Source of file MzIdentMlReader1Interface.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\Reader;

use pgb_liv\php_ms\Core\Spectra\PrecursorIon;

/**

 *

 * @author Andrew Collins

 */

interface MzIdentMlReader1Interface

{

    public function getInputs();

    public function getAnalysisProtocolCollection();

    /**

     *

     * @return PrecursorIon[]

     */

    public function getAnalysisData();

    public function getProteinDetectionList();

    /**

     * Gets the CvParam name attribute from any previously seen and indexed CvParam.

     * For this method to return a value the accession should already have been read by this parser.

     *

     * @param string $accession

     *            The accession to return the name value for.

     *

     * @throws \OutOfRangeException The accession was not found and consequently has not yet been parsed by this instance.

     * @return string

     */

    public function getCvParamName($accession);

}