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File plots.js has 693 lines of code (exceeds 250 allowed). Consider refactoring.
Open

/*
    GV - GeneValidator's JavaScript module

    Define a global GV (acronym for GeneValidator) object containing all
    GV associated methods:
Severity: Major
Found in aux/source_assets/js/plots.js - About 1 day to fix

    Similar blocks of code found in 3 locations. Consider refactoring.
    Open

        for (var j = 0; j < footer.length; j++) {

      var footer_array = footer[j].split(",");
      svg.append("rect")
          .attr("x", (width-total_len)/2 + offset)
    Severity: Major
    Found in aux/source_assets/js/plots.js and 2 other locations - About 1 day to fix
    aux/source_assets/js/plots.js on lines 682..696
    aux/source_assets/js/plots.js on lines 798..812

    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 223.

    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 3 locations. Consider refactoring.
    Open

        for (var j = 0; j < footer.length; j++) {
      var footer_array = footer[j].split(",");
      svg.append("rect")
           .attr("x", (width-total_len)/2 + offset)
           .attr("y", -30)
    Severity: Major
    Found in aux/source_assets/js/plots.js and 2 other locations - About 1 day to fix
    aux/source_assets/js/plots.js on lines 342..357
    aux/source_assets/js/plots.js on lines 682..696

    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 223.

    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 3 locations. Consider refactoring.
    Open

        for (var j = 0; j < footer.length; j++) {
      var footer_array = footer[j].split(",");
      svg.append("rect")
           .attr("x", (width-total_len)/2 + offset)
           .attr("y", -30)
    Severity: Major
    Found in aux/source_assets/js/plots.js and 2 other locations - About 1 day to fix
    aux/source_assets/js/plots.js on lines 342..357
    aux/source_assets/js/plots.js on lines 798..812

    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 223.

    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

        alldata.map( function(data) {
      svg.selectAll(".bar")
         .data(data)
         .enter().append("rect")
                 .attr("x", function(d) { return x(d.key); })
    Severity: Major
    Found in aux/source_assets/js/plots.js and 1 other location - About 7 hrs to fix
    aux/source_assets/js/plots.js on lines 308..317

    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 191.

    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

          alldata.map( function(data) {
        svg.selectAll(".bar")
          .data(data)
          .enter().append("rect")
            .attr("x", function(d) { return x(d.key); })
    Severity: Major
    Found in aux/source_assets/js/plots.js and 1 other location - About 7 hrs to fix
    aux/source_assets/js/plots.js on lines 427..436

    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 191.

    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

        if (yValues !== null){
      svg.append("g")
           .attr("class", "y axis")
           .call(yAxis.ticks(yValues.length)
                      .tickFormat(function() {
    Severity: Major
    Found in aux/source_assets/js/plots.js and 1 other location - About 6 hrs to fix
    aux/source_assets/js/plots.js on lines 618..644

    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 156.

    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

        if (yValues !== null){
      svg.append("g")
           .attr("class", "y axis")
           .call(yAxis.ticks(yValues.length)
                      .tickFormat(function() {
    Severity: Major
    Found in aux/source_assets/js/plots.js and 1 other location - About 6 hrs to fix
    aux/source_assets/js/plots.js on lines 753..779

    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 156.

    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.selectAll(".dot")
       .data(data)
       .enter().append("line")
                 .attr("x1", function(d) { return x(d.start); })
                 .attr("y1", function(d) { return y(d.y); })
    Severity: Major
    Found in aux/source_assets/js/plots.js and 1 other location - About 5 hrs to fix
    aux/source_assets/js/plots.js on lines 646..653

    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 141.

    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.selectAll(".dot")
         .data(data)
      .enter().append("line")
              .attr("x1", function(d) { return x(d.start); })
              .attr("y1", function(d) { return y(d.y); })
    Severity: Major
    Found in aux/source_assets/js/plots.js and 1 other location - About 5 hrs to fix
    aux/source_assets/js/plots.js on lines 781..788

    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 141.

    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

    Function plot_lines has 121 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

      GV.plot_lines = function (data, target, title, footer, xTitle, yTitle, no_lines, yValues) {
    var margin = {top: 70, right: 50, bottom: 75, left: 50},
    width = 600 - margin.left - margin.right,
    height = 500 - margin.top - margin.bottom;
    Severity: Major
    Found in aux/source_assets/js/plots.js - About 4 hrs to fix

      Identical blocks of code found in 4 locations. Consider refactoring.
      Open

          var svg = d3.select("#".concat(target)).append("svg")
      .attr("width", width + margin.left + margin.right)
      .attr("height", height + margin.top + margin.bottom)
      .append("g")
      .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
      Severity: Major
      Found in aux/source_assets/js/plots.js and 3 other locations - About 4 hrs to fix
      aux/source_assets/js/plots.js on lines 366..370
      aux/source_assets/js/plots.js on lines 464..468
      aux/source_assets/js/plots.js on lines 589..593

      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 122.

      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 4 locations. Consider refactoring.
      Open

          var svg = d3.select("#".concat(target)).append("svg")
                .attr("width", width + margin.left + margin.right)
                .attr("height", height + margin.top + margin.bottom)
                .append("g")
                .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
      Severity: Major
      Found in aux/source_assets/js/plots.js and 3 other locations - About 4 hrs to fix
      aux/source_assets/js/plots.js on lines 240..244
      aux/source_assets/js/plots.js on lines 366..370
      aux/source_assets/js/plots.js on lines 464..468

      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 122.

      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 4 locations. Consider refactoring.
      Open

          var svg = d3.select("#".concat(target)).append("svg")
                  .attr("width", width + margin.left + margin.right)
                  .attr("height", height + margin.top + margin.bottom)
                  .append("g")
                  .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
      Severity: Major
      Found in aux/source_assets/js/plots.js and 3 other locations - About 4 hrs to fix
      aux/source_assets/js/plots.js on lines 240..244
      aux/source_assets/js/plots.js on lines 366..370
      aux/source_assets/js/plots.js on lines 589..593

      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 122.

      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 4 locations. Consider refactoring.
      Open

          var svg = d3.select("#".concat(target)).append("svg")
      .attr("width", width + margin.left + margin.right)
      .attr("height", height + margin.top + margin.bottom)
      .append("g")
        .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
      Severity: Major
      Found in aux/source_assets/js/plots.js and 3 other locations - About 4 hrs to fix
      aux/source_assets/js/plots.js on lines 240..244
      aux/source_assets/js/plots.js on lines 464..468
      aux/source_assets/js/plots.js on lines 589..593

      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 122.

      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.append("g")
         .attr("class", "x axis")
         .attr("transform", "translate(0," + (height + height/no_lines) + ")")
         .call(xAxis)
       .append("text")
      Severity: Major
      Found in aux/source_assets/js/plots.js and 1 other location - About 4 hrs to fix
      aux/source_assets/js/plots.js on lines 742..751

      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 121.

      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.append("g")
         .attr("class", "x axis")
         .attr("transform", "translate(0," + (height+height/no_lines) + ")")
         .call(xAxis)
       .append("text")
      Severity: Major
      Found in aux/source_assets/js/plots.js and 1 other location - About 4 hrs to fix
      aux/source_assets/js/plots.js on lines 607..616

      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 121.

      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

      Function plot_bars has 104 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

        GV.plot_bars = function (alldata, target, title, footer, xTitle, yTitle, bar) {
    var margin = {top: 70, right: 50, bottom: 75, left: 50},
      width = 600 - margin.left - margin.right,
      height = 500 - margin.top - margin.bottom;
      Severity: Major
      Found in aux/source_assets/js/plots.js - About 4 hrs to fix

        Method hierarchical_clusterization has a Cognitive Complexity of 28 (exceeds 5 allowed). Consider refactoring.
        Open

            def hierarchical_clusterization(no_clusters = 0, distance_method = 0,
                                    vec = @values, debug = false)
      clusters = []
      vec = vec.sort
        Severity: Minor
        Found in lib/genevalidator/clusterization.rb - About 4 hrs 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 plot_scatter has 98 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

          GV.plot_scatter = function (data, target, title, footer, xTitle, yTitle, yLine, slope) {
    var margin = {top: 50, right: 30, bottom: 75, left: 50},
    width = 500 - margin.left - margin.right,
    height = 500 - margin.top - margin.bottom;
        Severity: Major
        Found in aux/source_assets/js/plots.js - About 3 hrs to fix
          Severity
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