Extension:DNASeq/V20100808

modified version (proposed by Niklas Laxström)

<?php
/**
Author: Pierre Lindenbaum PhD
Mail: plindenbaum@yahoo.fr

Installation:
        install this file in
        
                ${MWROOT}/extensions/dnaseq/dnaseq.php
        
        and add the following line at the end of ${MWROOT}/LocalSettings.php :
        
                require_once("$IP/extensions/dnaseq/dnaseq.php");
**/


/**
 * Protect against register_globals vulnerabilities.
 * This line must be present before any global variable is referenced.
 */
if(!defined('MEDIAWIKI')){
        echo("This is an extension to the MediaWiki package and cannot be run standalone.\n" );
        die(-1);
}

/**
 * An array of extension types and inside that their names, versions, authors
 * and urls. This credit information gets added to the wiki's Special:Version
 * page, allowing users to see which extensions are installed, and to find more
 * information about them.
 */
$wgExtensionCredits['parserhook'][] = array(
        'name'        => 'dnaseq',
        'version'     => '0.2',
        'author'      => '[http://plindenbaum.blogspot.com Pierre Lindenbaum]',
        'url'         => 'http://code.google.com/p/lindenb/source/browse/trunk/proj/mediawiki/extensions/dnaseq/dnaseq.php',
        'description' => 'Displays a DNA sequence'
);

$wgHooks['ParserFirstCallInit'][] = 'myDnaSequence';


function myDnaSequence( $parser )
        {
        $parser->setHook( 'dnaseq', 'myRenderDnaSequence' );
        return true;
        }

function myRenderDnaSequence( $input, $args, $parser )
        {
        if($input==null) return "";
        $len= mb_strlen($input);
        $n=0;
        $html="<div style='padding: 10px; font-size:10px; border-width: thin; border: 1px black solid; white-space: pre;background-color: white;font-family: courier, monospace;line-height:13px; font-size:12px;'>";
        for($i=0;$i< $len;$i++)
                {
                $c = mb_substr( $input, $i, 1 );
                if(ctype_space($c) || ctype_digit($c)) continue;
                if($n % 60 == 0)
                        {
                        if($n!=0) $html.="<br />";
                        $html.= sprintf("%06d  ",($n+1));
                        }
                else if($n % 10 ==0)
                        {
                        $html.=" ";
                        }
                $n++;
                switch(strtolower($c))
                        {
                        case "a":
                                $html.="<span style='color:green;'>".$c."</span>";
                                break;
                        case "c":
                                $html.="<span style='color:blue;'>".$c."</span>";
                                break;
                        case "g":
                                $html.="<span style='color:black;'>".$c."</span>";
                                break;
                        case "t":
                        case "u":
                                $html.="<span style='color:red'>".$c."</span>";
                                break;
                        default:
                                $html.="<span style='text-decoration: blink;color:gray'>".$c."</span>";
                                break;
                        }
                if($n % 60 == 0)
                        {
                        $html.= sprintf("  %06d",($n));
                        }
                }
        $html .= "</div>";
        return $html;
        }