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<?php

namespace DispatchModule\Models;

/**
 * FastaModel cooperates with Fasta36
 *
 */
class FastaModel extends \BaseModule\Models\BaseModel {

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

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

    /**
     * Executing query
     * @return array output of the fasta tool
     */
    public function executeFastaSearch() {
        exec('"' . FASTA_PATH . "ggsearch36\" -n -m 8 -d 0 \"" . $this->input . "\" \"" . CPPREDICT2_TEMPLATES . TEMPLATES_DATABASE . ".fasta\" | LC_ALL=C sort -g -k 11,11 -k 12,12nr | sort -s -u -k 1,1 | cut -f 1,2", $result);
        return $result;
    }

}