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<?php

namespace DispatchModule\Tools;

/**
 * AnnotationDbTool
 * - retrieves non-taxonomic information from database
 * - used (mainly) by search
 */
class AnnotationDbTool extends \DispatchModule\Tools\DbTool {

    /**
     * Constructor used to save container
     *
     * @param \Nette\DI\Container $container
     */
    public function __construct(\Nette\DI\Container $container) {
        parent::__construct($container,
                            'Annotation',
                            'Standard search using annotations stored in database',
                            array(
                                'molecule_type' => array('select', 'Molecule type', array(
                                          'items' => array('' => 'any'),
                                          'multiplicators' => array('or' => 5))),
                                'description' => array('text', 'Description contains',
                                    array('placeholder' => '18S sequenced from gene...')),
                                'accession' => array('text', 'Accession number', array(
                                        'multiplicators' => array('or' => 10),
                                        'placeholder' => 'AC091632'
                                    )),
                                'firstpublished' => array('text', 'First published', array(
                                        'date' => true,
                                        'modifiers' => array('firstpublished_direction' => array('select', '', array('items' => array(self::RULE_LT => 'before', self::RULE_GT => 'after')))),
                                        'multiplicators' => array('and' => 2)
                                    )),
                                'sequence_quality' => array('select', 'Minimal sequence quality', array('items' => array('' => '0%', '50' => '50%', '90' => '90%', '95' => '95%', '99' => '99%'))),
                                'region_length' => array('text', 'Length', array(
                                        'modifiers' => array('region_length_direction' => array('select', '', array('items' => array(self::RULE_LT => '<', self::RULE_GT => '>')))),
                                        'multiplicators' => array('and' => 2)
                                    )),
                            ));

        $base = $this->chooseBaseTable();
        $result = $this->prepareCriteria('DISTINCT dataset', $base);
        $result->order('dataset');
        foreach ($result as $res) {
            $type = $res['dataset'];
            $this->wantedParameters['molecule_type'][2]['items'][$type] = $type;
        }
    }

}