Function calculate_multipliers has 43 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    calculate_multipliers() {
        var sum_query_length = 0;
        var sum_hit_length = 0;
        _.each(
            this.query_arr,

Method defaults has 43 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def defaults
      @defaults ||= {
        host: '0.0.0.0',
        port: 4567,
        databases_widget: 'classic',

Function render has 41 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    render() {
        return (
            <div
                className="dnd-overlay absolute left-0 top-0 w-full h-full bg-gray-200 bg-opacity-75 z-40"
                style={{ display: 'none' }}>

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

Open

    render() {
        return (
            <div>
                <div id="overlay" style={{ position: 'absolute', top: 0, left: 0, width: '100vw', height: '100vw', background: 'rgba(0, 0, 0, 0.2)', display: 'none', zIndex: 99 }} />

Function ribbonV3 has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

var ribbonV3 = function() {
    var source = d3_source, target = d3_target, radius = d3_svg_chordRadius, startAngle = d3_svg_arcStartAngle, endAngle = d3_svg_arcEndAngle;
    function chord(d, i) {
        var s = subgroup(this, source, d, i), t = subgroup(this, target, d, i);
        result = "M" + s.p0 + arc(s.r, s.p1, s.a1 - s.a0) + (equals(s, t) ? curve(s.p0) : curve(t.p0) + arc(t.r, t.p1, t.a1 - t.a0) + curve(s.p0)) + "Z";

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Method convert_deprecated_options has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

    def convert_deprecated_options(options)
      options.each do |blast_algo, algo_config|
        if algo_config.is_a?(Array)
          # Very old config files may have a single array with CLI args.
          # e.g. { blastn: ['-task blastn', '-evalue 1e-5'] }

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Method sys has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

  def self.sys(command, options = {})
    # Available output channels
    channels = %i[stdout stderr]

    # Make temporary files to store output from stdout and stderr.

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Function render has 36 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  render() {
    const { formState, isModalVisible } = this.state;

    let content;
    switch (formState) {

Function render has 36 lines of code (exceeds 25 allowed). Consider refactoring.

Open

circosJS.Core.prototype.render = function(ids, removeTracks) {
    var name, ref, ref1, renderAll, svg, track, trackStore, trackType, tracks, translated;
    if (typeof ids === 'undefined') {
        renderAll = true;
        ids = [];

Function advancedParamsJSX has 36 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    advancedParamsJSX() {
        let classNames = 'flex-grow block px-4 py-1 text-gray-900 border border-gray-300 rounded-lg bg-gray-50 text-base font-mono';

        if (this.state.textValue) {
            classNames += ' bg-yellow-100';

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

Open

circosJS.Chord = function() {
    circosJS.Track.call(this);
    this.parseData = circosJS.parseChordData;
    this.applyRules = function(rules, data) {
        var datum, l, len, results, rule;

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

Open

    resultsJSX() {
        return (
            <div className="grid grid-cols-1 md:grid-cols-4 gap-4 print:grid-cols-1" id="results">
                <div className="hidden md:col-span-1 md:block print:hidden">
                    <Sidebar

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

Open

const RunSummary = (props) => {
    const renderContent = () => {
        return (
            <div className="overview mr-0 mb-0">
                <p className="m-0 text-sm">

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

Open

    componentDidMount() {
        /**
        * Fetch data to initialise the search interface from the server. These
        * include list of databases to search against, advanced options to
        * apply when an algorithm is selected, and a query sequence that

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

Open

    this.renderAxes = function(parentElement, conf, layout, data) {
        var axes, axis, x;
        if (conf.axes.minor.spacingType === 'pixel') {
            axes = (function() {
                var l, ref, ref1, ref2, results;

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

Open

    drawLegend(svg, options, width, height, hits) {
        var svg_legend = svg.append('g')
            .attr('transform',
                'translate(0,' + (height - 1.75 * options.margin) + ')');

Function hitLinks has 33 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    hitLinks() {
        var btns = [];
        if (!(this.props.imported_xml || this.props.non_parse_seqids)) {
            btns = btns.concat([
                this.viewSequenceButton(),

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

Open

    selectHit(id) {
        var checkbox = $('#' + id);
        var num_checked = $('.hit-links :checkbox:checked').length;

        if (!checkbox || !checkbox.val()) return;

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

Open

    const renderContent = () => {
        return (
            <div className="overview mr-0 mb-0">
                <p className="m-0 text-sm">
                    <strong>SequenceServer {props.seqserv_version}</strong> using{' '}

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

Open

circosJS.Core.prototype.smartBorders = function() {
    var border, borders, currentBorder, l, layout, len, ref, store, track, trackId, trackType, width;
    width = this.conf.defaultTrackWidth;
    layout = {
        'in': this._layout.conf.innerRadius,

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