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| <?php | |
| /** | |
| * Copyright 2019 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\Reader\FastaEntry; | |
| use pgb_liv\php_ms\Core\Protein; | |
| use pgb_liv\php_ms\Core\Database\DefaultDatabase; | |
| use pgb_liv\php_ms\Core\Entry\DatabaseEntry; | |
| /** | |
| * A fallback object to use if unable to safely parse fasta data | |
| * | |
| * @author Andrew Collins | |
| */ | |
| class DefaultFastaEntry implements FastaInterface | |
| { | |
| public static function parseIdentifier($identifier) | |
| { | |
| return array( | |
| $identifier | |
| ); | |
| } | |
| /** | |
| * | |
| * {@inheritdoc} | |
| */ | |
| public function getProtein($identifier, $description) | |
| { | |
| $protein = new Protein(); | |
| $database = new DefaultDatabase(); | |
| $dbEntry = new DatabaseEntry($database); | |
| $dbEntry->setUniqueIdentifier($identifier); | |
| $protein->setDatabaseEntry($dbEntry); | |
| $protein->setDescription($description); | |
| return $protein; | |
| } | |
| } |