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<?php

namespace DispatchModule\Tools;

/**
 * SimilarityTool
 */
class SimilarityTool extends \DispatchModule\Tools\BaseTool implements \DispatchModule\Tools\ToolInterface {

    /**
     * XML Parser
     * @var \DispatchModule\Models\BlastXMLParser
     */
    protected $xmlParser;

    /**
     * Representing query given to the blast tool
     * @var \BaseModule\Models\FileModel
     */
    protected $query;

    /**
     * Directory for temporary files
     * @var string 
     */
    protected $directory;

    /**
     * Short description of the tool
     * @var string
     */
    public $description = 'Basic Local Alignment Search Tool compares primary biological sequence information';

    /**
     * Saves parsed blast data
     * @var string
     */
    public $blastTempFile;

    /**
     * Flag whether any sequence is set
     * @var bool
     */
    protected $used = false;

    /**
     * Tells whether any sequence is set
     * @return boolean
     */
    public function used() {
        return $this->used;
    }

    /**
     * Array of wanted parameters
     * @var array
     */
    protected $wantedParameters = array(
        'min_coverage' => array('select', 'Min coverage', array("items" =>
                array(
                    '40' => '40%',
                    '65' => '65%',
                    '80' => '80%',
                    '85' => '85%',
                    '90' => '90%',
                    '93' => '93%',
                    '95' => '95%',
                    '97' => '97%',
                    '98' => '98%',
                    '99' => '99%',
                    '100' => '100%',
                ))),
        'min_identity' => array('select', 'Min identity', array("items" =>
                array(
                    '40' => '40%',
                    '65' => '65%',
                    '80' => '80%',
                    '85' => '85%',
                    '90' => '90%',
                    '93' => '93%',
                    '95' => '95%',
                    '97' => '97%',
                    '98' => '98%',
                    '99' => '99%',
                    '100' => '100%',
                ))),
        'sequence' => array('textarea', 'Sequence', array(
                'placeholder' => 'AGUUCGGCACCACGGUGCAA',
                'multiplicators' => array('or' => 10))),
        'fasta_file' => array('file', 'Fasta file'),
        'fasta_file_hidden' => array('hidden')
    );

    /**
     * Constructor used to save container
     *
     * @param \Nette\DI\Container $container
     */
    public function __construct(\Nette\DI\Container $container) {
        parent::__construct($container);
        $this->directory = TEMP_PATH . DIRECTORY_SEPARATOR . "blastTemp" . DIRECTORY_SEPARATOR;
    }

    /**
     * Adds search criteria
     * 
     * @param string $name
     * @param mixed $value
     * @return boolean
     */
    public function addCriteria($name, $value) {
        switch ($name) {
            case "sequence":
                if (isset($this->completeData['blast_sequence_array'])) {
                    $sequences = $this->completeData['blast_sequence_array'];
                }
                $value .= ((isset($sequences[0])) ? "\n" . implode("\n", $sequences) : "");
                if (!empty($value)) {
                    $this->used = true;
                }
                break;
            case "fasta_file":
                break;
            case "fasta_file_hidden":
                if (!empty($value)) {
                    $this->used = true;
                }
                break;
        }
        //return loaded result
        if (isset($this->completeData['offset']) && $this->completeData['offset'] > 0) {
            return true;
        }
        if (is_null($this->query)) {
            if (!isset($this->fileName) || empty($this->fileName)) {
                $this->fileName = (session_id()) ? session_id() : (time() . rand());
            }
            $this->blastTempFile = $this->directory . $this->fileName . ".txt";
            $this->query = new \BaseModule\Models\FileModel($this->directory . $this->fileName);
            $this->query->createFile();
            $this->xmlParser = new \DispatchModule\Models\BlastXMLParser($this->directory . $this->fileName . ".xml");
        }
        switch ($name) {
            case "min_coverage":
                $this->xmlParser->setMinCoverage($value / 100);
                break;
            case "min_identity":
                $this->xmlParser->setMinIdentity($value / 100);
                break;
            case "sequence":
                if (!empty($value)) {
                    $this->query->appendContent($value);
                }
                break;
            case "fasta_file":
                break;
            case "fasta_file_hidden":
                if (!empty($value)) {
                    if ($this->query->getContent()) {
                        $this->query->appendContent("\n");
                    }
                    $this->query->appendContent($value);
                }
                break;
        }
    }

    /**
     * Executes query
     * 
     * @return ResultSet
     */
    public function execute() {
        //Blast tool is been executed just once
        if (isset($this->completeData['offset']) && $this->completeData['offset'] > 0) {
            return null;
        }
        //executes blast
        $blast = new \DispatchModule\Models\BlastModel($this->query->getFile());
        $blast->executeBlastSearch($this->xmlParser->getFileName());

        //parses xml and saves result
        $seq = $this->xmlParser->execute();

        //deletes older files
        $this->query->deleteFile();
        $this->xmlParser->deleteFile();
        \BaseModule\Models\FileModel::deleteOldFiles($this->directory);

        return $seq;
    }

    /**
     * Gets human-readable short description (name) of the tool
     * @return string human-readable short description of the tools
     */
    public function getLabel() {
        return 'Sequence';
    }

}