🚀 Here's the PR! #96

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Step 1: 🔎 Searching

I found the following snippets in your repository. I will now analyze these snippets and come up with a plan.

Some code snippets I think are relevant in decreasing order of relevance (click to expand). If some file is missing from here, you can mention the path in the ticket description.

https://github.com/liberu-genealogy/php-dna/blob/10dea8c35836765b57e421475854607f9b352831/phpconvcount.py#L1-L85

I also found the following external resources that might be helpful:

**Summaries of links found in the content:** https://github.com/apriha/lineage/blob/master/src%2Flineage%2Fvisualization.py: The page is a Python file named `visualization.py` from the `lineage` repository on GitHub. It contains code for chromosome plotting functions. The code defines several functions, including `plot_chromosomes`, `_chromosome_collections`, and `_patch_chromosomal_features`. These functions are used to plot chromosomes with designated markers and highlight segments on the chromosomes representing shared chromosomes. The code also includes import statements, variable definitions, and comments explaining the purpose of the functions. The user wants to convert this Python file to a PHP file named `Visualisation.php`.

Step 2: ⌨️ Coding

[X] Create src/Visualisation.php ✓ https://github.com/liberu-genealogy/php-dna/commit/04a1ba9c266bcc9844e7c53b3d43b6888c748f7b Edit
Create src/Visualisation.php with contents:
• Begin by creating a new PHP file named `Visualisation.php` in the `src` directory. This file will contain the PHP translation of the Python code found in the `visualization.py` file from the `lineage` repository.
• Start the file with the `• Import any necessary PHP libraries or modules at the top of the file. Given the nature of the visualization tasks, it may be necessary to use PHP's GD library for image creation and manipulation or any other relevant visualization library available in PHP. Include statements such as `use GDLibrary;` or the appropriate import statement for the library chosen for graphical operations.
• Define the PHP class `Visualisation` with the opening `class Visualisation {` followed by the closing brace `}`. This class will encapsulate all the functions translated from the Python file.
• Inside the `Visualisation` class, translate the `plot_chromosomes` function from Python to PHP. This will involve converting Python's function syntax to PHP, adapting any Python-specific constructs (like list comprehensions or dictionary operations) to their PHP equivalents, and ensuring that any data manipulation or mathematical operations are correctly implemented in PHP.
• Similarly, translate the `_chromosome_collections` and `_patch_chromosomal_features` functions from Python to PHP within the `Visualisation` class. Pay special attention to the translation of any graphical operations, ensuring that PHP's graphical library functions are used correctly to replicate the visualization functionality.
• After translating the main functions, review the code for any Python-specific idioms or constructs that do not have direct equivalents in PHP and find appropriate PHP idioms or patterns to achieve the same functionality.
• Ensure that the PHP code follows the PHP 8.3 standards and conventions, making use of new features where appropriate for cleaner or more efficient code.
• Finally, add comments throughout the `Visualisation.php` file explaining the purpose of each function and any complex or non-obvious code blocks, mirroring the commenting style found in the Python source file to maintain readability and maintainability.

[X] Running GitHub Actions for src/Visualisation.php ✓ Edit
Check src/Visualisation.php with contents:

Ran GitHub Actions for 04a1ba9c266bcc9844e7c53b3d43b6888c748f7b:

Step 3: 🔁 Code Review

I have finished reviewing the code for completeness. I did not find errors for sweep/finish_visulation.

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liberu-genealogy / php-dna

Sweep: finish visulation #95

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