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<?php

namespace AnalyseModule\Models;

/**
 * BaseTool contains method for loading the sequences from the database
 * - it is the recommended model tha other tool models sohuld inherit from
 */
class BaseTool extends \BaseModule\Services\BaseService {

    /**
     * Load complete sequences (given by list of accessions) from database
     *
     * @param array $accessions accession numbers (along with start and stops) to load
     * @return array complete sequences
     */
    protected function loadSequencesFromDb($accessions) {
        $accClear = array();
        $starts = array();
        $stops = array();
        foreach ($accessions as $i => $acc) {
            $accRecord = explode(':', $acc);
            $accClear[] = $accRecord[0];
            $stops[] = $accRecord[2];
            $starts[] = $accRecord[2];
        }
        // load sequence records for accessions from database
        $dbTool = new \DispatchModule\Tools\DbTool($this->container);
        for ($i = 1; $i < count($accClear); $i++) {
            $dbTool->completeData['db_accession_array'][] = $accClear[$i];
        }
        $dbTool->addCriteria('accession', $accClear[0]);
        $result = $dbTool->execute();
        $sequences = $result->data;
        foreach ($sequences as $i => $sequence) {
            $key = array_search($sequence->accession, $accClear);
            if ($sequence->startPosition != $starts[$key] && $sequence->stopPosition != $stops[$key]) {
                unset($sequences[$i]);
            }
        }
        return $sequences;
    }

}