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Similar blocks of code found in 3 locations. Consider refactoring.
Open

          createElement(
            'li',
            {
              class: 'list-group-item col-xs-12 col-sm-12',
              'data-toggle': 'combobox-panel',
Severity: Major
Found in demo/src/scripts/ui/Menu.js and 2 other locations - About 2 hrs to fix
demo/src/scripts/ui/Menu.js on lines 658..681
demo/src/scripts/ui/Menu.js on lines 712..735

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 85.

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

Function joinComplexes has 62 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  joinComplexes(complexes) {
    // clear target complex
    this._chains = []
    this._components = []
    this._helices = []
Severity: Major
Found in packages/miew/src/chem/Complex.js - About 2 hrs to fix

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

    var arrayWithHoles = createCommonjsModule(function (module) {
function _arrayWithHoles(arr) {
  if (Array.isArray(arr)) return arr;
}
module.exports = _arrayWithHoles, module.exports.__esModule = true, module.exports["default"] = module.exports;
    Severity: Major
    Found in packages/miew-cli/dist/index.js and 1 other location - About 2 hrs to fix
    packages/miew-cli/dist/index.modern.js on lines 3173..3178

    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 84.

    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

    var arrayWithHoles = createCommonjsModule(function (module) {
function _arrayWithHoles(arr) {
  if (Array.isArray(arr)) return arr;
}
module.exports = _arrayWithHoles, module.exports.__esModule = true, module.exports["default"] = module.exports;
    Severity: Major
    Found in packages/miew-cli/dist/index.modern.js and 1 other location - About 2 hrs to fix
    packages/miew-cli/dist/index.js on lines 3177..3182

    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 84.

    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

    function bytesToBase64(
buffer) {
  var bytes = new Uint8Array(buffer);
  var binary = '';
  for (var i = 0; i < bytes.byteLength; i++) {
    Severity: Major
    Found in packages/miew-cli/dist/index.js and 1 other location - About 2 hrs to fix
    packages/miew-cli/dist/index.modern.js on lines 3438..3446

    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 84.

    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

      collectMask() {
    let mask = 0xffffffff
    const residues = this._residues
    for (let i = 0, n = residues.length; i < n; ++i) {
      mask &= residues[i]._mask
    Severity: Major
    Found in packages/miew/src/chem/Chain.js and 1 other location - About 2 hrs to fix
    packages/miew/src/chem/Residue.js on lines 158..165

    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 84.

    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

      collectMask() {
    let mask = 0xffffffff
    const atoms = this._atoms
    for (let i = 0, n = atoms.length; i < n; ++i) {
      mask &= atoms[i].mask
    Severity: Major
    Found in packages/miew/src/chem/Residue.js and 1 other location - About 2 hrs to fix
    packages/miew/src/chem/Chain.js on lines 184..191

    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 84.

    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

    function bytesToBase64(
buffer) {
  var bytes = new Uint8Array(buffer);
  var binary = '';
  for (var i = 0; i < bytes.byteLength; i++) {
    Severity: Major
    Found in packages/miew-cli/dist/index.modern.js and 1 other location - About 2 hrs to fix
    packages/miew-cli/dist/index.js on lines 3442..3450

    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 84.

    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

    Function iterableToArrayLimit has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
    Open

    var iterableToArrayLimit = createCommonjsModule(function (module) {
function _iterableToArrayLimit(arr, i) {
  var _i = arr == null ? null : typeof Symbol !== "undefined" && arr[Symbol.iterator] || arr["@@iterator"];
  if (_i == null) return;
  var _arr = [];
    Severity: Minor
    Found in packages/miew-cli/dist/index.modern.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 iterableToArrayLimit has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
    Open

    var iterableToArrayLimit = createCommonjsModule(function (module) {
function _iterableToArrayLimit(arr, i) {
  var _i = arr == null ? null : typeof Symbol !== "undefined" && arr[Symbol.iterator] || arr["@@iterator"];
  if (_i == null) return;
  var _arr = [];
    Severity: Minor
    Found in packages/miew-cli/dist/index.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 _updateIndices has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
    Open

      _updateIndices() {
    // Algorithm:
    // 1. Get plane vertices (from 3 to 6 vertices)
    // 2. Get "right" vector in plane
    // 3. Sort vertices using Graham-like method
    Severity: Minor
    Found in packages/miew/src/gfx/VolumeMesh.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 _fromArray has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
    Open

    function _fromArray(entries) {
  repIndex = 0
  const opts = {}
  for (let i = 0, n = entries.length; i < n; ++i) {
    const /** string[] */ entry = entries[i]
    Severity: Minor
    Found in packages/miew/src/options.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 _traverseData has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
    Open

      _traverseData(dom) {
    function isArray(o) {
      return Object.prototype.toString.apply(o) === '[object Array]'
    }
    Severity: Minor
    Found in packages/miew/src/io/parsers/CMLParser.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

    File Palette.js has 267 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    import { assign } from 'lodash'

function clamp(x, a, b) {
  return x <= b ? (x < 0 ? 0 : x) : b
}
    Severity: Minor
    Found in packages/miew/src/gfx/palettes/Palette.js - About 2 hrs to fix

      Function _updateIndices has 60 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

        _updateIndices() {
    // Algorithm:
    // 1. Get plane vertices (from 3 to 6 vertices)
    // 2. Get "right" vector in plane
    // 3. Sort vertices using Graham-like method
      Severity: Major
      Found in packages/miew/src/gfx/VolumeMesh.js - About 2 hrs to fix

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

              if (opts.min === opts.max) {
        factor = residue.temperature > opts.max ? 1 : 0
      } else {
        factor = (residue.temperature - opts.min) / (opts.max - opts.min)
      }
        Severity: Major
        Found in packages/miew/src/gfx/colorers/TemperatureColorer.js and 1 other location - About 2 hrs to fix
        packages/miew/src/gfx/colorers/TemperatureColorer.js on lines 22..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 83.

        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

                const scale =
          dist *
          (order % 2 === 0
            ? (((j / 2) | 0) + 0.5) * (1 - 2 * (j % 2))
            : (((j + 1) / 2) | 0) * (-1 + 2 * (j % 2)))
        Severity: Major
        Found in packages/miew/src/gfx/modes/groups/BondsCylinderGroup.js and 1 other location - About 2 hrs to fix
        packages/miew/src/gfx/modes/groups/BondsCylinderGroup.js on lines 39..43

        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 83.

        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

          setValues(values) {
    if (typeof values === 'undefined') {
      return
    }
        Severity: Major
        Found in packages/miew/src/gfx/shaders/FXAAMaterial.js and 1 other location - About 2 hrs to fix
        packages/miew/src/gfx/shaders/OutlineMaterial.js on lines 38..53

        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 83.

        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

              if (opts.min === opts.max) {
        factor = atom.temperature > opts.max ? 1 : 0
      } else {
        factor = (atom.temperature - opts.min) / (opts.max - opts.min)
      }
        Severity: Major
        Found in packages/miew/src/gfx/colorers/TemperatureColorer.js and 1 other location - About 2 hrs to fix
        packages/miew/src/gfx/colorers/TemperatureColorer.js on lines 39..43

        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 83.

        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

          setValues(values) {
    if (typeof values === 'undefined') {
      return
    }
        Severity: Major
        Found in packages/miew/src/gfx/shaders/OutlineMaterial.js and 1 other location - About 2 hrs to fix
        packages/miew/src/gfx/shaders/FXAAMaterial.js on lines 37..52

        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 83.

        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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        Status
        Source
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