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lib/rubabel/molecule/fragmentable/asms_2002_scheme1.rb

Summary

Maintainability
F
5 days
Test Coverage

File asms_2002_scheme1.rb has 490 lines of code (exceeds 250 allowed). Consider refactoring.
Open

require_relative "../fragmentable"

module Rubabel
  class Molecule
    module Fragmentable
Severity: Minor
Found in lib/rubabel/molecule/fragmentable/asms_2002_scheme1.rb - About 7 hrs to fix

    Method jasms_2002_scheme1_b_d1_water_loss has 35 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

          ::Rearrangements << def jasms_2002_scheme1_b_d1_water_loss(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |lo, lc, lh|
          #duplications and mapping
          nmol = self.dup
    Severity: Minor
    Found in lib/rubabel/molecule/fragmentable/asms_2002_scheme1.rb - About 1 hr to fix

      Method jasms_2002_scheme1_c_e2aprime_formaldehyde_loss has 34 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

            ::Rule_names << def jasms_2002_scheme1_c_e2aprime_formaldehyde_loss(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |*arr|
          #duplications and mapping
          (nmol,(carbon1, carbon2, oxygen, carbon3)) = self.dup_molecule(arr)
      Severity: Minor
      Found in lib/rubabel/molecule/fragmentable/asms_2002_scheme1.rb - About 1 hr to fix

        Method jasms_2002_scheme1_c_e1aprime has 34 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

              ::Rule_names << def jasms_2002_scheme1_c_e1aprime(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |co, c1, c3, lo, n|
          #duplications and mapping
          nmol = self.dup
        Severity: Minor
        Found in lib/rubabel/molecule/fragmentable/asms_2002_scheme1.rb - About 1 hr to fix

          Method jasms_2002_scheme1_c_e1b_to_d1bprime has 32 lines of code (exceeds 25 allowed). Consider refactoring.
          Open

                ::Rule_names << def jasms_2002_scheme1_c_e1b_to_d1bprime(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |co, c, n|
          #duplications and mapping
          nmol = self.dup
          Severity: Minor
          Found in lib/rubabel/molecule/fragmentable/asms_2002_scheme1.rb - About 1 hr to fix

            Method jasms_2002_scheme1_c_e1bprime has 32 lines of code (exceeds 25 allowed). Consider refactoring.
            Open

                  ::Rule_names << def jasms_2002_scheme1_c_e1bprime(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |n, c2, lo|
          #duplications and mapping
          nmol = self.dup
            Severity: Minor
            Found in lib/rubabel/molecule/fragmentable/asms_2002_scheme1.rb - About 1 hr to fix

              Method jasms_2002_scheme1_c_e1 has 32 lines of code (exceeds 25 allowed). Consider refactoring.
              Open

                    ::Rule_names << def jasms_2002_scheme1_c_e1(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |n, cc, o, tbvc|
          #duplications and mapping
          nmol = self.dup
              Severity: Minor
              Found in lib/rubabel/molecule/fragmentable/asms_2002_scheme1.rb - About 1 hr to fix

                Method jasms_2002_scheme1_c_e1_aprimeprime_formaldehyde_loss has 31 lines of code (exceeds 25 allowed). Consider refactoring.
                Open

                      ::Rearrangements << def jasms_2002_scheme1_c_e1_aprimeprime_formaldehyde_loss(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |*arr|
          #duplications and mapping
          (nmol,(cyclized_oxygen, freed_carbon, carbon_linked_to_nitrogen, carbon_linker, nitrogen)) = self.dup_molecule(arr)
                Severity: Minor
                Found in lib/rubabel/molecule/fragmentable/asms_2002_scheme1.rb - About 1 hr to fix

                  Method jasms_2002_scheme1_b_d1_formaldehyde_loss has 31 lines of code (exceeds 25 allowed). Consider refactoring.
                  Open

                        ::Rearrangements << def jasms_2002_scheme1_b_d1_formaldehyde_loss(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |tco, leavingc, leftc|
          #duplications and mapping
          nmol = self.dup
                  Severity: Minor
                  Found in lib/rubabel/molecule/fragmentable/asms_2002_scheme1.rb - About 1 hr to fix

                    Method jasms_2002_scheme1_b_d1 has 31 lines of code (exceeds 25 allowed). Consider refactoring.
                    Open

                          ::Rule_names << def jasms_2002_scheme1_b_d1(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |n, tcc, o|
          #duplications and mapping
          nmol = self.dup
                    Severity: Minor
                    Found in lib/rubabel/molecule/fragmentable/asms_2002_scheme1.rb - About 1 hr to fix

                      Method jasms_2002_scheme1_a_c1 has 31 lines of code (exceeds 25 allowed). Consider refactoring.
                      Open

                            ::Rule_names << def jasms_2002_scheme1_a_c1(only_uniqs: true, fragment_adduct_state: :as_published)
        # Create a fragmentation block method
        fragment_sets = []
        fragment = lambda do |tbcc, o, lc|
          # Duplication and mapping identity to new atoms
                      Severity: Minor
                      Found in lib/rubabel/molecule/fragmentable/asms_2002_scheme1.rb - About 1 hr to fix

                        Method jasms_2002_scheme1_c_e2bprime has 29 lines of code (exceeds 25 allowed). Consider refactoring.
                        Open

                              ::Rule_names << def jasms_2002_scheme1_c_e2bprime(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |*arr|
          #duplications and mapping
          (nmol,(nitrogen, carbon, leaving_oxygen)) = self.dup_molecule(arr)
                        Severity: Minor
                        Found in lib/rubabel/molecule/fragmentable/asms_2002_scheme1.rb - About 1 hr to fix

                          Method jasms_2002_scheme1_c_e1_abprimeprime_water_loss has 29 lines of code (exceeds 25 allowed). Consider refactoring.
                          Open

                                ::Rearrangements << def jasms_2002_scheme1_c_e1_abprimeprime_water_loss(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |*arr|
          #duplications and mapping
          (nmol,(carbon_linker, alcohol_carbon, oxygen, nitrogen)) = self.dup_molecule(arr)
                          Severity: Minor
                          Found in lib/rubabel/molecule/fragmentable/asms_2002_scheme1.rb - About 1 hr to fix

                            Method jasms_2002_scheme1_c_e2aprime has 29 lines of code (exceeds 25 allowed). Consider refactoring.
                            Open

                                  ::Rule_names << def jasms_2002_scheme1_c_e2aprime(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |*arr|
          #duplications and mapping
          (nmol,(nitrogen, branch_carbon, leaving_oxygen, cyclized_oxygen)) = self.dup_molecule(arr)
                            Severity: Minor
                            Found in lib/rubabel/molecule/fragmentable/asms_2002_scheme1.rb - About 1 hr to fix

                              Method jasms_2002_scheme1_c_e2bprime_water_loss has 29 lines of code (exceeds 25 allowed). Consider refactoring.
                              Open

                                    ::Rule_names << def jasms_2002_scheme1_c_e2bprime_water_loss(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |*arr|
          #duplications and mapping
          (nmol,(ring_carbon2, alcohol_carbon, oxygen, nitrogen)) = self.dup_molecule(arr)
                              Severity: Minor
                              Found in lib/rubabel/molecule/fragmentable/asms_2002_scheme1.rb - About 1 hr to fix

                                Method jasms_2002_scheme1_c_e2aprime_formaldehyde_loss has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
                                Open

                                      ::Rule_names << def jasms_2002_scheme1_c_e2aprime_formaldehyde_loss(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |*arr|
          #duplications and mapping
          (nmol,(carbon1, carbon2, oxygen, carbon3)) = self.dup_molecule(arr)
                                Severity: Minor
                                Found in lib/rubabel/molecule/fragmentable/asms_2002_scheme1.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 3 locations. Consider refactoring.
                                Open

                                      ::Rearrangements << def jasms_2002_scheme1_c_e1_aprimeprime_formaldehyde_loss(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |*arr|
          #duplications and mapping
          (nmol,(cyclized_oxygen, freed_carbon, carbon_linked_to_nitrogen, carbon_linker, nitrogen)) = self.dup_molecule(arr)
                                Severity: Major
                                Found in lib/rubabel/molecule/fragmentable/asms_2002_scheme1.rb and 2 other locations - About 3 hrs to fix
                                lib/rubabel/molecule/fragmentable/asms_2002_scheme2.rb on lines 190..224
                                lib/rubabel/molecule/fragmentable/asms_2002_scheme3-5.rb on lines 435..469

                                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 136.

                                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

                                      ::Rule_names << def jasms_2002_scheme1_c_e1bprime(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |n, c2, lo|
          #duplications and mapping
          nmol = self.dup
                                Severity: Major
                                Found in lib/rubabel/molecule/fragmentable/asms_2002_scheme1.rb and 1 other location - About 3 hrs to fix
                                lib/rubabel/molecule/fragmentable/asms_2002_scheme1.rb on lines 303..340

                                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 128.

                                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

                                      ::Rule_names << def jasms_2002_scheme1_c_e1b_to_d1bprime(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |co, c, n|
          #duplications and mapping
          nmol = self.dup
                                Severity: Major
                                Found in lib/rubabel/molecule/fragmentable/asms_2002_scheme1.rb and 1 other location - About 3 hrs to fix
                                lib/rubabel/molecule/fragmentable/asms_2002_scheme1.rb on lines 262..299

                                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 128.

                                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 3 locations. Consider refactoring.
                                Open

                                      ::Rule_names << def jasms_2002_scheme1_c_e2bprime_water_loss(only_uniqs: true, fragment_adduct_state: :as_published)
        fragment_sets = []
        fragment = lambda do |*arr|
          #duplications and mapping
          (nmol,(ring_carbon2, alcohol_carbon, oxygen, nitrogen)) = self.dup_molecule(arr)
                                Severity: Major
                                Found in lib/rubabel/molecule/fragmentable/asms_2002_scheme1.rb and 2 other locations - About 3 hrs to fix
                                lib/rubabel/molecule/fragmentable/asms_2002_scheme2.rb on lines 338..370
                                lib/rubabel/molecule/fragmentable/asms_2002_scheme2.rb on lines 374..406

                                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 125.

                                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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