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

        fragment = lambda do |leaving_oxygen, attacked_carbon, anionic_oxygen|
          # Duplication and mapping identity to new atoms
          nmol = self.dup
          leaving_group_oxygen = nmol.atom(leaving_oxygen.id)
          product_carbon_to_link = nmol.atom(attacked_carbon.id)
Severity: Minor
Found in lib/rubabel/molecule/fragmentable/fragmentable_rule_example.rb and 1 other location - About 45 mins to fix
lib/rubabel/molecule/fragmentable/paoc_rule.rb on lines 12..26

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 39.

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

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

        fragment = lambda do |leaving_oxygen, attacked_carbon, anionic_oxygen|
          # Duplication and mapping identity to new atoms
          nmol = self.dup
          leaving_group_oxygen = nmol.atom(leaving_oxygen.id)
          product_carbon_to_link = nmol.atom(attacked_carbon.id)
Severity: Minor
Found in lib/rubabel/molecule/fragmentable/paoc_rule.rb and 1 other location - About 45 mins to fix
lib/rubabel/molecule/fragmentable/fragmentable_rule_example.rb on lines 15..29

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 39.

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

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

        fragment = lambda do |electrophile, center, center_nbr|
          (nmol, (nele, ncarb, ncarb_nbr)) = self.dup_molecule([electrophile, center, center_nbr])
          nmol.delete_bond(nele, ncarb)
          ncarb_nbr.get_bond(ncarb) + 1
          nmol.split
Severity: Minor
Found in lib/rubabel/molecule/fragmentable/tamil_rules.rb and 1 other location - About 25 mins to fix
lib/rubabel/molecule/fragmentable/tamil_rules.rb on lines 12..16

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 31.

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

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

  matches = q_lists.map.with_index do |list, i|
    scores = list.map do |peak|
      # finds closest match in the GS spectrum
      closest_match = gold_standard_spectrum[gold_standard_spectrum.find_nearest_index(peak.first)]
Severity: Minor
Found in generate_comparison_scores.rb and 1 other location - About 25 mins to fix
andromeda.rb on lines 54..60

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 31.

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

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

    matches = q_lists.map.with_index do |list, i|
      scores = list.map do |peak|
        closest_match = gold_standard_spectrum[gold_standard_spectrum.find_nearest_index(peak.first)]
        
        #putsv "Potential problem with #{closest_match}: bigger peak nearby" if larger_peaks_nearby(gold_standard_spectrum, closest_match)
Severity: Minor
Found in andromeda.rb and 1 other location - About 25 mins to fix
generate_comparison_scores.rb on lines 132..139

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 31.

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

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

        fragment = lambda do |electrophile, center, center_nbr|
          (nmol, (nele, ncarb, ncarb_nbr)) = self.dup_molecule([electrophile, center, center_nbr])
          nmol.delete_bond(nele, ncarb)
          ncarb_nbr.get_bond(ncarb) + 1
          nmol.split
Severity: Minor
Found in lib/rubabel/molecule/fragmentable/tamil_rules.rb and 1 other location - About 25 mins to fix
lib/rubabel/molecule/fragmentable/tamil_rules.rb on lines 29..33

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 31.

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

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

        fragment = lambda do |carbon, oxygen|
          nmol = self.dup
          ncarbon = nmol.atom(carbon.id)
          noxygen = nmol.atom(oxygen.id)
          nmol.delete_bond(ncarbon, noxygen)
Severity: Minor
Found in lib/rubabel/molecule/fragmentable/tamil_rules.rb and 1 other location - About 20 mins to fix
lib/rubabel/molecule/fragmentable/tamil_rules.rb on lines 44..51

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 28.

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

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

        fragment = lambda do |carbon, oxygen|
          nmol = self.dup
          ncarbon = nmol.atom(carbon.id)
          noxygen = nmol.atom(oxygen.id)
          nmol.delete_bond(ncarbon, noxygen)
Severity: Minor
Found in lib/rubabel/molecule/fragmentable/tamil_rules.rb and 1 other location - About 20 mins to fix
lib/rubabel/molecule/fragmentable/tamil_rules.rb on lines 61..68

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 28.

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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