Function _build has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _build() {
    const self = this
    this._hbonds = new HBondInfo(this._complex)
    this._ss = [] // DSSP map by residue

Function extractArgs has 32 lines of code (exceeds 25 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),

Function _enableMRT has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _enableMRT(on, renderBuffer, textureBuffer) {
    const gfx = this._gfx
    const gl = gfx.renderer.getContext()
    const ext = gl.getExtension('WEBGL_draw_buffers')
    const { properties } = gfx.renderer

Function _parseData has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function _parseData(data, opts, job) {
  if (job.shouldCancel()) {
    return Promise.reject(new Error('Operation cancelled'))
  }

Function addVertexToGeo has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

  addVertexToGeo(geoOut, vAdd) {
    let entry
    const oneHynberes = 0.01
    const n815851 = 815851
    const n37633 = 37633

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Function _buildInner has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

  _buildInner(radOffset, addChunk) {
    const chunksToIdx = this._selection.chunks

    const prevVector = new Vector3()
    const currVector = new Vector3()

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Function updateToFrame has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

  updateToFrame(frameData) {
    const bondsIdc = this._selection.chunks
    const { bonds } = this._selection
    const mode = this._mode
    const colorer = this._colorer

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Function _forEachVoxelWithinRadiusSimple has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

  _forEachVoxelWithinRadiusSimple(center, radius, process) {
    const xRange = VoxelWorld._xRange
    const yRange = VoxelWorld._yRange
    const zRange = VoxelWorld._zRange
    const vCenter = VoxelWorld._vCenter

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Function writeEntireString has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

  writeEntireString(string, maxStrPos, concat) {
    if (!maxStrPos) {
      maxStrPos = 81
    }
    for (let j = 0; j < string.length; j++) {

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Function resetReps has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

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

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Function _extractSheets has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

  _extractSheets(complex, sheetData) {
    const { asymDict } = this
    if (
      !sheetData.sheet_id ||
      !sheetData.id ||

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Function center has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

  center(selector) {
    // no arguments - center on current selection;
    if (selector === undefined) {
      this.setPivotSubset()
      this._needRender = true

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Function _onKeyDown has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

  _onKeyDown(event) {
    if (!this._running || !this._hotKeysEnabled) {
      return
    }

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Function begin has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

  begin() {
    const visual = this._complexVisual
    const selection = this._complexVisual.getSelectionGeo()

    const atoms = this._getSelectionBorderAtoms()

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Function view has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

  view(expression) {
    const VIEW_VERSION = '1'
    const self = this
    const { pivot } = this._gfx
    let transform = []

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Function DebugTracer has 31 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function DebugTracer(namespace) {
  var enabled = false;
  this.enable = function (on) {
    enabled = on;
  };

Function DebugTracer has 31 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function DebugTracer(namespace) {
  var enabled = false;
  this.enable = function (on) {
    enabled = on;
  };

Function constructor has 31 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  constructor(instanceCount, opts) {
    super()
    this._opts = opts
    this.items = []
    this.needsUpdate = false

Function _createExtrudedChunkGeometry has 31 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function _createExtrudedChunkGeometry(shape, ringsCount) {
  const geo = new BufferGeometry()
  const ptsCount = shape.length
  const totalPts = ptsCount * ringsCount
  const type = totalPts <= 65536 ? Uint16Array : Uint32Array

Function _init has 31 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _init(chunkGeo, chunksCount) {
    const chunkSize = (this._chunkSize = chunkGeo.attributes.position.count)
    const chunkIndex = chunkGeo.index.array
    const chunkIndexSize = chunkIndex.length
    const pointsCount = this._chunkSize * chunksCount