Source of file ProteinTrait.php

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src/Core/ProteinTrait.php

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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\Core;

use pgb_liv\php_ms\Core\Entry\ProteinEntry;

/**

 * Trait for methods associated with attaching a protein to another object

 * @author Andrew Collins

*/

trait ProteinTrait

/**

     * An array of all proteins this object maps to

     * @var ProteinEntry[]

*/

    private $proteins = array();

/**

     * Add a new protein mapping to this object.

     * Start and end positions on the protein sequence can be specified

     * @param Protein $protein

     *            The protein to map to

     * @param int $start

     *            The start position of this peptide in the sequence

     * @param int $end

     *            The end position this peptide in the sequence

*/

    public function addProtein(Protein $protein, $start = null, $end = null)

        $entry = new ProteinEntry($protein);

        if (! is_null($start)) {

            $entry->setStart($start);

        if (! is_null($end)) {

            $entry->setEnd($end);

        $this->addProteinEntry($entry);

/**

     * This provides direct access to add new entity records and should be used when subclasses are expected

     * @param ProteinEntry $entity

*/

    public function addProteinEntry(ProteinEntry $entry)

        $this->proteins[] = $entry;

/**

     * Gets the set of proteins that this object links to

     * @return ProteinEntry[]

*/

    public function getProteins()

        return $this->proteins;