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<?php

namespace DispatchModule\Models;

/**
 * Blast XML Parser parses XML document generated by Blast
 *
 */
class BlastXMLParser extends \BaseModule\Models\BaseModel {

    /** 
     * Min coverage of the result and query
     * @var int
     */
    private $minCoverage;

    /** 
     * Min identity of the result and query
     * @var int
     */
    private $minIdentity;

    /** 
     * Length of the query
     * @var int
     */
    private $length;

    /**
     * Temp variable for sequence
     * @var \DispatchModule\Sequence
     */
    private $sequence;

    /**
     * Temp variable for match
     * @var \DispatchModule\BlastMatch
     */
    private $match;

    /**
     * Returned result set
     * @var \DispatchModule\ResultSet
     */
    private $result;

    /**
     * String node 
     * @var String
     */
    private $text;

    /**
     * Input XML file for parsing
     * @var FileModel
     */
    private $file;

    /**
     * Constructor - creates FileModel instance
     *
     * @param string $fileName name of the file
     */
    public function __construct($fileName) {
        $this->file = new \BaseModule\Models\FileModel($fileName);
    }

    /**
     * Get XML file name (including rel. path)
     * @return String
     */
    public function getFileName() {
        return $this->file->getFile();
    }

    /**
     * Removes file
     */
    public function deleteFile() {
        $this->file->deleteFile();
    }

    /**
     * Sets minimal required coverage
     * @param integer $minMatch
     */
    public function setMinCoverage($minCoverage) {
        $this->minCoverage = $minCoverage;
    }

    /**
     * Sets minimal required identity

     * @param integer $minMatch

     */
    public function setMinIdentity($minIdentity) {
        $this->minIdentity = $minIdentity;
    }

    /**
     * Parses Blast XML and return the result set
     * @return \DispatchModule\ResultSet Result set of sequences
     */
    public function execute() {
        $this->result = new \DispatchModule\ResultSet();
        $parser = xml_parser_create();
        xml_set_element_handler($parser, array($this, "tagStart"), array($this, "tagEnd"));
        xml_set_character_data_handler($parser, array($this, "chars"));
        if (!($file = @fopen($this->file->getFile(), "r"))) {
            return new \DispatchModule\ResultSet();
        } else {
            while ($d = fread($file, 4096)) {
                if (!xml_parse($parser, $d, feof($file))) {
                    return new \DispatchModule\ResultSet();
                }
            }
        }
        $this->result->sortByScore();
        return $this->result;
    }


    /**
     * XML node start
     * @param parser $parser
     * @param string $elementName
     * @param array $attributes
     */
    public function tagStart($parser, $elementName, $attributes) {
        $this->text = "";
        switch ($elementName) {
            case "HIT":
                $this->sequence = new \DispatchModule\Sequence;
                break;
            case "HSP":
                $this->match = new \DispatchModule\BlastMatch;
                break;
        }
    }

    /**
     * XML node end
     * @param parser $parser
     * @param string $elementName
     */
    public function tagEnd($parser, $elementName) {
        switch ($elementName) {
            case "BLASTOUTPUT_QUERY-LEN":
                $this->length = $this->text;
                break;
            case "HIT":
                if (!empty($this->sequence->matches)) {
                    $this->result->addSequence($this->sequence);
                }
                break;
            case "HIT_DEF":
        $splitted = explode(".", explode(" ", $this->text)[0]);
                $this->sequence->accession = $splitted[0];
        $this->sequence->startPosition = $splitted[1];
        $this->sequence->stopPosition = $splitted[2];
                $this->sequence->regionLength = $this->sequence->stopPosition - $this->sequence->startPosition + 1;
                break;
            case "HSP":
                if ($this->match->getCoverage() >= $this->minCoverage && $this->match->getIdentity() >= $this->minIdentity) {
                    $this->sequence->matches[] = $this->match;
                }
                break;
            case "HSP_QSEQ":
                $this->match->subsequence = str_replace("T", "U", $this->text);
                break;
            case "HSP_QUERY-FROM":
                $this->match->queryStartPosition = $this->text;
                $this->match->setCoverage(($this->match->queryStopPosition + 1 - $this->text) / $this->length);
                break;
            case "HSP_QUERY-TO":
                $this->match->queryStopPosition = $this->text;
                $this->match->setCoverage(($this->text + 1 - $this->match->queryStartPosition) / $this->length);
                break;
            case "HSP_HIT-FROM":
                $this->match->dbStartPosition = $this->sequence->startPosition + $this->text - 1;
                break;
            case "HSP_HIT-TO":
                $this->match->dbStopPosition = $this->sequence->startPosition + $this->text - 1;
                break;
            case "HSP_EVALUE":
                $this->match->setEValue($this->text);
                break;
            case "HSP_BIT-SCORE":
                $this->match->setBitScore($this->text);
                break;
            case "HSP_SCORE":
                $this->match->setScore($this->text);
                break;
            case "HSP_MIDLINE":
                $match = substr_count($this->text, "|");
                $length = strlen($this->text);
                $matchRatio = $match / $length;
                $this->match->setIdentity($matchRatio);
                break;
        }
    }

    /**
     * Processing of the element
     * @param parser $parser
     * @param string $data
     */
    public function chars($parser, $data) {
        $this->text .= $data;
    }

}