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wurmlab/GeneValidator

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lib/genevalidator/validation_alignment.rb

Summary

Maintainability
D
2 days
Test Coverage
A
94%

Method run has a Cognitive Complexity of 25 (exceeds 5 allowed). Consider refactoring.
Open

    def run
      n = opt[:min_blast_hits] < 10 ? 10 : opt[:min_blast_hits]
      n = 50 if n > 50

      raise NotEnoughHitsError if hits.length < n
Severity: Minor
Found in lib/genevalidator/validation_alignment.rb - About 3 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

File validation_alignment.rb has 281 lines of code (exceeds 250 allowed). Consider refactoring.
Open

require 'bio'
require 'forwardable'

require 'genevalidator/exceptions'
require 'genevalidator/get_raw_sequences'
Severity: Minor
Found in lib/genevalidator/validation_alignment.rb - About 2 hrs to fix

    Method run has 63 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

        def run
      n = opt[:min_blast_hits] < 10 ? 10 : opt[:min_blast_hits]
      n = 50 if n > 50

      raise NotEnoughHitsError if hits.length < n
    Severity: Major
    Found in lib/genevalidator/validation_alignment.rb - About 2 hrs to fix

      Method multiple_align_mafft has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
      Open

          def multiple_align_mafft(prediction, hits)
      raise unless prediction.is_a?(Query) && hits[0].is_a?(Query)

      opt = ['--maxiterate', '1000', '--localpair', '--anysymbol', '--quiet',
             '--thread', @num_threads.to_s]
      Severity: Minor
      Found in lib/genevalidator/validation_alignment.rb - About 1 hr to fix

      Cognitive Complexity

      Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

      A method's cognitive complexity is based on a few simple rules:

      • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
      • Code is considered more complex for each "break in the linear flow of the code"
      • Code is considered more complex when "flow breaking structures are nested"

      Further reading

      Method plot_alignment has 29 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

          def plot_alignment(freq, ma = @multiple_alignment)
      # get indeces of consensus in the multiple alignment
      consensus = get_consensus(ma[0..ma.length - 2])
      consensus_idxs = consensus.split(//).each_index.select { |j| isalpha(consensus[j]) }
      consensus_ranges = array_to_ranges(consensus_idxs)
      Severity: Minor
      Found in lib/genevalidator/validation_alignment.rb - About 1 hr to fix

        Method get_sm_pssm has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
        Open

            def get_sm_pssm(ma, threshold = 0.7)
      sm = ''
      freq = []
      (0..ma[0].length - 1).each do |i|
        freqs = Hash.new(0)
        Severity: Minor
        Found in lib/genevalidator/validation_alignment.rb - About 1 hr to fix

        Cognitive Complexity

        Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

        A method's cognitive complexity is based on a few simple rules:

        • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
        • Code is considered more complex for each "break in the linear flow of the code"
        • Code is considered more complex when "flow breaking structures are nested"

        Further reading

        Method conclude has 26 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

            def conclude
      if @result == :yes
        'There is no evidence based on the top 10 BLAST hits to suggest any' \
        ' problems with the query sequence.'
      else
        Severity: Minor
        Found in lib/genevalidator/validation_alignment.rb - About 1 hr to fix

          Method initialize has 8 arguments (exceeds 4 allowed). Consider refactoring.
          Open

              def initialize(short_header, header, description, gaps = 0, extra_seq = 0,
                   consensus = 1, threshold = 20, expected = :yes)
          Severity: Major
          Found in lib/genevalidator/validation_alignment.rb - About 1 hr to fix

            Method conclude has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
            Open

                def conclude
      if @result == :yes
        'There is no evidence based on the top 10 BLAST hits to suggest any' \
        ' problems with the query sequence.'
      else
            Severity: Minor
            Found in lib/genevalidator/validation_alignment.rb - About 45 mins to fix

            Cognitive Complexity

            Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

            A method's cognitive complexity is based on a few simple rules:

            • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
            • Code is considered more complex for each "break in the linear flow of the code"
            • Code is considered more complex when "flow breaking structures are nested"

            Further reading

            Method remove_isolated_residues has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
            Open

                def remove_isolated_residues(seq, len = 2)
      gap_starts = seq.to_enum(:scan, /(-\w{1,#{len}}-)/i).map { |_m| $`.size + 1 }
      # remove isolated residues
      gap_starts.each do |i|
        (i..i + len - 1).each { |j| seq[j] = '-' if isalpha(seq[j]) }
            Severity: Minor
            Found in lib/genevalidator/validation_alignment.rb - About 25 mins to fix

            Cognitive Complexity

            Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

            A method's cognitive complexity is based on a few simple rules:

            • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
            • Code is considered more complex for each "break in the linear flow of the code"
            • Code is considered more complex when "flow breaking structures are nested"

            Further reading

            Similar blocks of code found in 2 locations. Consider refactoring.
            Open

                def extra_sequence_validation(prediction_raw, sm)
      return 1 if prediction_raw.length != sm.length
      # find residues that are in the prediction
      # but not in the statistical model
      no_insertions = 0
            Severity: Minor
            Found in lib/genevalidator/validation_alignment.rb and 1 other location - About 50 mins to fix
            lib/genevalidator/validation_alignment.rb on lines 270..278

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 43.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 2 locations. Consider refactoring.
            Open

                def gap_validation(prediction_raw, sm)
      return 1 if prediction_raw.length != sm.length
      # find gaps in the prediction and
      # not in the statistical model
      no_gaps = 0
            Severity: Minor
            Found in lib/genevalidator/validation_alignment.rb and 1 other location - About 50 mins to fix
            lib/genevalidator/validation_alignment.rb on lines 289..297

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 43.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

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