Class: Bioinform::MotifModel::PCM

Inherits:
PM
  • Object
show all
Defined in:
lib/bioinform/data_models/pcm.rb

Instance Attribute Summary

Attributes inherited from PM

#alphabet, #matrix

Instance Method Summary collapse

Methods inherited from PM

#==, #complemented, #each_position, from_file, from_string, #initialize, #length, #named, #reverse_complemented, #reversed, #to_s

Constructor Details

This class inherits a constructor from Bioinform::MotifModel::PM

Instance Method Details

#count ⇒ Object

Raises:



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# File 'lib/bioinform/data_models/pcm.rb', line 16

def count
  counts = each_position.map{|pos| pos.inject(0.0, &:+)}
  count = counts.first
  diffs = counts.map{|pos_count| (pos_count - count).abs }
  counts_are_same = (diffs.max < count * 1e-3)
  raise Error, 'Different columns have different count'  unless counts_are_same
  count
end

#validation_errors ⇒ Object 



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# File 'lib/bioinform/data_models/pcm.rb', line 10

def validation_errors
  errors = super
  errors << "elements of PCM should be non-negative"  unless matrix.all?{|pos| pos.all?{|el| el >= 0 } }
  errors
end