Function updateToFrame has 40 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  updateToFrame(frameData) {
    // This method looks like a copy paste. However, it
    // was decided to postpone animation refactoring until GFX is fixed.

    const residues = frameData.getResidues()

Function _parseAtomsInf has 40 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _parseAtomsInf() {
    const het = true
    const altLoc = ' '
    const occupancy = 1
    const tempFactor = 1

Function updateCMLData has 40 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    function updateCMLData(complex) {
      const { root } = self._gfx
      const mat = extractRotation(root.matrixWorld)
      const v4 = new Vector4(0, 0, 0, 0)
      const vCenter = new Vector4(0, 0, 0, 0)

Function _addReprListItem has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

Menu.prototype._addReprListItem = function (panel, index, repr) {
  const self = this
  const reprList = $(
    `${self._menuId} [data-panel-type=miew-menu-panel-representation] .miew-repr-list`
  )

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Function pickObject has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

Picker.prototype.pickObject = function (screenPos) {
  if (!this.gfxObj) {
    this.picked = {}
    this.dispatchEvent({ type: 'newpick', obj: {} })
    return

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Function rebuildSelectionGeometry has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

  rebuildSelectionGeometry() {
    const mask = 1 << this._selectionBit

    gfxutils.clearTree(this._selectionGeometry)

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Function parse has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

  parse(stream) {
    /** @type {?Assembly} */
    let assembly = this._assembly
    /** @type {?Matrix4} */
    let matrix = this._matrix

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Function extractArgs has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

function extractArgs(input, defaultsDict, params) {
  if (input) {
    const bang = input.indexOf(cOptsSep)
    const inputVal = parseParams(
      input.substr(0, bang >= 0 ? bang : undefined),

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Function toScript has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

function toScript(opts) {
  const commandsList = []
  let idx = 0
  function checkAndAdd(command, value, saveQuotes) {
    if (value !== null && value !== undefined) {

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Function _resetComponentTransform has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

  _resetComponentTransform() {
    const visual = this._complexVisual
    const selection = this._complexVisual.getSelectionGeo()
    let i
    let j

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Function _onPick has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

  _onPick(event) {
    if (!settings.now.picking) {
      // picking is disabled
      return
    }

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Function _build has 39 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _build() {
    const { residues, parent } = this._selection
    const mode = this._mode
    const colorer = this._colorer
    const geo = this._geo

Function toScript has 39 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function toScript(opts) {
  const commandsList = []
  let idx = 0
  function checkAndAdd(command, value, saveQuotes) {
    if (value !== null && value !== undefined) {

Function fillSingleWords has 38 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  function fillSingleWords() {
    const frag = document.createDocumentFragment()
    let newItem
    const group = selectionPanel.find('[data-tab-content=singleword]').get(0)
    let i

Function _loopThrough has 38 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function _loopThrough(
  subDiv,
  residues,
  segmentsHeight,
  tension,

Function _initVertices has 38 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _initVertices(segmentsCount) {
    this._buffersSize = segmentsCount * VERTEX_PER_SEGMENT
    const pointsCount = this._buffersSize
    const use32bitIndex = pointsCount > MAX_IDC_16BIT
    this._index = utils.allocateTyped(

Function constructor has 38 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  constructor(volume, width, height) {
    const planeGeo = this._initPlaneGeo(width, height)

    const mat = new VolumeMaterial.BackFacePosMaterialFarPlane()
    this._plane = new meshes.Mesh(planeGeo, mat)

Function _fillCmpEdit has 38 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _fillCmpEdit() {
    const self = this
    const components = this._components

    function addComp() {

Function resetReps has 38 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  resetReps(reps) {
    // Create all necessary representations
    if (this._complex) {
      this._complex.clearAtomBits(~0)
    }

Function _traverseData has 38 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _traverseData(dom) {
    function isArray(o) {
      return Object.prototype.toString.apply(o) === '[object Array]'
    }