ods.php

<?php

	//  ________________________________                          ____________________________
	// /  PromKappa                     \________________________/       v2.00                |
	// |                                                                                      |
	// |                   Name:  PromKappa (ported from VB6 to PHP)                          |
	// |     Original language :  Visual Basic 6                                              |
	// |    Original source V1 :  http://www.biomedcentral.com/1471-2164/13/512/additional    |
	// |    Original source V2 :  http://www.biomedcentral.com/1471-2164/14/278/additional    |
	// |               Category:  Open source software                                        |
	// |                 Author:  Paul A. Gagniuc                                             |
	// |                  Email:  paul_gagniuc@acad.ro                                        |
	// |                                                                                      |
	// |           Date Created:  October 2013                                                |
	// |               Language:  PHP                                                         |
	// |                    Use:  DNA patterns, analysis of DNA sequences                     |
	// |                                                                                      |
	// |                  _____________________________                                       |
	// |_________________/                             \______________________________________|
	//

	$sequence = $_GET["s"];

	function Sliding_Windw($sequence)
	{
		$window = 30;
		$step = 1;

		for ($u=0; $u<=strlen($sequence) - $window; $u += $step)
		{
			echo substr($sequence, $u, $window) . "<br>";
		}
	}


	function CG($sequence)
	{
		$a = 0;
		$t = 0;
		$c = 0;
		$g = 0;

		for ($u=0; $u<=strlen($sequence); $u ++)
		{
			$nucleotida = strtolower(substr($sequence, $u, 1));

			if ($nucleotida == "a") {$a = $a + 1;}
			if ($nucleotida == "t") {$t = $t + 1;}
			if ($nucleotida == "g") {$g = $g + 1;}
			if ($nucleotida == "c") {$c = $c + 1;}
		}

		return (100 / ($c + $g + $t + $a)) * ($c + $g);
	}



	function IC($sequence)
	{
		$count = 0;
		$total = 0;
		$S1 = strtolower($sequence);
		$max = strlen($S1) - 1;

		for ($u=1; $u<=$max; $u++)
		{
			$s2 = substr($S1, $u + 1, strlen($S1));

			for ($i=1; $i<=strlen($s2); $i++)
			{
				if (substr($S1, $i, 1) == substr($s2, $i, 1)) {
					$count = $count + 1;
				}
			} 


			if ($count <= 0) {
				$count = 0;
			} else {
				$total = $total + ($count / strlen($s2) * 100);
				$count = 0;
			}
		}
		return round(($total / $max), 2);
	}


	$width = 255;
	$height = 255;
	$image = imagecreatetruecolor($width, $height);

	$window = 30;
	$step = 1;


	$no_points = strlen($sequence) - $window;

	for ($u=0; $u<=$no_points; $u += $step)
  	{
		$window_string = substr($sequence, $u, $window);

		$CGP = CG($window_string);
		$KIC = IC($window_string);

		$X_CG = round(($width/100) * $CGP);
		$Y_IC = round(($height/100) * $KIC);
		

		$line_with = round($width/$no_points);

		$x1 =$X_CG;
		$y1 =$height - $Y_IC;

		$x2 =$X_CG + $line_with;
		$y2 =$height - $Y_IC;

		$color = imagecolorallocate($image, 255, 0, 0); ;

		imageline($image, $x1, $y1, $x2, $y2, $color);
	}

	header("Content-type: image/png");
	imagepng($image);
	imagedestroy($image);
?>