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.query.current.isEmpty()) {

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

Open

    render() {
        var methods = this.state.methods;
        var method = methods[0];
        var multi = methods.length > 1;

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

Open

    warningJSX() {
        return(
            <div className="mx-auto max-w-7xl px-4 sm:px-6 lg:px-8">
                <div className="grid grid-cols-6 gap-4">
                    <div className="col-start-1 col-end-7 text-center">

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

Open

circosJS.Core.prototype.removeTracks = function(trackIds) {
    var id, l, len, ref, store, svg, trackId, type;
    svg = d3.select(this.conf.container);
    ref = this.tracks;
    for (type in ref) {

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

Open

    handleLoadTree(category) {
        var tree_id = '#' + category + '_database_tree';
        // hack that is needed to sync the selected tree db with the hidden main db
        window.jstree_node_change_timeout = null;

Function renderChords has 8 arguments (exceeds 4 allowed). Consider refactoring.

Open

    this.renderChords = function(parentElement, name, conf, data, layout, ratio, getSource, getTarget) {

Method retrieve has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

      def retrieve(loci)
        # Exit early if loci is nil.
        return unless loci

        # String -> Array

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

Open

circosJS.Layout = function(conf, data) {
    var block_nb, gap, k, offset, ref, ref1, size, v;
    if (data == null) {
        circosJS.log(2, 'no layout data', '');
    }

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Method init_database has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

    def init_database
      fail DATABASE_DIR_NOT_SET unless config[:database_dir]

      config[:database_dir] = File.expand_path(config[:database_dir])
      unless File.exist?(config[:database_dir]) &&

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Function ratio has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

    this.ratio = function(value, min, max, scope, reverse, logScale) {

Method parse_advanced has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

      def parse_advanced(param_line)
        param_list = (param_line || '').split(' ')
        res = {}

        param_list.each_with_index do |word, i|

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Function ratio has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

    this.ratio = function(value, min, max, scope, reverse, logScale) {

Method open_in_browser has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def open_in_browser(server_url)
      return if using_ssh? || verbose?
      if RUBY_PLATFORM =~ /linux/ && xdg?
        sys("xdg-open #{server_url}")
      elsif RUBY_PLATFORM =~ /darwin/

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Avoid deeply nested control flow statements.

Open

                    if (Object.prototype.hasOwnProperty.call(source, key)) {
                        target[key] = source[key];
                    }

Avoid deeply nested control flow statements.

Open

            for (trackId in store) {
                svg.select('.' + trackId).remove();
                delete store[trackId];
            }

Consider simplifying this complex logical expression.

Open

    if ('source_id' in sample && 'source_start' in sample && 'source_end' && 'target_id' in sample && 'target_start' in sample && 'target_end' in sample) {
        data = data.map(function(datum) {
            var elts;
            elts = [datum.source_id, datum.source_start, datum.source_end, datum.target_id, datum.target_start, datum.target_end];
            if (datum.value != null) {

Method make_blast_database has 5 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def make_blast_database(action, file, title, type, non_parse_seqids = false)