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

    const rows = (() => {
      const result = [];
      for (let x = 0; 0 < len ? x <= len : x >= len; 0 < len ? x++ : x--) {
        result.push(0);
      }
Severity: Major
Found in src/model/FeatureCol.js and 1 other location - About 2 hrs to fix
src/model/FeatureCol.js on lines 77..83

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 86.

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

    const rows = ((() => {
      const result = [];
      for (let x = 0; 0 < len ? x <= len : x >= len; 0 < len ? x++ : x--) {
        result.push(0);
      }
Severity: Major
Found in src/model/FeatureCol.js and 1 other location - About 2 hrs to fix
src/model/FeatureCol.js on lines 43..49

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 86.

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

gulp.task('build-gzip-css', ['min-css'], function() {
  return gulp.src(path.join(buildDir, "msa.min.css"))
    .pipe(gzip({append: false, gzipOptions: { level: 9 }}))
    .pipe(rename("msa.min.gz.css"))
    .pipe(gulp.dest(buildDir));
Severity: Major
Found in gulpfile.js and 1 other location - About 2 hrs to fix
gulpfile.js on lines 38..43

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 83.

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

gulp.task('build-gzip-js', function() {
   return gulp.src(path.join(buildDir, "msa.js"))
     .pipe(gzip({append: false, gzipOptions: { level: 9 }}))
     .pipe(rename("msa.min.gz.js"))
     .pipe(gulp.dest(buildDir));
Severity: Major
Found in gulpfile.js and 1 other location - About 2 hrs to fix
gulpfile.js on lines 44..49

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 83.

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 initialize has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
Open

  initialize: function(data) {

    if (!(typeof data !== "undefined" && data !== null)) { data = {}; }
    // check for default arrays
    if (!(data.colorscheme != null)) { data.colorscheme = {}; }
Severity: Minor
Found in src/msa.js - About 2 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 getComparators has 56 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  getComparators: function() {
    var models = [];

    models.push({text: "ID " + arrowUp, comparator: "id"});
Severity: Major
Found in src/menu/views/OrderingMenu.js - About 2 hrs to fix

    Function showTree has 54 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

        showTree: function(newickStr) {
      var newick = window.require("biojs-io-newick");
      var mt = window.require("msa-tnt");

      if (typeof newickStr === "string") {
    Severity: Major
    Found in src/utils/tree.js - About 2 hrs to fix

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

          if (this.g.vis.get("seqlogo")) {
      var seqlogo = new SeqLogoWrapper({model: this.model, g: this.g});
      seqlogo.ordering = -30;
      this.addView("seqlogo",seqlogo);
    }
      Severity: Major
      Found in src/views/header/RightHeaderBlock.js and 2 other locations - About 2 hrs to fix
      src/views/header/RightHeaderBlock.js on lines 39..43
      src/views/header/RightHeaderBlock.js on lines 45..49

      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 78.

      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

          if (this.g.vis.get("conserv")) {
      var conserv = new ConservationView({model: this.model, g: this.g});
      conserv.ordering = -20;
      this.addView("conserv",conserv);
    }
      Severity: Major
      Found in src/views/header/RightHeaderBlock.js and 2 other locations - About 2 hrs to fix
      src/views/header/RightHeaderBlock.js on lines 45..49
      src/views/header/RightHeaderBlock.js on lines 51..55

      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 78.

      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

          if (this.g.vis.get("markers")) {
      var marker = new MarkerView({model: this.model, g: this.g});
      marker.ordering = -10;
      this.addView("marker",marker);
    }
      Severity: Major
      Found in src/views/header/RightHeaderBlock.js and 2 other locations - About 2 hrs to fix
      src/views/header/RightHeaderBlock.js on lines 39..43
      src/views/header/RightHeaderBlock.js on lines 51..55

      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 78.

      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 getComparators has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
      Open

        getComparators: function() {
    var models = [];

    models.push({text: "ID " + arrowUp, comparator: "id"});
      Severity: Minor
      Found in src/menu/views/OrderingMenu.js - About 2 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 render has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
      Open

        render: function() {
    dom.removeAllChilds(this.el);

    this.el.style.display = "inline-block";
      Severity: Minor
      Found in src/views/labels/MetaView.js - About 2 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

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

          if (true) {
      var headerblock = new HeaderBlock({model: this.model, g: this.g});
      headerblock.ordering = this.g.visorder.get('headerBox');
      this.addView("headerBox", headerblock);
    }
      Severity: Major
      Found in src/views/Stage.js and 1 other location - About 2 hrs to fix
      src/views/Stage.js on lines 55..59

      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 76.

      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

        initialize: function(data) {
    this.g = data.g;
    this.listenTo(this.g.vis, "change:metacell", this.render);
    return this.listenTo(this.g.zoomer, "change:metaWidth", this.render);
  },
      Severity: Major
      Found in src/views/labels/MetaView.js and 1 other location - About 2 hrs to fix
      src/views/header/LabelHeader.js on lines 9..14

      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 76.

      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

        initialize: function(data) {
    this.g = data.g;

    this.listenTo(this.g.vis, "change:metacell change:labels", this.render);
    return this.listenTo(this.g.zoomer, "change:labelWidth change:metaWidth", this.render);
      Severity: Major
      Found in src/views/header/LabelHeader.js and 1 other location - About 2 hrs to fix
      src/views/labels/MetaView.js on lines 11..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 76.

      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 (true) {
      var searchblock = new Search({model: this.model, g: this.g});
      searchblock.ordering = this.g.visorder.get('searchBox');
      this.addView("searchbox", searchblock);
    }
      Severity: Major
      Found in src/views/Stage.js and 1 other location - About 2 hrs to fix
      src/views/Stage.js on lines 49..53

      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 76.

      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 initialize has 51 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

        initialize: function(data) {

    if (!(typeof data !== "undefined" && data !== null)) { data = {}; }
    // check for default arrays
    if (!(data.colorscheme != null)) { data.colorscheme = {}; }
      Severity: Major
      Found in src/msa.js - About 2 hrs to fix

        Function _renderSelection has 50 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

          _renderSelection: function(data) {

    let xZero = data.xZero;
    const yZero = data.yZero;
    const n = data.n;
        Severity: Minor
        Found in src/views/canvas/CanvasSelection.js - About 2 hrs to fix

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

            hide: function() {
    this.isVisible = false;
    this.$el.find(".msa-scale-minimised").removeClass(this.toggleClass);
    this.$el.find(".msa-scale-maximised").addClass(this.toggleClass);
  },
          Severity: Major
          Found in src/views/ScaleSlider.js and 1 other location - About 2 hrs to fix
          src/views/ScaleSlider.js on lines 94..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

          Function render has 50 lines of code (exceeds 25 allowed). Consider refactoring.
          Open

            render: function() {
    var conserv = this.g.stats.scale(this.g.stats.conservation());

    dom.removeAllChilds(this.el);
          Severity: Minor
          Found in src/views/header/ConservationView.js - About 2 hrs to fix
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