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wilzbach/msa

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Showing 149 of 149 total issues

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

xhr("./data/fer1.gff3", 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 45..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 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

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

    this.listenTo(this.g.zoomer, "change:rowHeight", function() {
      return this.el.style.height = this.g.zoomer.get("rowHeight") + "px";
    });
Severity: Minor
Found in src/views/labels/LabelRowView.js and 1 other location - About 30 mins to fix
src/views/labels/LabelBlock.js on lines 59..61

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

Function _endSelection has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  _endSelection: function(dragEnd) {
    // remove listeners
    jbone(document.body).off('.overmove');
    jbone(document.body).off('.overup');
Severity: Minor
Found in src/views/OverviewBox.js - About 25 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 _reduceColumns has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  _reduceColumns: function() {
    return this.each(function(el, index, arr) {
      const cols = filter(arr, (el) => el.get('type') === 'column');
      const xStart = el.get('xStart');
      const xEnd = el.get('xEnd');
Severity: Minor
Found in src/g/selection/SelectionCol.js - About 25 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 draw has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  draw: function() {

    this.removeViews();

    this.addView("stage",new Stage({model: this.seqs, g: this.g}));
Severity: Minor
Found in src/msa.js - About 25 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 importFile has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  importFile: function(file, opt) {
    opt = opt || {};
    opt.name = file.name;
    var fileName;
    var [objs, type] = this.parseText(file, opt);
Severity: Minor
Found in src/utils/file.js - About 25 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 _proxyToG has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  _proxyToG: function(key) {
    return this.listenTo(this.g[key], "all",function(name,prev,now,opts) {
      // suppress duplicate events
      if (name === "change") { return; }
      // backbone uses the second argument for the next value -> swap
Severity: Minor
Found in src/msa.js - About 25 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 drawSeq has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  drawSeq: function(data, callback) {
    const seq = data.model.get("seq");
    const y = data.yPos;
    const rectWidth = this.rectWidth;
    const rectHeight = this.rectHeight;
Severity: Minor
Found in src/views/canvas/CanvasSeqDrawer.js - About 25 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

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