Source of file FastaInterface.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;

/**

 * Interface to fasta file formats

 *

 * @author Andrew Collins

 */

interface FastaInterface

{

    /**

     * Gets the header text should be written at the start of the file output

     *

     * @return string

     */

    public function getHeader();

    /**

     * Gets the description text line that should be written for the protein entry

     *

     * @param Protein $protein

     *            The protein to get the plain text format for

     * @return string

     */

    public function getDescription(Protein $protein);

    /**

     * Gets a protein object from the FASTA fields

     *

     * @param string $identifier

     *            The identifier string

     * @param string $description

     *            The description string without identifier

     * @param string $sequence

     *            The full sequence block

     * @return Protein

     */

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

}