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public/javascripts/d3.phylogram.js

Summary

Maintainability
D
2 days
Test Coverage

Function build has 107 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  d3.phylogram.build = function(selector, nodes, options) {
    options = options || {}
    var w = options.width || d3.select(selector).style('width') || d3.select(selector).attr('width'),
        h = options.height || d3.select(selector).style('height') || d3.select(selector).attr('height'),
        w = parseInt(w),
Severity: Major
Found in public/javascripts/d3.phylogram.js - About 4 hrs to fix

    File d3.phylogram.js has 261 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    /*
d3.phylogram.js
Wrapper around a d3-based phylogram (tree where branch lengths are scaled)
Also includes a radial dendrogram visualization (branch lengths not scaled)
along with some helper methods for building angled-branch trees.
    Severity: Minor
    Found in public/javascripts/d3.phylogram.js - About 2 hrs to fix

      Function buildRadial has 43 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

        d3.phylogram.buildRadial = function(selector, nodes, options) {
    options = options || {}
    var w = options.width || d3.select(selector).style('width') || d3.select(selector).attr('width'),
        r = w / 2,
        labelWidth = options.skipLabels ? 10 : options.labelWidth || 120;
      Severity: Minor
      Found in public/javascripts/d3.phylogram.js - About 1 hr to fix

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

              vis.selectAll('g.leaf.node').append("svg:text")
        .attr("dx", 8)
        .attr("dy", 3)
        .attr("text-anchor", "start")
        .attr('font-family', 'Helvetica Neue, Helvetica, sans-serif')
        Severity: Major
        Found in public/javascripts/d3.phylogram.js and 1 other location - About 2 hrs to fix
        public/javascripts/d3.phylogram.js on lines 257..264

        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

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

              vis.selectAll('g.leaf.node').append("svg:text")
        .attr("dx", 8)
        .attr("dy", 3)
        .attr("text-anchor", "start")
        .attr('font-family', 'Helvetica Neue, Helvetica, sans-serif')
        Severity: Major
        Found in public/javascripts/d3.phylogram.js and 1 other location - About 2 hrs to fix
        public/javascripts/d3.phylogram.js on lines 277..284

        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

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

              vis.selectAll('g.inner.node')
        .append("svg:text")
          .attr("dx", -6)
          .attr("dy", -6)
          .attr("text-anchor", 'end')
        Severity: Major
        Found in public/javascripts/d3.phylogram.js and 1 other location - About 1 hr to fix
        public/javascripts/d3.phylogram.js on lines 268..275

        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 71.

        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

              vis.selectAll('g.inner.node')
        .append("svg:text")
          .attr("dx", -6)
          .attr("dy", -6)
          .attr("text-anchor", 'end')
        Severity: Major
        Found in public/javascripts/d3.phylogram.js and 1 other location - About 1 hr to fix
        public/javascripts/d3.phylogram.js on lines 248..255

        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 71.

        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

            var vis = options.vis || d3.select(selector).append("svg:svg")
        .attr("width", w + 300)
        .attr("height", h + 30)
      .append("svg:g")
        .attr("transform", "translate(20, 20)");
        Severity: Major
        Found in public/javascripts/d3.phylogram.js and 1 other location - About 1 hr to fix
        public/javascripts/d3.phylogram.js on lines 296..300

        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 56.

        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

            var vis = d3.select(selector).append("svg:svg")
        .attr("width", r * 2)
        .attr("height", r * 2)
      .append("svg:g")
        .attr("transform", "translate(" + r + "," + r + ")");
        Severity: Major
        Found in public/javascripts/d3.phylogram.js and 1 other location - About 1 hr to fix
        public/javascripts/d3.phylogram.js on lines 182..186

        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 56.

        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

            vis.selectAll('g.leaf.node')
      .append("svg:circle")
        .attr("r", 4.5)
        .attr('stroke', 'yellowGreen')
        .attr('fill', 'greenYellow')
        Severity: Major
        Found in public/javascripts/d3.phylogram.js and 1 other location - About 1 hr to fix
        public/javascripts/d3.phylogram.js on lines 137..142

        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 55.

        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

            vis.selectAll('g.root.node')
      .append('svg:circle')
        .attr("r", 4.5)
        .attr('fill', 'steelblue')
        .attr('stroke', '#369')
        Severity: Major
        Found in public/javascripts/d3.phylogram.js and 1 other location - About 1 hr to fix
        public/javascripts/d3.phylogram.js on lines 130..135

        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 55.

        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

                h = options.height || d3.select(selector).style('height') || d3.select(selector).attr('height'),
        Severity: Major
        Found in public/javascripts/d3.phylogram.js and 2 other locations - About 40 mins to fix
        public/javascripts/d3.phylogram.js on lines 171..171
        public/javascripts/d3.phylogram.js on lines 292..292

        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 49.

        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

            var w = options.width || d3.select(selector).style('width') || d3.select(selector).attr('width'),
        Severity: Major
        Found in public/javascripts/d3.phylogram.js and 2 other locations - About 40 mins to fix
        public/javascripts/d3.phylogram.js on lines 172..172
        public/javascripts/d3.phylogram.js on lines 292..292

        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 49.

        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

            var w = options.width || d3.select(selector).style('width') || d3.select(selector).attr('width'),
        Severity: Major
        Found in public/javascripts/d3.phylogram.js and 2 other locations - About 40 mins to fix
        public/javascripts/d3.phylogram.js on lines 171..171
        public/javascripts/d3.phylogram.js on lines 172..172

        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 49.

        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

              vis.selectAll("text.rule")
          .data(yscale.ticks(10))
        .enter().append("svg:text")
          .attr("class", "rule")
        Severity: Minor
        Found in public/javascripts/d3.phylogram.js and 1 other location - About 30 mins to fix
        public/javascripts/d3.phylogram.js on lines 198..201

        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

              vis.selectAll('line')
          .data(yscale.ticks(10))
        .enter().append('svg:line')
          .attr('y1', 0)
        Severity: Minor
        Found in public/javascripts/d3.phylogram.js and 1 other location - About 30 mins to fix
        public/javascripts/d3.phylogram.js on lines 207..210

        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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