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

Open

  change(repSettings, complex, mode, color) {
    const diff = {}

    // modify selector
    if (repSettings.selector) {

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

Open

  _extractAtoms(complex, complexData) {
    let aids = complexData.atoms && complexData.atoms.aid
    let elements = aids && complexData.atoms.element
    if (!elements || aids.length !== elements.length) {
      throw new Error('Unable to parse atom elements')

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

Open

  _finalize(serialAtomMap, residueHash, complex) {
    if (this.init instanceof Residue && this.term instanceof Residue) {
      return
    }

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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

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

Open

  _updateInfoPanel() {
    const info = this._msgAtomInfo.getElementsByTagName('p')[0]
    let atom
    let residue

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

Open

  _getAltObj() {
    if (this._editors) {
      let altObj = null
      for (let i = 0; i < this._editors.length; ++i) {
        const nextAltObj = this._editors[i].getAltObj()

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Function _fillSourceList has 35 lines of code (exceeds 25 allowed). Consider refactoring.

Open

Menu.prototype._fillSourceList = function () {
  const self = this
  const names = this._viewer.getVisuals()
  $('#miew-source-dropdown').toggle(names.length > 1)

Function constructor has 35 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  constructor(params) {
    super()
    // add fog
    this.fog = true
    // used for instanced geometry

Function constructor has 35 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  constructor(
    BondsGroup,
    geoParams,
    complex,
    colorer,

Function _writeRelations has 35 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _writeRelations() {
    let modelsList = ''
    for (let i = 0; i < this._info.models.length; ++i) {
      modelsList += `
  Model: "Model::${this._info.name}_${i}", "Mesh" {

Function _continueAnimation has 35 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _continueAnimation() {
    this._isAnimating = true
    let minFrameTime = 1000 / settings.now.maxfps
    minFrameTime = Number.isNaN(minFrameTime) ? 0 : minFrameTime
    const self = this

Function checkArg has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    value: function checkArg(key, arg, modificate) {
      if (key !== undefined && arg !== undefined) {
        if (keyRemap(key) === 'selector') {
          var res = selectors.parse(arg);
          if (res.error !== undefined) {

Function checkArg has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    value: function checkArg(key, arg, modificate) {
      if (key !== undefined && arg !== undefined) {
        if (keyRemap(key) === 'selector') {
          var res = selectors.parse(arg);
          if (res.error !== undefined) {

Function constructor has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  constructor(
    AtomsGroup,
    geoParams,
    complex,
    colorer,

Function getBoundingBox has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  getBoundingBox(atoms, vBoxMin, vBoxMax) {
    const bigNum = 10000000.0

    vBoxMin.x = vBoxMin.y = vBoxMin.z = bigNum
    vBoxMax.x = vBoxMax.y = vBoxMax.z = 0 - bigNum

Function _countNormalsInRing has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _countNormalsInRing(ptsCount, vtxIdx, isSlope, shiftToExtraPt) {
    const tmpShape = this._tmpShape
    const normals = this._normals

    tmpShape[0].fromArray(this._positions, vtxIdx)

Function update has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

ObjectHandler.prototype.update = (function () {
  const axis = new Vector3()

  return function (timeSinceLastUpdate, timeSinceMove) {
    if (settings.now.autoRotation !== 0.0) {

Function _build has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _build() {
    const self = this

    for (let i = 0; i < this._complex._residues.length - 1; ++i) {
      const ri = this._complex._residues[i]

Function _fixDir has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _fixDir(refPoint, currDir, posGetter) {
    // count atoms to the right and to the left of the current plane
    let rightCount = 0
    let leftCount = 0
    const tmpVec = refPoint.clone()

Function _flattenModels has 34 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _flattenModels() {
    let overallVertsCount = 0
    function shift(x) {
      return x + overallVertsCount
    }