Class: GeneValidator::DuplicationValidationOutput
- Inherits:
-
ValidationReport
- Object
- ValidationReport
- GeneValidator::DuplicationValidationOutput
- Defined in:
- lib/genevalidator/validation_duplication.rb
Overview
Class that stores the validation output information
Instance Attribute Summary collapse
-
#average ⇒ Object
readonly
Returns the value of attribute average.
-
#pvalue ⇒ Object
readonly
Returns the value of attribute pvalue.
-
#result ⇒ Object
readonly
Returns the value of attribute result.
-
#threshold ⇒ Object
readonly
Returns the value of attribute threshold.
Attributes inherited from ValidationReport
#approach, #conclusion, #description, #errors, #expected, #explanation, #header, #message, #plot_files, #run_time, #short_header, #validation_result
Instance Method Summary collapse
- #color ⇒ Object
- #conclude ⇒ Object
- #explain ⇒ Object
-
#initialize(short_header, header, description, pvalue, averages, threshold = 0.05, expected = :yes) ⇒ DuplicationValidationOutput
constructor
A new instance of DuplicationValidationOutput.
- #print ⇒ Object
- #validation ⇒ Object
Constructor Details
#initialize(short_header, header, description, pvalue, averages, threshold = 0.05, expected = :yes) ⇒ DuplicationValidationOutput
Returns a new instance of DuplicationValidationOutput.
20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 |
# File 'lib/genevalidator/validation_duplication.rb', line 20 def initialize(short_header, header, description, pvalue, averages, threshold = 0.05, expected = :yes) @short_header = short_header @header = header @description = description @pvalue = pvalue @threshold = threshold @result = validation @expected = expected @average = averages.mean @approach = 'We expect each BLAST hit to match each region of the' \ ' query at most once. Here, we calculate the' \ ' distribution of hit coverage against the query' \ ' sequence and use the Wilcoxon test to determine if it' \ ' is higher than 1.' @explanation = explain @conclusion = conclude end |
Instance Attribute Details
#average ⇒ Object (readonly)
Returns the value of attribute average.
16 17 18 |
# File 'lib/genevalidator/validation_duplication.rb', line 16 def average @average end |
#pvalue ⇒ Object (readonly)
Returns the value of attribute pvalue.
15 16 17 |
# File 'lib/genevalidator/validation_duplication.rb', line 15 def pvalue @pvalue end |
#result ⇒ Object (readonly)
Returns the value of attribute result.
18 19 20 |
# File 'lib/genevalidator/validation_duplication.rb', line 18 def result @result end |
#threshold ⇒ Object (readonly)
Returns the value of attribute threshold.
17 18 19 |
# File 'lib/genevalidator/validation_duplication.rb', line 17 def threshold @threshold end |
Instance Method Details
#color ⇒ Object
62 63 64 |
# File 'lib/genevalidator/validation_duplication.rb', line 62 def color validation == :yes ? 'success' : 'danger' end |
#conclude ⇒ Object
44 45 46 47 48 49 50 51 52 |
# File 'lib/genevalidator/validation_duplication.rb', line 44 def conclude if @result == :yes 'This suggests that the query sequence contains no erroneous' \ ' duplications.' else 'The null hypothesis is rejected - thus a region of the query' \ ' sequence is likely repeated more than once.' end end |
#explain ⇒ Object
39 40 41 42 |
# File 'lib/genevalidator/validation_duplication.rb', line 39 def explain "The Wilcoxon test produced a p-value of #{prettify_evalue(@pvalue)}" \ "#{@result == :no ? " (average = #{@average.round(2)})." : '.'}" end |
#print ⇒ Object
54 55 56 |
# File 'lib/genevalidator/validation_duplication.rb', line 54 def print @pvalue.round(2).to_s end |
#validation ⇒ Object
58 59 60 |
# File 'lib/genevalidator/validation_duplication.rb', line 58 def validation @pvalue > @threshold ? :yes : :no end |