Source of file FragmentFactory.php
Size: 3,066 Bytes - Last Modified: 2019-05-10T12:24:09+01:00
src/Utility/Fragment/FragmentFactory.php
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| <?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\Utility\Fragment; use pgb_liv\php_ms\Core\ModifiableSequenceInterface; /** * Helper methods to get fragmentation types by instrument type * * @author Andrew Collins */class FragmentFactory {/** * List of all methods currently supported * * @var string[] */private static $methods = array( 'CID', 'HCD', 'ECD', 'ETD', 'CTD', 'EDD', 'NETD', 'ETHCD' ); public static function getFragmentMethods() { return self::$methods; } /** * For a specified method, returns the possible fragmentat ion types that may be produced * * @param string $method * The method to get fragment types for * @param ModifiableSequenceInterface $sequence * The peptide or protein sequence object to get fragment types for * @return FragmentInterface[] */public static function getMethodFragments($method, ModifiableSequenceInterface $sequence) { $fragmentTypes = array(); switch (strtoupper($method)) { case 'CID': case 'HCD': $fragmentTypes['B'] = new BFragment($sequence); $fragmentTypes['Y'] = new YFragment($sequence); break; case 'ECD': $fragmentTypes['C'] = new CFragment($sequence); $fragmentTypes['Z'] = new ZFragment($sequence); $fragmentTypes['B'] = new BFragment($sequence); break; case 'ETD': $fragmentTypes['C'] = new CFragment($sequence); $fragmentTypes['Z'] = new ZFragment($sequence); break; case 'CTD': case 'EDD': case 'NETD': $fragmentTypes['A'] = new AFragment($sequence); $fragmentTypes['X'] = new XFragment($sequence); break; case 'ETHCD': $fragmentTypes['B'] = new BFragment($sequence); $fragmentTypes['Y'] = new YFragment($sequence); $fragmentTypes['C'] = new CFragment($sequence); $fragmentTypes['Z'] = new ZFragment($sequence); break; default: throw new \InvalidArgumentException('Unknown fragmentation method type "' . $method . '"'); } return $fragmentTypes; } } |