Function parse has 136 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    parse: function parse(input) {
      var self = this,
          stack = [0],
          tstack = [],
          vstack = [null],

Function modifyExcludedFromGeo has a Cognitive Complexity of 36 (exceeds 5 allowed). Consider refactoring.

Open

  modifyExcludedFromGeo(
    side,
    probeSphereRadius,
    vBoxMin,
    vBoxMax,

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File Miew-cli.js has 392 lines of code (exceeds 250 allowed). Consider refactoring.

Open

import { Miew } from 'miew'
import { parser as parsercli } from './MiewCLIParser'
import clihelp from './MiewCLIHelp'
import logger from './logger'
import { slice, sortBy, get, keys, isUndefined, set, assign } from 'lodash'

Function constructor has 134 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  constructor(
    radiusTop,
    radiusBottom,
    height,
    radialSegments,

File PDBParser.js has 381 lines of code (exceeds 250 allowed). Consider refactoring.

Open

import { isString, isUndefined } from 'lodash'
import Parser from './Parser'
import chem from '../../chem'
import Remark290 from './pdb/Remark290'
import Remark350 from './pdb/Remark350'

Function _fillReprList has 128 lines of code (exceeds 25 allowed). Consider refactoring.

Open

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

Function _initializeTerminal has a Cognitive Complexity of 34 (exceeds 5 allowed). Consider refactoring.

Open

Menu.prototype._initializeTerminal = function () {
  const self = this
  let res = null
  let urlSubString = ''
  const element = $(

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Function _doGridPosNorms has 123 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _doGridPosNorms(isoValue, step, appendSimple) {
    const vol = this._volumetricData
    const volData = this._volumetricData.getData()
    const dim = vol.getDimensions()
    const xSize = dim[0]

Function K has 121 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  function K(r, t, n) {
    n = n || {}
    var e,
      i,
      o,

ComplexVisual has 37 functions (exceeds 20 allowed). Consider refactoring.

Open

class ComplexVisual extends Visual {
  constructor(name, dataSource) {
    super(name, dataSource)
    this._complex = dataSource

File VolumeMesh.js has 368 lines of code (exceeds 250 allowed). Consider refactoring.

Open

import VolumeMaterial from './shaders/VolumeMaterial'
import settings from '../settings'
import {
  BufferAttribute,
  BufferGeometry,

File FBXResult.js has 366 lines of code (exceeds 250 allowed). Consider refactoring.

Open

// Forming default definitions block
const defaultDefinitions = `
Definitions:  {
  Version: 100
  Count: 3

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

Open

function AVHash(posRad, min, max, maxDistance) {
  const itemSize = 4
  const nAtoms = posRad.length / itemSize

  const minX = min[0]

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

Open

  _parseAssemblyInfo(mmtfData) {
    let i
    let j
    let k
    const assemblies = []

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Function _doGridPosNorms has a Cognitive Complexity of 30 (exceeds 5 allowed). Consider refactoring.

Open

  _doGridPosNorms(isoValue, step, appendSimple) {
    const vol = this._volumetricData
    const volData = this._volumetricData.getData()
    const dim = vol.getDimensions()
    const xSize = dim[0]

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Function _selectComponents has 110 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _selectComponents(text) {
    const parser = new DOMParser()
    const doc = parser.parseFromString(text, 'application/xml')
    const traversedData = this._traverseData(doc)
    let rawData

Function createVoxels has 106 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  createVoxels() {
    let numAtomsRefs
    let rad
    const ATOM_VOXEL_REF_SCALE = 4.5

Function _updateVertices has 105 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _updateVertices() {
    // Algorithm:
    // 1. Get plane parameters
    // 2. Compute culling flags for all vertices
    // 3. If intersection occurs => compute from 3 to 6 intersection points

Function _buildAlphaHelices has 104 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  _buildAlphaHelices(inResidues, chainLength, inPreferPiHelices) {
    // Helix and Turn
    for (let stride = 3; stride <= 5; ++stride) {
      if (inResidues.length < stride) {
        break

Function _presetsPanelActionsPdbInputsRefresh has a Cognitive Complexity of 28 (exceeds 5 allowed). Consider refactoring.

Open

Menu.prototype._presetsPanelActionsPdbInputsRefresh = function (self) {
  const loadPdbButton = $(
    `${self._menuId} .presets-panel-action[data-presets-panel-action=pdb-load]`
  )
  const clearInputsButton = $(

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