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<?php

namespace DispatchModule\Models;

/**
 * BlastModel cooperates with Blast
 *
 */
class BlastModel extends \BaseModule\Models\BaseModel {

    /**
     * Input query file (relative path from "www" folder)
     * @var String
     */
    private $input;

    /**
     * Constructor of BlasModel - sets input file
     *
     * @param string $input input path
     */
    public function __construct($input) {
        $this->input = $input;
    }

    /**
     * Executing query saved in the blastTemp directory
     * @param string $output path where to store output
     * @param string $format format of output
     * @param string $database blast database that should be used for alignment
     * @return array output of the blast tool
     */
    public function executeBlastSearch($output = "", $format = "", $database = "") {
        if (empty($database)) {
            $database = BLAST_DATABASE;
        }
        if (!empty($output)) {
            $output = " -out \"" . $output . '"';
        }
        if (empty($format)) {
            $format = 5;
        }
        exec("\"" . BLAST_PATH . "blastn\" -db \"" . $database . "\" -query \"" . $this->input . "\" -outfmt \"" . $format . '"' . $output, $result);
        return $result;
    }

}