+    end
+
+    def validation_errors(options = {})
+      validation_errors = []
+      validation_errors << "PCM matrix should contain only non-negative elements"  unless matrix.all?{|pos| pos.all?{|el| el >=0 } }
+      super + validation_errors
+    end
   end
 end

data/lib/bioinform/data_models/pm.rb

@@ -43,16 +43,20 @@ module Bioinform
       self.name = result.name
 #      self.tags = result.tags || []
       self.background = result.background || [1, 1, 1, 1]
-      raise 'matrix not valid'  unless valid?
     end
 
+    def self.new_with_validation(input, parser = nil)
+      obj = self.new(input, parser)
+      raise 'matrix not valid'  unless obj.valid?
+      obj
+    end
     def ==(other)
       @matrix == other.matrix && background == other.background && name == other.name
     rescue
       false
     end
 
-    def self.valid_matrix?(matrix)
+    def self.valid_matrix?(matrix, options = {})
       matrix.is_a?(Array) &&
       ! matrix.empty? &&
       matrix.all?{|pos| pos.is_a?(Array)} &&
@@ -62,8 +66,24 @@ module Bioinform
       false
     end
 
-    def valid?
-      self.class.valid_matrix?(@matrix)
+    def validation_errors(options = {})
+      errors = []
+      if !matrix.is_a?(Array)
+        errors << 'Matrix is not an array'
+      elsif matrix.empty?
+        errors << 'Matrix is not an array'
+      elsif ! matrix.all?{|pos| pos.is_a?(Array)}
+        errors << 'Some of matrix positions aren\'t represented as arrays'
+      elsif ! matrix.all?{|pos| pos.size == 4}
+        errors << 'Some of matrix positions have number of columns other than 4'
+      elsif ! matrix.all?{|pos| pos.all?{|el| el.is_a?(Numeric)}}
+        errors << 'Some of matrix elements aren\'t represented by numbers'
+      end
+      errors
+    end
+
+    def valid?(options = {})
+      self.class.valid_matrix?(@matrix, options)
     end
 
     def each_position

data/lib/bioinform/data_models/ppm.rb

@@ -6,5 +6,16 @@ module Bioinform
     def to_ppm
       self
     end
+    def self.valid_matrix?(matrix, options = {})
+      precision = options[:precision] || 0.01
+      super && matrix.all?{|pos| ((pos.inject(0, &:+) - 1.0).abs <= precision)  && pos.all?{|el| el >=0 } }
+    end
+    def validation_errors(options = {})
+      precision = options[:precision] || 0.01
+      validation_errors = []
+      validation_errors << "PPM matrix should contain only non-negative elements"  unless matrix.all?{|pos| pos.all?{|el| el >=0 } }
+      validation_errors << "Sum of PPM matrix elements for each position should equal to 1"  unless matrix.all?{|pos| ((pos.inject(0, &:+) - 1.0).abs <= precision) }
+      super + validation_errors
+    end
   end
 end

data/lib/bioinform/version.rb

@@ -1,3 +1,3 @@
 module Bioinform
-  VERSION = "0.1.14"
+  VERSION = "0.1.15"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bioinform
 version: !ruby/object:Gem::Version
-  version: 0.1.14
+  version: 0.1.15
 platform: ruby
 authors:
 - Ilya Vorontsov
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-12-16 00:00:00.000000000 Z
+date: 2014-02-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: docopt
@@ -180,7 +180,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.1.11
+rubygems_version: 2.2.1
 signing_key: 
 specification_version: 4
 summary: Classes for work with different input formats of positional matrices and