$test->execute();
//fais
print_r($test->tab);

<?php

ini_set ('max_execution_time', 0); // Aucune limite d'execution
require_once("./selection.php");  

 $test=new selection();

 $test->execute();

 


?>		

$this->subsequence($sequence)

$selection = new Selection();
$selection->execute();

class selection {
public function __construct($way="/home/guillaume/Desktop/Seq-matrice/sequences.fasta") {

		$this->way=$way;

		$this->b=10;
		$this->tab = array();
		//$this->i=0;
}
public function execute() {
				

		if(file_exists($this->way)) {                              

			$lignes= file ($this->way); 
			                         

			//print_r($lignes);

			$cpt=0;                                                

			foreach($lignes as $ligne) {                           

				if(strpos($ligne,'>')!== false){
										

					if($cpt>0) {
					

						echo "$sequence<br \>";
						$sequence=trim($sequence," "); 

						$this->subsequence($sequence);   // L'appel se fait à ce niveau
						$sequence="";
						
               

					}
					$this->id=$ligne;

					$sequence="";

					$cpt++;

				}
				else{
				
					$sequence.=$ligne;  

					$sequence=trim($sequence);
				}

				

			}

			if($sequence!="") {     
				echo "$sequence<br \>"; 
				echo "$this->id<br \>";	
				#echo "$sequence<br \>";	
				$this->subsequence($sequence);
   //Ou bien à ce niveau
			}

		}
		else {   
			die("impossible d'ouvrir le fichier FASTA");

			

		}

	}

	public function subsequence($sequence) {

		$arr=array();
		$jen="/home/guillaume/Desktop/Seq-matrice/data.fasta";
		$pro=fopen($jen,"w+");
		fwrite($pro,$this->id);
		fwrite($pro,$sequence."\n");
		fclose($pro);
		chmod($jen,0777);

		for($a=0;$a<=strlen($sequence)-$this->b;$a++){                       

			$this->files=substr($sequence,$a,$this->b);

           		$align=array(0=>$this->files);	

		
			//print_r($align);  

	
			#msf

			$msa=new Msa($align);
			$msa->toMSF("/opt/lampp/htdocs/profils/test.msa");
		

			$file="/opt/lampp/htdocs/profils/test.msa";
			
			$msf=file_get_contents("$file");
				
		
			#pfmake

			$pfmake=new pfMake($file);			

			$pfmake->setAlignmentMode(-1);

			$pfmake->setLinearMode();

			$pfmake->execute();

			

					

			$pfmake->autoscale($db=0);

			$prf=$pfmake->getProfile();
			//echo $prf;
			$profil=file_get_contents("$prf");			
			#echo $profil;
		

			

			#  pfsearch
			$pfsearch=new pfSearch($prf,$jen);

			$pfsearch->execute();
			$pr=$pfsearch->getResult();

			#$prr=$pfsearch=file_get_contents($pr);
			#echo $pr;
				
			$this->tab[$this->i]=array ($msf,$profil,$pr);     // Voilà donc le tableau récapitulatif avec ou sans $this->i c'est la même
			print_r ($this->tab);
			//$this->i++;                                

		}
		
		#Recherche séquence significative
		$score=new score();
		$score->execute();
		$mx=$score->getResult();
				
		#Renvoie clé de $mx (valeur maximale)
		function recursive_array_search($needle,$haystack) {
    			foreach($haystack as $key=>$value) {
       			 $current_key=$key;
        			if($needle===$value OR (is_array($value) && recursive_array_search($needle,$value))) {
			  	  return $current_key;
				}
		    	}
		return false ;  // A ce niveau le script me retoune "false"
		}
		$found = recursive_array_search($mx,$tab);
		var_dump($found);
 
	

		
	}
}

$this->tab[$this->i]=array ($msf,$profil,$pr);   

 $this->tab[]=array ($msf,$profil,$pr);

$this->tab[]=array  ($msf,$profil,$pr);

   

       public function __construct() {

		$this->tab = array();
		$this->i=0;

                       $this->tab[$this->i]=array ($msf,$profil,$pr);
			print_r ($this->tab);
			$this->i++;