Source of file PeffFastaEntry.php

<?php

/**

 * Copyright 2016 University of Liverpool

 *

 * Licensed under the Apache License, Version 2.0 (the "License");

 * you may not use this file except in compliance with the License.

 * You may obtain a copy of the License at

 *

 * http://www.apache.org/licenses/LICENSE-2.0

 *

 * Unless required by applicable law or agreed to in writing, software

 * distributed under the License is distributed on an "AS IS" BASIS,

 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

 * See the License for the specific language governing permissions and

 * limitations under the License.

 */

namespace pgb_liv\php_ms\Core\Database\Fasta;

use pgb_liv\php_ms\Core\Protein;

use pgb_liv\php_ms\Core\Modification;

/**

 * A sequence Database Entry object.

 * By default the identifier, description

 * and sequence are available. Additional fields will be available if the

 * description has been able to be parsed in the case of FASTA data.

 *

 * @author Andrew Collins

 */

class PeffFastaEntry implements FastaInterface

{

    /**

     *

     * {@inheritdoc}

     *

     * @see \pgb_liv\php_ms\Core\Database\Fasta\FastaInterface::getHeader()

     */

    public function getHeader()

    {

        return '# PEFF 1.0draft24' . PHP_EOL;

    }

    /**

     *

     * {@inheritdoc}

     *

     * @see \pgb_liv\php_ms\Core\Database\Fasta\FastaInterface::getDescription()

     */

    public function getDescription(Protein $protein)

    {

        $description = '>' . $protein->getDatabasePrefix() . ':' . $protein->getAccession();

        if ($protein->getAccession()) {

            $description .= ' \DbUniqueId=' . $protein->getAccession();

        }

        if ($protein->getEntryName()) {

            $description .= ' \CC=' . $protein->getEntryName();

        }

        if ($protein->getName()) {

            $description .= ' \Pname=' . $protein->getName();

        }

        if ($protein->getGeneName()) {

            $description .= ' \Gname=' . $protein->getGeneName();

        }

        if ($protein->getOrganismName()) {

            $description .= ' \TaxName=' . $protein->getOrganismName();

        }

        if ($protein->getSequenceVersion()) {

            $description .= ' \SV=' . $protein->getSequenceVersion();

        }

        if ($protein->getProteinExistence()) {

            $description .= ' \PE=' . $protein->getProteinExistence();

        }

        return $description;

    }

    /**

     *

     * {@inheritdoc}

     *

     * @see \pgb_liv\php_ms\Core\Database\Fasta\FastaInterface::getProtein()

     */

    public function getProtein($identifier, $description, $sequence)

    {

        // Parse identifier

        $identifierParts = explode(':', $identifier, 3);

        $protein = new Protein();

        $protein->setUniqueIdentifier($identifier);

        $protein->setSequence($sequence);

        $protein->setDatabasePrefix($identifierParts[0]);

        $protein->setAccession($identifierParts[1]);

        $protein->setDescription($description);

        // Parse description

        preg_match_all('/\\\\(\\w+)=(.+?(?= \\\\|$))/', $description, $matches);

        $attributes = array();

        foreach ($matches[1] as $index => $key) {

            $attributes[$key] = $matches[2][$index];

        }

        $this->parseAttributes($protein, $attributes);

        return $protein;

    }

    /**

     * Parses the attribute array and inputs the data into the protein

     *

     * @param Protein $protein

     *            Object to input values to

     * @param array $attributes

     *            Array to read from

     * @return void

     */

    private function parseAttributes(Protein $protein, array $attributes)

    {

        foreach ($attributes as $key => $value) {

            switch (strtolower($key)) {

                case 'dbuniqueid':

                    $protein->setAccession($value);

                    break;

                case 'cc':

                    $protein->setEntryName($value);

                    break;

                case 'gname':

                    $protein->setGeneName($value);

                    break;

                case 'sv':

                    $protein->setSequenceVersion($value);

                    break;

                case 'pe':

                    $protein->setProteinExistence($value);

                    break;

                case 'pname':

                    $protein->setName($value);

                    break;

                case 'taxname':

                    $protein->setOrganismName($value);

                    break;

                case 'modrespsi':

                case 'modresunimod':

                    $modifications = self::parseModifications($value);

                    $protein->addModifications($modifications);

                    break;

                default:

                    // Invalid or not yet supported fields

                    break;

            }

        }

    }

    /**

     * Parses ModResPsi/ModResUnimod element and returns the parsed modifications

     *

     * @param string $value

     *            The ModResXXX value

     * @return Modification[]

     */

    private static function parseModifications($value)

    {

        preg_match_all('/\(([0-9,]+)\|((?>UNIMOD|MOD):[0-9]+)\|(.+?)(?>\)|\|(.+?)\))/', $value, $matches, PREG_SET_ORDER);

        $modifications = array();

        foreach ($matches as $match) {

            $locations = explode(',', $match[1]);

            foreach ($locations as $location) {

                $modification = new Modification();

                $modification->setLocation((int) $location);

                $modification->setName($match[3]);

                $modification->setAccession($match[2]);

                $modifications[] = $modification;

            }

        }

        return $modifications;

    }

}