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Function _onmousemove has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
Open

  _onmousemove: function(e, reversed) {
    if (this.dragStart.length === 0) { return; }

    const dragEnd = mouse.abs(e);
    // relative to first click
Severity: Minor
Found in src/views/canvas/CanvasSeqBlock.js - About 1 hr 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

    for (var i = 0; i <= 1; i++) {
      rect[1][i] = this.coords.screen_to_model(rect[1][i], 'y');
    }
Severity: Major
Found in src/views/OverviewBox.js and 1 other location - About 1 hr to fix
src/views/OverviewBox.js on lines 247..249

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 63.

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 (0 <= maxLen) {
            while (i1 <= maxLen) {
              result.push(i1++);
            }
          } else {
Severity: Major
Found in src/g/selection/SelectionCol.js and 1 other location - About 1 hr to fix
src/menu/views/SelectionMenu.js on lines 22..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 63.

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

    for (var i = 0; i <= 1; i++) {
      rect[0][i] = this.coords.screen_to_model(rect[0][i], 'x');
    }
Severity: Major
Found in src/views/OverviewBox.js and 1 other location - About 1 hr to fix
src/views/OverviewBox.js on lines 252..254

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 63.

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

    while (counter < clickedRows && i < this.model.length) {
      counter += this.model.at(i).attributes.height || 1;
      i++;
    }
Severity: Major
Found in src/views/canvas/CanvasSeqDrawer.js and 1 other location - About 1 hr to fix
src/views/canvas/CanvasSeqDrawer.js on lines 74..77

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 63.

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 (0 <= end) {
          while (i <= end) {
            result.push(i++);
          }
        } else {
Severity: Major
Found in src/menu/views/SelectionMenu.js and 1 other location - About 1 hr to fix
src/g/selection/SelectionCol.js on lines 73..81

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 63.

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

    while (counter < start && i < this.model.length) {
      counter += this.model.at(i).attributes.height || 1;
      i++;
    }
Severity: Major
Found in src/views/canvas/CanvasSeqDrawer.js and 1 other location - About 1 hr to fix
src/views/canvas/CanvasSeqDrawer.js on lines 90..93

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 63.

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 34 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  render: function() {
    var gaps = this.g.stats.gaps();

    dom.removeAllChilds(this.el);
Severity: Minor
Found in src/views/header/GapView.js - About 1 hr to fix

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

        models.push({text: "Label " + arrowDown, comparator: function(a, b) {
        return - a.get("name").localeCompare(b.get("name"));
    }});
    Severity: Major
    Found in src/menu/views/OrderingMenu.js and 1 other location - About 1 hr to fix
    src/menu/views/OrderingMenu.js on lines 73..75

    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 62.

    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

        models.push({text: "Seq " + arrowDown, comparator: function(a,b) {
        return - a.get("seq").localeCompare(b.get("seq"));
    }});
    Severity: Major
    Found in src/menu/views/OrderingMenu.js and 1 other location - About 1 hr to fix
    src/menu/views/OrderingMenu.js on lines 67..69

    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 62.

    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 _appendSelection has 33 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

      _appendSelection: function(data) {
    const seq = data.model.get("seq");
    const selection = this._getSelection(data.model);
    // get the status of the upper and lower row
    const getNextPrev= this._getPrevNextSelection(data.model);
    Severity: Minor
    Found in src/views/canvas/CanvasSelection.js - About 1 hr to fix

      Function render has 33 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

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

    const fontSize = this.g.zoomer.get("markerFontsize");
    const cellWidth = this.g.zoomer.get("columnWidth");
      Severity: Minor
      Found in src/views/header/MarkerView.js - About 1 hr to fix

        Function render has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
        Open

          render: function() {
    var gaps = this.g.stats.gaps();

    dom.removeAllChilds(this.el);
        Severity: Minor
        Found in src/views/header/GapView.js - About 1 hr 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

          initialize: function(data) {
    this.g = data.g;
    this.el.style.display = "inline-block";
    return this.msa = data.msa;
  },
        Severity: Major
        Found in src/menu/views/ExtraMenu.js and 1 other location - About 1 hr to fix
        src/menu/views/ImportMenu.js on lines 6..10

        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 60.

        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

              for (var i = 0; 0 < end ? i <= end : i >= end; 0 < end ? i++ : i--) {
        avgHeight += conserv[n];
      }
        Severity: Major
        Found in src/views/header/ConservationView.js and 1 other location - About 1 hr to fix
        src/views/header/GapView.js on lines 46..48

        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 60.

        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;
    this.el.style.display = "inline-block";
    return this.msa = data.msa;
  },
        Severity: Major
        Found in src/menu/views/ImportMenu.js and 1 other location - About 1 hr to fix
        src/menu/views/ExtraMenu.js on lines 8..12

        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 60.

        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 joinCb has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
        Open

          joinCb: function(retCb, finalLength, finalScope) {
    finalLength = finalLength || 1;
    var cbsFinished = 0;

    var callbackWrapper = function(cb, scope) {
        Severity: Minor
        Found in src/utils/loader.js - About 1 hr 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

              for (var i = 0; 0 < end ? i <= end : i >= end; 0 < end ? i++ : i--) {
        avgHeight += gaps[n];
      }
        Severity: Major
        Found in src/views/header/GapView.js and 1 other location - About 1 hr to fix
        src/views/header/ConservationView.js on lines 99..101

        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 60.

        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 drawFeature has 31 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

          drawFeature: function(data) {
    var seq = data.model.get("seq");
    var rectWidth = this.g.zoomer.get("columnWidth");
    var rectHeight = this.g.zoomer.get("rowHeight");
        Severity: Minor
        Found in src/views/FeatureBlock.js - About 1 hr to fix

          Function _onmousemove has 31 lines of code (exceeds 25 allowed). Consider refactoring.
          Open

            _onmousemove: function(e, reversed) {
    if (this.dragStart.length === 0) { return; }

    const dragEnd = mouse.abs(e);
    // relative to first click
          Severity: Minor
          Found in src/views/canvas/CanvasSeqBlock.js - About 1 hr to fix
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