Source of file DefaultFastaEntry.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;

/**

 * 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 DefaultFastaEntry implements FastaInterface

{

    /**

     *

     * {@inheritdoc}

     *

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

     */

    public function getHeader()

    {

        return '';

    }

    /**

     *

     * {@inheritdoc}

     *

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

     */

    public function getDescription(Protein $protein)

    {

        $description = '>' . $protein->getUniqueIdentifier();

        if (! is_null($protein->getDescription())) {

            $description .= ' ' . $protein->getDescription();

        }

        return $description;

    }

    /**

     *

     * {@inheritdoc}

     *

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

     */

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

    {

        $protein = new Protein();

        $protein->setUniqueIdentifier($identifier);

        $protein->setDescription($description);

        $protein->setSequence($sequence);

        return $protein;

    }

}