Class: GeneValidator::ValidationTest
- Inherits:
-
Object
- Object
- GeneValidator::ValidationTest
- Extended by:
- Forwardable
- Defined in:
- lib/genevalidator/validation_test.rb
Overview
This is an abstract class extended by all validation classes
Direct Known Subclasses
AlignmentValidation, BlastReadingFrameValidation, DuplicationValidation, GeneMergeValidation, LengthClusterValidation, LengthRankValidation, OpenReadingFrameValidation
Instance Attribute Summary collapse
-
#cli_name ⇒ Object
Returns the value of attribute cli_name.
-
#description ⇒ Object
Returns the value of attribute description.
-
#header ⇒ Object
Returns the value of attribute header.
-
#hits ⇒ Object
Returns the value of attribute hits.
-
#prediction ⇒ Object
Returns the value of attribute prediction.
-
#run_time ⇒ Object
Returns the value of attribute run_time.
-
#short_header ⇒ Object
Returns the value of attribute short_header.
-
#type ⇒ Object
Returns the value of attribute type.
-
#validation_report ⇒ Object
Returns the value of attribute validation_report.
Instance Method Summary collapse
-
#initialize(prediction, hits = nil, *_argv) ⇒ ValidationTest
constructor
Initilizes the object Params:
type
: type of the predicted sequence (:nucleotide or :protein)prediction
: aSequence
object representing the blast queryhits
: a vector ofSequence
objects (representing blast hits)argv
: aditional arguments if needed. - #run ⇒ Object
Constructor Details
#initialize(prediction, hits = nil, *_argv) ⇒ ValidationTest
Initilizes the object Params: type
: type of the predicted sequence (:nucleotide or :protein) prediction
: a Sequence
object representing the blast query hits
: a vector of Sequence
objects (representing blast hits) argv
: aditional arguments if needed
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# File 'lib/genevalidator/validation_test.rb', line 26 def initialize(prediction, hits = nil, *_argv) @type = config[:type] @prediction = prediction @hits = hits @short_header = 'NewVal' @header = 'New Validation' @run_time = 0 @cli_name = 'all' @description = 'No description available.' @validation_report = ValidationReport.new('Not enough evidence') end |
Instance Attribute Details
#cli_name ⇒ Object
Returns the value of attribute cli_name.
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# File 'lib/genevalidator/validation_test.rb', line 14 def cli_name @cli_name end |
#description ⇒ Object
Returns the value of attribute description.
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# File 'lib/genevalidator/validation_test.rb', line 15 def description @description end |
#header ⇒ Object
Returns the value of attribute header.
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# File 'lib/genevalidator/validation_test.rb', line 13 def header @header end |
#hits ⇒ Object
Returns the value of attribute hits.
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# File 'lib/genevalidator/validation_test.rb', line 11 def hits @hits end |
#prediction ⇒ Object
Returns the value of attribute prediction.
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# File 'lib/genevalidator/validation_test.rb', line 10 def prediction @prediction end |
#run_time ⇒ Object
Returns the value of attribute run_time.
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# File 'lib/genevalidator/validation_test.rb', line 17 def run_time @run_time end |
#short_header ⇒ Object
Returns the value of attribute short_header.
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# File 'lib/genevalidator/validation_test.rb', line 12 def short_header @short_header end |
#type ⇒ Object
Returns the value of attribute type.
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# File 'lib/genevalidator/validation_test.rb', line 9 def type @type end |
#validation_report ⇒ Object
Returns the value of attribute validation_report.
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# File 'lib/genevalidator/validation_test.rb', line 16 def validation_report @validation_report end |
Instance Method Details
#run ⇒ Object
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# File 'lib/genevalidator/validation_test.rb', line 38 def run fail 'run method should be implemented by all classes that extend' \ ' ValidationTest' end |