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packages/miew/src/io/parsers/MMTFParser.js

Summary

Maintainability
D
2 days
Test Coverage

File MMTFParser.js has 395 lines of code (exceeds 250 allowed). Consider refactoring.
Open

import Parser from './Parser'
import chem from '../../chem'
import MMTF from '../../vendors/mmtf'
import StructuralElement from '../../chem/StructuralElement'
import { isArrayBuffer, isUndefined } from 'lodash'
Severity: Minor
Found in packages/miew/src/io/parsers/MMTFParser.js - About 5 hrs to fix

    Function _parseAssemblyInfo has a Cognitive Complexity of 32 (exceeds 5 allowed). Consider refactoring.
    Open

      _parseAssemblyInfo(mmtfData) {
    let i
    let j
    let k
    const assemblies = []
    Severity: Minor
    Found in packages/miew/src/io/parsers/MMTFParser.js - About 4 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

    Function _markHeteroAtoms has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.
    Open

      _markHeteroAtoms(mmtfData) {
    const chainsInModel0 = mmtfData.chainsPerModel[0]
    for (let i = 0; i < mmtfData.entityList.length; ++i) {
      const entity = mmtfData.entityList[i]
      if (entity.type !== 'polymer') {
    Severity: Minor
    Found in packages/miew/src/io/parsers/MMTFParser.js - About 2 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

    Function _parseAssemblyInfo has 59 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

      _parseAssemblyInfo(mmtfData) {
    let i
    let j
    let k
    const assemblies = []
    Severity: Major
    Found in packages/miew/src/io/parsers/MMTFParser.js - About 2 hrs to fix

      Function _updateSecStructure has 49 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

        _updateSecStructure(complex, residue, groupData) {
    const helixClasses = [3, -1, 1, -1, 5]

    if (!isUndefined(groupData) && groupData.secStruct === this._ssType) {
      residue._secondary = this._ssStruct
      Severity: Minor
      Found in packages/miew/src/io/parsers/MMTFParser.js - About 1 hr to fix

        Function _updateSecStructure has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
        Open

          _updateSecStructure(complex, residue, groupData) {
    const helixClasses = [3, -1, 1, -1, 5]

    if (!isUndefined(groupData) && groupData.secStruct === this._ssType) {
      residue._secondary = this._ssStruct
        Severity: Minor
        Found in packages/miew/src/io/parsers/MMTFParser.js - 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

        Function _traverse has 30 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

          _traverse(mmtfData) {
    const self = this

    // get metadata
    const { metadata } = this._complex
        Severity: Minor
        Found in packages/miew/src/io/parsers/MMTFParser.js - About 1 hr to fix

          Avoid deeply nested control flow statements.
          Open

                      for (let m = 0; m < res._atoms.length; ++m) {
              res._atoms[m].het = true
            }
          Severity: Major
          Found in packages/miew/src/io/parsers/MMTFParser.js - About 45 mins to fix

            Function _updateMolecules has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
            Open

              _updateMolecules(mmtfData) {
    const entities = mmtfData.entityList
    if (!entities) {
      return
    }
            Severity: Minor
            Found in packages/miew/src/io/parsers/MMTFParser.js - About 35 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

            Function compare has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
            Open

              compare(candidate) {
    const len = candidate.length
    if (len !== this._original.length) {
      return false
    }
            Severity: Minor
            Found in packages/miew/src/io/parsers/MMTFParser.js - 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

            Function _onGroup has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
            Open

              _onGroup(groupData) {
    if (groupData.modelIndex !== 0) {
      return
    }
            Severity: Minor
            Found in packages/miew/src/io/parsers/MMTFParser.js - 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 4 locations. Consider refactoring.
            Open

                this._complex.finalize({
      needAutoBonding: false,
      detectAromaticLoops: this.settings.now.aromatic,
      enableEditing: this.settings.now.editing,
      serialAtomMap: this._serialAtomMap
            Severity: Major
            Found in packages/miew/src/io/parsers/MMTFParser.js and 3 other locations - About 1 hr to fix
            packages/miew/src/io/parsers/GROParser.js on lines 173..178
            packages/miew/src/io/parsers/MOL2Parser.js on lines 294..299
            packages/miew/src/io/parsers/XYZParser.js on lines 100..105

            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 64.

            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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