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yannickwurm/sequenceserver

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public/js/hits_overview.js

Summary

Maintainability
F
3 days
Test Coverage

Function graphIt has 140 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    graphIt($queryDiv, $graphDiv, index, howMany, opts, inhits) {
    /* barHeight: Height of each hit track.
     * legend: Height reserved for the overview legend.
     * margin: Margin around the svg element.
     */
Severity: Major
Found in public/js/hits_overview.js - About 5 hrs to fix

    Function graphControls has 78 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

        graphControls($queryDiv, $graphDiv, isInit, opts, hits) {
        var MIN_HITS_TO_SHOW = 20;

        var totalHits, shownHits, lessButton, moreButton;
    Severity: Major
    Found in public/js/hits_overview.js - About 3 hrs to fix

      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) + ')');
      Severity: Minor
      Found in public/js/hits_overview.js - About 1 hr to fix

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

            graphIt($queryDiv, $graphDiv, index, howMany, opts, inhits) {
    /* barHeight: Height of each hit track.
     * legend: Height reserved for the overview legend.
     * margin: Margin around the svg element.
     */
        Severity: Minor
        Found in public/js/hits_overview.js - About 35 mins to fix

        Cognitive Complexity

        Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

        A method's cognitive complexity is based on a few simple rules:

        • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
        • Code is considered more complex for each "break in the linear flow of the code"
        • Code is considered more complex when "flow breaking structures are nested"

        Further reading

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

            graphControls($queryDiv, $graphDiv, isInit, opts, hits) {
        var MIN_HITS_TO_SHOW = 20;

        var totalHits, shownHits, lessButton, moreButton;
        Severity: Minor
        Found in public/js/hits_overview.js - About 35 mins to fix

        Cognitive Complexity

        Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

        A method's cognitive complexity is based on a few simple rules:

        • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
        • Code is considered more complex for each "break in the linear flow of the code"
        • Code is considered more complex when "flow breaking structures are nested"

        Further reading

        Similar blocks of code found in 2 locations. Consider refactoring.
        Open

                var gradScale = d3.scale
            .log()
            .domain([
                d3.min([1e-5, d3.min(hits.map(function (d) {
                    if (parseFloat(d.hitEvalue) === 0.0) return undefined;
        Severity: Major
        Found in public/js/hits_overview.js and 1 other location - About 4 hrs to fix
        public/js/visualisation_helpers.js on lines 4..15

        Duplicated Code

        Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

        Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

        When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

        Tuning

        This issue has a mass of 128.

        We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

        The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

        If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

        See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

        Refactorings

        Further Reading

        Similar blocks of code found in 2 locations. Consider refactoring.
        Open

                svg_legend.append('text')
            .attr('class',' legend-text')
            .attr('transform', 'translate(0, ' +options.legend +')')
            .attr('x', 9.5 * (width - 2 * options.margin) / 10 + options.margin / 2)
            .text('Weaker hits');
        Severity: Major
        Found in public/js/hits_overview.js and 1 other location - About 2 hrs to fix
        public/js/hits_overview.js on lines 189..193

        Duplicated Code

        Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

        Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

        When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

        Tuning

        This issue has a mass of 89.

        We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

        The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

        If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

        See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

        Refactorings

        Further Reading

        Similar blocks of code found in 2 locations. Consider refactoring.
        Open

                svg_legend.append('text')
            .attr('class',' legend-text')
            .attr('transform', 'translate(0, ' + options.legend + ')')
            .attr('x', 6.7 * (width - 2 * options.margin) / 10 - options.margin / 2)
            .text('Stronger hits');
        Severity: Major
        Found in public/js/hits_overview.js and 1 other location - About 2 hrs to fix
        public/js/hits_overview.js on lines 180..184

        Duplicated Code

        Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

        Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

        When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

        Tuning

        This issue has a mass of 89.

        We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

        The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

        If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

        See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

        Refactorings

        Further Reading

        Similar blocks of code found in 2 locations. Consider refactoring.
        Open

                            $('<button/>')
                        .addClass('btn btn-link more')
                        .attr('type', 'button')
                        .attr('data-parent-query', $queryDiv.attr('id'))
                        .html('View More&nbsp;')
        Severity: Major
        Found in public/js/hits_overview.js and 1 other location - About 2 hrs to fix
        public/js/hits_overview.js on lines 99..108

        Duplicated Code

        Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

        Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

        When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

        Tuning

        This issue has a mass of 75.

        We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

        The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

        If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

        See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

        Refactorings

        Further Reading

        Similar blocks of code found in 2 locations. Consider refactoring.
        Open

                            $('<button/>')
                        .addClass('btn btn-link less')
                        .attr('type', 'button')
                        .attr('data-parent-query', $queryDiv.attr('id'))
                        .html('View Less&nbsp;')
        Severity: Major
        Found in public/js/hits_overview.js and 1 other location - About 2 hrs to fix
        public/js/hits_overview.js on lines 89..98

        Duplicated Code

        Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

        Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

        When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

        Tuning

        This issue has a mass of 75.

        We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

        The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

        If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

        See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

        Refactorings

        Further Reading

        Identical blocks of code found in 2 locations. Consider refactoring.
        Open

            setupTooltip() {
        this.svg_container.find('[data-toggle="tooltip"]').tooltip({
            'placement': 'top', 'container': 'body', 'html': 'true',
            'delay': 0, 'white-space': 'nowrap'
        });
        Severity: Major
        Found in public/js/hits_overview.js and 1 other location - About 1 hr to fix
        public/js/length_distribution.js on lines 86..91

        Duplicated Code

        Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

        Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

        When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

        Tuning

        This issue has a mass of 57.

        We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

        The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

        If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

        See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

        Refactorings

        Further Reading

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