feat: Updated src/Snps/SNPs.php

src/Snps/SNPs.php

@@ -1,5 +1,6 @@
 <?php
 
+declare(strict_types=1);
 
 namespace Dna\Snps;
 
@@ -17,34 +18,15 @@
 
 // import copy // In PHP, you don't need to import the 'copy' module, as objects are automatically copied when assigned to variables
 
-// from itertools import groupby, count // PHP has built-in support for array functions that can handle these operations natively
-
-// import logging // For logging in PHP, you can use Monolog: https://github.com/Seldaek/monolog
-// use Monolog\Logger;
-// use Monolog\Handler\StreamHandler;
-
-// import os, re, warnings
-// PHP has built-in support for file operations, regex, and error handling, so no need to import these modules
-
-// import numpy as np // See the note above about using MathPHP or another PHP library for numerical operations
-// import pandas as pd // See the note above about using php-dataframe or another PHP library for data manipulation
-
-// from pandas.api.types import CategoricalDtype // If using php-dataframe, check documentation for similar functionality
-
-// For snps.ensembl, snps.resources, snps.io, and snps.utils, you'll need to find suitable PHP alternatives or adapt the Python code
 use Dna\Snps\Ensembl;
 use Dna\Snps\IO\SnpFileReader;
 use Dna\Snps\Analysis\BuildDetector;
 use Dna\Snps\Analysis\ClusterOverlapCalculator;
-// from snps.utils import Parallelizer
 
-// Set up logging
-// $logger = new Logger('my_logger');
-// $logger->pushHandler(new StreamHandler('php://stderr', Logger::DEBUG));
+class SNPs implements Countable, Iterator
 
 class SNPs implements Countable, Iterator
 {
-
     private array $_source = [];
     private array $_snps = [];
     private int $_build = 0;
@@ -56,14 +38,13 @@ class SNPs implements Countable, Iterator
     private ?string $_cluster = null;
     private int $_position = 0;
     private array $_keys = [];
-    private array $_duplicate;
-    private array $_discrepant_XY;
-    private array $_heterozygous_MT;
-    private $_chip;
-    private $_chip_version;
-    private $_cluster;
+    private array $_duplicate = [];
+    private array $_discrepant_XY = [];
+    private array $_heterozygous_MT = [];
 
 
+    /**
+    
     /**
      * SNPs constructor.
      *