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Avoid deeply nested control flow statements.
Open

            if (showLowerCase) { c = c.toUpperCase(); }
Severity: Major
Found in src/views/OverviewBox.js - About 45 mins to fix

    Avoid deeply nested control flow statements.
    Open

                if (seq_hidden[i]) {
              colors.push("grey");
              continue;
            }
    Severity: Major
    Found in src/views/OverviewBox.js - About 45 mins to fix

      Avoid deeply nested control flow statements.
      Open

                  if ((typeof color !== "undefined" && color !== null)) {
              colors.push(color);
            }
      Severity: Major
      Found in src/views/OverviewBox.js - About 45 mins to fix

        Function invertCol has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
        Open

          invertCol: function(columns) {
    const selColumns = this.where({type:"column"}).reduce((memo,el) => {
      return memo.concat(((() => {
        const result = [];
        let i = el.attributes.xStart;
        Severity: Minor
        Found in src/g/selection/SelectionCol.js - About 45 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 getMinRows has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
        Open

          getMinRows: function() {

    const len = (this.max(function(el) { return el.get("xEnd"); })).attributes.xEnd;
    const rows = ((() => {
      const result = [];
        Severity: Minor
        Found in src/model/FeatureCol.js - About 45 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 markerHidden has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
        Open

          markerHidden: function(n,stepSize) {
    const hidden = this.g.columns.get("hidden").slice(0);

    const min = Math.max(0, n - stepSize);
    let prevHidden = true;
        Severity: Minor
        Found in src/views/header/MarkerView.js - About 45 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 _drawSelection has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
        Open

          _drawSelection: function() {
    // hide during selection
    if (this.dragStart.length > 0 && !this.prolongSelection) { return; }

    this.ctx.fillStyle = "#666666";
        Severity: Minor
        Found in src/views/OverviewBox.js - About 45 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

        Avoid deeply nested control flow statements.
        Open

                    if (hidden.indexOf(j) >= 0) {
              color = "grey";
            }
        Severity: Major
        Found in src/views/OverviewBox.js - About 45 mins to fix

          Function assignRows has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
          Open

            assignRows: function() {

    const len = (this.max(function(el) { return el.get("xEnd"); })).attributes.xEnd;
    const rows = (() => {
      const result = [];
          Severity: Minor
          Found in src/model/FeatureCol.js - About 45 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

              this.listenTo(this.g.columns, "change:hidden", function() {
      this.draw();
      return this.render();
    });
          Severity: Minor
          Found in src/views/header/RightHeaderBlock.js and 1 other location - About 40 mins to fix
          src/views/header/SeqLogoWrapper.js on lines 24..27

          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 48.

          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

              this.listenTo(this.g.stats, "reset", function() {
      this.draw();
      return this.render();
    });
          Severity: Minor
          Found in src/views/header/SeqLogoWrapper.js and 1 other location - About 40 mins to fix
          src/views/header/RightHeaderBlock.js on lines 23..26

          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 48.

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

            calcHiddenSeqs: function(n) {
    let nNew = n;
    for (let i = 0; 0 < nNew ? i <= nNew : i >= nNew; 0 < nNew ? i++ : i--) {
      if (this.at(i).get("hidden")) {
        nNew++;
          Severity: Minor
          Found in src/model/SeqCollection.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 drawSeqs has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
          Open

            drawSeqs: function(callback, target) {
    const hidden = this.g.columns.get("hidden");

    target = target || this;
          Severity: Minor
          Found in src/views/canvas/CanvasSeqDrawer.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

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

              this.dragStartScroll = [this.g.zoomer.get('_alignmentScrollLeft'), this.g.zoomer.get('_alignmentScrollTop')];
          Severity: Minor
          Found in src/views/canvas/CanvasSeqBlock.js and 1 other location - About 35 mins to fix
          src/views/canvas/CanvasSeqBlock.js on lines 248..248

          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 46.

          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

              this.dragStartScroll = [this.g.zoomer.get('_alignmentScrollLeft'), this.g.zoomer.get('_alignmentScrollTop')];
          Severity: Minor
          Found in src/views/canvas/CanvasSeqBlock.js and 1 other location - About 35 mins to fix
          src/views/canvas/CanvasSeqBlock.js on lines 258..258

          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 46.

          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

          xhr("./data/fer1.gff_jalview", function(err, request, body) {
  var features = gffParser.parseSeqs(body);
  m.seqs.addFeatures(features);
});
          Severity: Minor
          Found in snippets/fer1_annoted.js and 1 other location - About 30 mins to fix
          snippets/fer1_annoted.js on lines 40..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 45.

          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 (this.g.vis.get("labels")) {
      this.el.appendChild(this.labelDOM());
    }
          Severity: Minor
          Found in src/views/header/LabelHeader.js and 1 other location - About 30 mins to fix
          src/views/header/LabelHeader.js on lines 28..30

          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 45.

          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 (this.g.vis.get("metacell")) {
      this.el.appendChild(this.metaDOM());
    }
          Severity: Minor
          Found in src/views/header/LabelHeader.js and 1 other location - About 30 mins to fix
          src/views/header/LabelHeader.js on lines 24..26

          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 45.

          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

            initialize: function(data) {
    this.g = data.g;
    return this.el.style.display = "inline-block";
  },
          Severity: Minor
          Found in src/menu/views/FilterMenu.js and 1 other location - About 30 mins to fix
          src/menu/views/DebugMenu.js on lines 5..8

          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 45.

          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

            _setHeight: function() {
    return this.el.style.height = this.g.zoomer.get("alignmentHeight") + "px";
  }
          Severity: Minor
          Found in src/views/labels/LabelBlock.js and 1 other location - About 30 mins to fix
          src/views/labels/LabelRowView.js on lines 13..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 45.

          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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