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

Open

    this.renderDatum = function(parentElement, conf, layout, utils) {
        var bin;
        bin = parentElement.selectAll('.bin').data(function(d) {
            return d.values;
        }).enter().append('path').attr('class', 'bin').attr('opacity', function(d) {

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

Open

                        _.bind(function (hit) {
                            if (hit.number < num_hits) {
                                var hsp_details = _.map(
                                    hit.hsps,
                                    _.bind(function (hsp) {

Function renderAxes has 33 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 overviewJSX has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    overviewJSX() {
        return (
            <div className="overview">
                <p>
                    <strong>SequenceServer {this.state.seqserv_version}</strong> using{' '}

Method tree has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.

Open

      def tree
        all.each_with_object({}) do |db, data|
          data[db.type] ||= []
          use_parent = '#'
          db.categories.each_with_index do |entry, index|

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

Open

    parsedOptions(textValue) {
        const words = textValue.split(" ");
        let parsedOptions = this.defaultObjectValue();
        // Iterate through the words in steps of 2, treating each pair as an option and its potential value
        for (let i = 0; i < words.length; i += 2) {

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

Open

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

    let content;
    switch (formState) {

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

Open

    this.renderChords = function(parentElement, name, conf, data, layout, ratio, getSource, getTarget) {
        var link, track;
        track = parentElement.append('g').attr('class', conf.colorPalette);
        link = track.selectAll('.chord').data(data).enter().append('path').attr('class', 'chord').attr('d', d3.svg.chord().source(function(d) {
            return getSource(d, layout);

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

Open

    render() {
        return (
            <div className="relative">
                <div
                    className="sequence">

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

Open

    warningJSX() {
        return(
            <div className="container">
                <div className="row">
                    <div className="col-md-6 col-md-offset-3 text-center">

Function componentDidMount has 30 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 applyRules has 29 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    this.applyRules = function(rules, data) {
        var datum, i, k, results, rule, v;
        rules = rules || [];
        results = [];
        for (k in data) {

Function renderBlock has 29 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    this.renderBlock = function(parentElement, data, layout, conf) {
        var block, scope;
        scope = conf.outerRadius - conf.innerRadius;
        block = parentElement.selectAll('.block').data(data).enter().append('g').attr('class', 'block').attr('transform', function(d) {
            return 'rotate(' + layout.blocks[d.key].start * 360 / (2 * Math.PI) + ')';

Function determineBlastMethods has 28 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    determineBlastMethods() {
        var database_type = this.databaseType;
        var sequence_type = this.sequenceType;

        if (this.refs.query.isEmpty()) {

Function Text has 28 lines of code (exceeds 25 allowed). Consider refactoring.

Open

circosJS.Text = function() {
    circosJS.Track.call(this);
    this.parseData = circosJS.parsePositionTextData;
    this.renderDatumContainer = (function(_this) {
        return function(instance, parentElement, name, data, conf) {

Function renderDatum has 28 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    this.renderDatum = function(parentElement, conf, layout, utils) {
        var tile;
        tile = parentElement.selectAll('.tile').data(function(d) {
            return d.values;
        }).enter().append('path').attr('class', 'tile').attr('d', d3.svg.arc().innerRadius(utils.datumInnerRadius).outerRadius(utils.datumOuterRadius).startAngle(function(d) {

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

Open

    ratioCalculate(value, min, max, scope, reverse, logScale) {
        var fraction, scaleLogBase, x;
        scaleLogBase = logScale ? 2.3 : 1;
        if (
            min === max ||

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

Open

    constructor(props) {
        super(props);
        // Properties below are internal state used to render results in small
        // slices (see updateState).
        this.numUpdates = 0;