KarrLab/SynNetGen

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Showing 39 of 39 total issues

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

<?php
/******************************************************************************
 *
 * $Id:$
 *
Severity: Major
Found in lib/m2html/templates/blue/doxysearch.php and 2 other locations - About 1 wk to fix
lib/m2html/templates/brain/doxysearch.php on lines 1..329
lib/m2html/templates/frame/doxysearch.php on lines 1..329

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 2233.

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 3 locations. Consider refactoring.
Open

<?php
/******************************************************************************
 *
 * $Id:$
 *
Severity: Major
Found in lib/m2html/templates/brain/doxysearch.php and 2 other locations - About 1 wk to fix
lib/m2html/templates/blue/doxysearch.php on lines 1..329
lib/m2html/templates/frame/doxysearch.php on lines 1..329

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 2233.

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 3 locations. Consider refactoring.
Open

<?php
/******************************************************************************
 *
 * $Id:$
 *
Severity: Major
Found in lib/m2html/templates/frame/doxysearch.php and 2 other locations - About 1 wk to fix
lib/m2html/templates/blue/doxysearch.php on lines 1..329
lib/m2html/templates/brain/doxysearch.php on lines 1..329

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 2233.

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 search has a Cognitive Complexity of 33 (exceeds 5 allowed). Consider refactoring.
Open

function search($file,$word,&$statsList)
{
  $index = computeIndex($word);
  if ($index!=-1) // found a valid index
  {
Severity: Minor
Found in lib/m2html/templates/frame/doxysearch.php - About 4 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 filter_results has a Cognitive Complexity of 33 (exceeds 5 allowed). Consider refactoring.
Open

function filter_results($docs,&$requiredWords,&$forbiddenWords)
{
  $filteredDocs=array();
  while (list ($key, $val) = each ($docs)) 
  {
Severity: Minor
Found in lib/m2html/templates/frame/doxysearch.php - About 4 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 filter_results has a Cognitive Complexity of 33 (exceeds 5 allowed). Consider refactoring.
Open

function filter_results($docs,&$requiredWords,&$forbiddenWords)
{
  $filteredDocs=array();
  while (list ($key, $val) = each ($docs)) 
  {
Severity: Minor
Found in lib/m2html/templates/blue/doxysearch.php - About 4 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 filter_results has a Cognitive Complexity of 33 (exceeds 5 allowed). Consider refactoring.
Open

function filter_results($docs,&$requiredWords,&$forbiddenWords)
{
  $filteredDocs=array();
  while (list ($key, $val) = each ($docs)) 
  {
Severity: Minor
Found in lib/m2html/templates/brain/doxysearch.php - About 4 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 search has a Cognitive Complexity of 33 (exceeds 5 allowed). Consider refactoring.
Open

function search($file,$word,&$statsList)
{
  $index = computeIndex($word);
  if ($index!=-1) // found a valid index
  {
Severity: Minor
Found in lib/m2html/templates/brain/doxysearch.php - About 4 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 search has a Cognitive Complexity of 33 (exceeds 5 allowed). Consider refactoring.
Open

function search($file,$word,&$statsList)
{
  $index = computeIndex($word);
  if ($index!=-1) // found a valid index
  {
Severity: Minor
Found in lib/m2html/templates/blue/doxysearch.php - About 4 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

File doxysearch.php has 289 lines of code (exceeds 250 allowed). Consider refactoring.
Open

<?php
/******************************************************************************
 *
 * $Id:$
 *
Severity: Minor
Found in lib/m2html/templates/brain/doxysearch.php - About 2 hrs to fix

    File doxysearch.php has 289 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    <?php
    /******************************************************************************
     *
     * $Id:$
     *
    Severity: Minor
    Found in lib/m2html/templates/frame/doxysearch.php - About 2 hrs to fix

      File doxysearch.php has 289 lines of code (exceeds 250 allowed). Consider refactoring.
      Open

      <?php
      /******************************************************************************
       *
       * $Id:$
       *
      Severity: Minor
      Found in lib/m2html/templates/blue/doxysearch.php - About 2 hrs to fix

        Method search has 62 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

        function search($file,$word,&$statsList)
        {
          $index = computeIndex($word);
          if ($index!=-1) // found a valid index
          {
        Severity: Major
        Found in lib/m2html/templates/frame/doxysearch.php - About 2 hrs to fix

          Method search has 62 lines of code (exceeds 25 allowed). Consider refactoring.
          Open

          function search($file,$word,&$statsList)
          {
            $index = computeIndex($word);
            if ($index!=-1) // found a valid index
            {
          Severity: Major
          Found in lib/m2html/templates/blue/doxysearch.php - About 2 hrs to fix

            Method search has 62 lines of code (exceeds 25 allowed). Consider refactoring.
            Open

            function search($file,$word,&$statsList)
            {
              $index = computeIndex($word);
              if ($index!=-1) // found a valid index
              {
            Severity: Major
            Found in lib/m2html/templates/brain/doxysearch.php - About 2 hrs to fix

              Method main has 41 lines of code (exceeds 25 allowed). Consider refactoring.
              Open

              function main($idxfile)
              {
                if(strcmp('4.1.0', phpversion()) > 0) 
                {
                  die("Error: PHP version 4.1.0 or above required!");
              Severity: Minor
              Found in lib/m2html/templates/brain/doxysearch.php - About 1 hr to fix

                Method main has 41 lines of code (exceeds 25 allowed). Consider refactoring.
                Open

                function main($idxfile)
                {
                  if(strcmp('4.1.0', phpversion()) > 0) 
                  {
                    die("Error: PHP version 4.1.0 or above required!");
                Severity: Minor
                Found in lib/m2html/templates/blue/doxysearch.php - About 1 hr to fix

                  Method main has 41 lines of code (exceeds 25 allowed). Consider refactoring.
                  Open

                  function main($idxfile)
                  {
                    if(strcmp('4.1.0', phpversion()) > 0) 
                    {
                      die("Error: PHP version 4.1.0 or above required!");
                  Severity: Minor
                  Found in lib/m2html/templates/frame/doxysearch.php - About 1 hr to fix

                    Method report_results has 38 lines of code (exceeds 25 allowed). Consider refactoring.
                    Open

                    function report_results(&$docs)
                    {
                      echo "<table cellspacing=\"2\">\n";
                      echo "  <tr>\n";
                      echo "    <td colspan=\"2\"><h2>Search Results</h2></td>\n";
                    Severity: Minor
                    Found in lib/m2html/templates/blue/doxysearch.php - About 1 hr to fix

                      Method report_results has 38 lines of code (exceeds 25 allowed). Consider refactoring.
                      Open

                      function report_results(&$docs)
                      {
                        echo "<table cellspacing=\"2\">\n";
                        echo "  <tr>\n";
                        echo "    <td colspan=\"2\"><h2>Search Results</h2></td>\n";
                      Severity: Minor
                      Found in lib/m2html/templates/frame/doxysearch.php - About 1 hr to fix
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