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<?php

namespace DispatchModule\Models;

/**
 * BlatModel cooperates with Blat
 *
 */
class BlatModel extends \BaseModule\Models\BaseModel {

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

    /**
     * Filename for Blat output file
     * @var String
     */
    private $output;

    /**
     * Results returned from python encoded by json
     * @var Array 
     */
    private $dumpedResults;

    /**
     * Results returned from python as a string (still encoded by json) 
     * @var String
     */
    private $stringResults;

    /**
     * Results returned from python decoded by json 
     * @var String
     */
    private $decodedResults;

    /**
     * Constructor sets input
     *
     * @param string $input input file path
     * @param string $fileId identifier of the output file
     */
    public function __construct($input, $fileId = null) {
        $this->input = $input;

        // generate output filename
        $this->output = TEMP_PATH . "/blatTemp/";
        if (isset($fileId) && !empty($fileId)) {
            $this->output = $this->output . $fileId;
        } else {
            $this->output = $this->output . (session_id() ? session_id() : (time() . rand()));
        }
        $this->output = $this->output .  ".output.pslx";
    }

    /**
     * Executing query saved in the blatTemp directory 
     * 
     * @param integer $minMatch Minimal (percentage) match with query
     * @param integer $minCoverage Minimal (percentage) coverage of query
     * @return String 
     */
    public function executeBlatSearch($minMatch, $minCoverage) {
        // run Blat client
        exec("\"" . BLAT_PATH . "gfClient\" localhost 7776 \"\" " . $this->input . " -out=pslx " . "\"" . $this->output . "\"" . " -minIdentity=" . $minMatch);
        /** exec("\"" . BLAT_PATH . "gfClient\" localhost 7776 \"\" " . $this->input . " -out=psl " . "\"" . $this->output . ".psl\"" . " -minIdentity=" . $minMatch);
        exec("\"" . BLAT_PATH . "gfClient\" localhost 7776 \"\" " . $this->input . " -out=pslx " . "\"" . $this->output . ".pslx\"" . " -minIdentity=" . $minMatch);
        exec("\"" . BLAT_PATH . "gfClient\" localhost 7776 \"\" " . $this->input . " -out=axt " . "\"" . $this->output . ".axt\"" . " -minIdentity=" . $minMatch);
        exec("\"" . BLAT_PATH . "gfClient\" localhost 7776 \"\" " . $this->input . " -out=maf " . "\"" . $this->output . ".maf\"" . " -minIdentity=" . $minMatch);
        exec("\"" . BLAT_PATH . "gfClient\" localhost 7776 \"\" " . $this->input . " -out=sim4 " . "\"" . $this->output . ".sim4\"" . " -minIdentity=" . $minMatch);
        exec("\"" . BLAT_PATH . "gfClient\" localhost 7776 \"\" " . $this->input . " -out=wublast " . "\"" . $this->output . ".wublast\"" . " -minIdentity=" . $minMatch);
        exec("\"" . BLAT_PATH . "gfClient\" localhost 7776 \"\" " . $this->input . " -out=blast " . "\"" . $this->output . ".blast\"" . " -minIdentity=" . $minMatch);
        exec("\"" . BLAT_PATH . "gfClient\" localhost 7776 \"\" " . $this->input . " -out=blast8 " . "\"" . $this->output . ".blast8\"" . " -minIdentity=" . $minMatch);
        exec("\"" . BLAT_PATH . "gfClient\" localhost 7776 \"\" " . $this->input . " -out=blast9 " . "\"" . $this->output . ".blast9\"" . " -minIdentity=" . $minMatch); /**/

        // parsing results returned by Blat client using Biopython
        // (the path to parsing.py is from the directory where the BlatTool
        //  is actually run)
        exec("python ../app/DispatchModule/models/parsing.py " . "\"" . $this->output . "\" " . $minCoverage, $this->dumpedResults);
        // convert array returned from exec in dumpedResults variable into string
        $this->stringResults = implode("\n", $this->dumpedResults);

        // unpack parsed results from python
        $this->decodedResults = json_decode($this->stringResults, true);

        return $this->decodedResults;
    }

}