Function _getSelection has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

  _getSelection: function(model) {
    const maxLen = model.get("seq").length;
    const selection = [];
    const sels = this.g.selcol.getSelForRow(model.get("id"));
    const rows = find(sels, function(el) { return el.get("type") === "row"; });

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Function saveSelection has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

  saveSelection: function(that,name) {
    let selection = that.g.selcol.pluck("seqId");
    console.log(selection);
    if (selection.length > 0) {
      // filter those seqids

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Function render has 27 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  render: function() {
    this.setName("Extras");
    var stats = this.g.stats;
    var msa = this.msa;
    this.addNode("Add consensus seq", () => {

Function addFeatures has 26 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  addFeatures: function(features) {
    if ((features.config != null)) {
      const obj = features;
      features = features.seqs;
      if ((obj.config.colors != null)) {

Function guessFileFromText has 26 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  { guessFileFromText: function(text, opt) {
    if (!(typeof text !== "undefined" && text !== null)) {
      console.warn("invalid file format");
      return ["", "error"];
    }

Function colorer has 26 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  colorer: function(colorRange) {
    let colorer = function() { return "none" };

    if( typeof colorRange === 'string' ) {
      colorer = function() { return colorRange };

Function render has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

  render: function() {
    this.setName("Export");

    this.addNode("Share view (URL)" + ShareSym, () => {
      return Exporter.shareLink(this.msa, function(link) {

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Function render has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

  render: function() {
    dom.removeAllChilds(this.el);

    this.el.style.width = `${this.g.zoomer.getLabelWidth()}px`;
    //@el.style.height = "#{@g.zoomer.get "rowHeight"}px"

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Function getDummySequences has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

  getDummySequences: function(len, seqLen) {
    const seqs = [];
    if (!(typeof len !== "undefined" && len !== null)) { len = BMath.getRandomInt(3,5); }
    if (!(typeof seqLen !== "undefined" && seqLen !== null)) { seqLen = BMath.getRandomInt(50,200); }

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Function invertCol has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  invertCol: function(columns) {
    const selColumns = this.where({type:"column"}).reduce((memo,el) => {
      return memo.concat(((() => {
        const result = [];
        let i = el.attributes.xStart;

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Function _drawSelection has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  _drawSelection: function() {
    // hide during selection
    if (this.dragStart.length > 0 && !this.prolongSelection) { return; }

    this.ctx.fillStyle = "#666666";

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Avoid deeply nested control flow statements.

Open

            if (hidden.indexOf(j) >= 0) {
              color = "grey";
            }

Avoid deeply nested control flow statements.

Open

            if (seq_hidden[i]) {
              colors.push("grey");
              continue;
            }

Function markerHidden has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  markerHidden: function(n,stepSize) {
    const hidden = this.g.columns.get("hidden").slice(0);

    const min = Math.max(0, n - stepSize);
    let prevHidden = true;

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Avoid deeply nested control flow statements.

Open

            if ((typeof color !== "undefined" && color !== null)) {
              colors.push(color);
            }

Function getMinRows has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  getMinRows: function() {

    const len = (this.max(function(el) { return el.get("xEnd"); })).attributes.xEnd;
    const rows = ((() => {
      const result = [];

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Function importFiles has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  importFiles: function(files) {
    return (() => {
      var result = [];
      var end = files.length - 1;
      for (var i = 0; 0 < end ? i <= end : i >= end; 0 < end ? i++ : i--) {

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Avoid deeply nested control flow statements.

Open

            if (showLowerCase) { c = c.toUpperCase(); }

Function assignRows has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

  assignRows: function() {

    const len = (this.max(function(el) { return el.get("xEnd"); })).attributes.xEnd;
    const rows = (() => {
      const result = [];

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Function calcHiddenSeqs has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

  calcHiddenSeqs: function(n) {
    let nNew = n;
    for (let i = 0; 0 < nNew ? i <= nNew : i >= nNew; 0 < nNew ? i++ : i--) {
      if (this.at(i).get("hidden")) {
        nNew++;

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