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

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

/* Avoid unstubbing $wgParser on setHook() too early on modern (1.12+) MW versions */
if ( defined( 'MW_SUPPORTS_PARSERFIRSTCALLINIT' ) ) {
	$wgHooks['ParserFirstCallInit'][] = 'myUcscIFrame';
} else {
	$wgExtensionFunctions[] = 'myUcscIFrame';
}


/**
 * 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'          =>      'ucsciframe',
        'version'       =>      '0.1',
        'author'        =>      '[http://plindenbaum.blogspot.com Pierre Lindenbaum]',
        'url'           =>      'http://code.google.com/p/code915/source/browse/trunk/mediawiki/extensions/ucsciframe/ucsciframe.php',
        'description'   =>      'Creates an iframe for the UCSC genome browser'
);

function myUcscIFrame()
	{
	global $wgParser;
	$wgParser->setHook( 'ucsciframe', 'myRenderUcscIFrame' );
	return true;
	}

function myRenderUcscIFrame( $input, $args, $parser )
	{
	if( !(isset($args['chrom']))) return "<span style='color:red;'>@chrom missing</span>";
	if( !(isset($args['start']))) return "<span style='color:red;'>@start missing</span>";
	if( !(isset($args['end']))) return "<span style='color:red;'>@end missing</span>";
	$chrom=trim($args['chrom']);
	if(strlen($chrom)==0)  return "<span style='color:red;'>bad @chrom</span>";
	if(substr($chrom,0,3)!='chr') $chrom="chr".$chrom;
	$start=(int)trim(str_replace(',','',$args['start']));
	$end=(int)trim(str_replace(',','',$args['end']));
	if(!is_int($start)) return 	"<span style='color:red;'>bad @start</span>";
	if(!is_int($end)) return 	"<span style='color:red;'>bad @end</span>";

	$url="http://genome.ucsc.edu/cgi-bin/hgTracks?org=".
		(isset($args['org'])?$args['org']:"Human").
		"&db=".(isset($args['db'])?$args['db']:"hg18").
		"&position=".$chrom."%3A".$start."-".$end;
	
	$html=	"<div style='text-align:center;margin:10pt;'>".
		"<a href='".$url."' target='_blank'>".$chrom.":".$start."-".$end."</a><br/>".
		"<iframe height='".(isset($args['height'])?$args['height']:"500px")."' width='90%' src ='".$url."' />".
		"</iframe></div>"
		;
	return $html;
	}

?>