Source of file FilterMass.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\Utility\Filter;

use pgb_liv\php_ms\Core\Peptide;

use pgb_liv\php_ms\Core\Spectra\IonInterface;

/**

 * Creates an instance of a filter than can be used with a list to

 * remove those which do not fit the criteria.

 *

 * @author Andrew Collins

 */

class FilterMass extends AbstractFilter

{

    /**

     * Minimum mass, inclusive

     *

     * @var float

     */

    private $minMass;

    /**

     * Maximum mass, inclusive

     *

     * @var float

     */

    private $maxMass;

    /**

     * Creates a new instance with the specified minimum and maximum mass values.

     * Specify null for minimum or maximum for no limit.

     *

     * @param float $minMass

     *            Minimum mass, inclusive

     * @param float $maxMass

     *            Maximum mass, inclusive

     */

    public function __construct($minMass, $maxMass)

    {

        if (! is_float($minMass) && ! is_int($minMass) && ! is_null($minMass)) {

            throw new \InvalidArgumentException(

                'Argument 1 must be of type float. Value is of type ' . gettype($minMass));

        }

        if (! is_float($maxMass) && ! is_int($maxMass) && ! is_null($maxMass)) {

            throw new \InvalidArgumentException(

                'Argument 2 must be of type float. Value is of type ' . gettype($maxMass));

        }

        $this->minMass = $minMass;

        $this->maxMass = $maxMass;

    }

    /**

     *

     * {@inheritdoc}

     *

     * @see \pgb_liv\php_ms\Utility\Filter\AbstractFilter::isValidSpectra()

     */

    public function isValidSpectra(IonInterface $spectra)

    {

        if (! is_null($this->minMass) && $spectra->getMass() < $this->minMass) {

            return false;

        }

        if (! is_null($this->maxMass) && $spectra->getMass() > $this->maxMass) {

            return false;

        }

        return true;

    }

    /**

     *

     * {@inheritdoc}

     *

     * @see \pgb_liv\php_ms\Utility\Filter\AbstractFilter::isValidPeptide()

     */

    public function isValidPeptide(Peptide $peptide)

    {

        // Mass is calculated at request so must be cached

        $mass = $peptide->getMonoisotopicMass();

        if (! is_null($this->minMass) && $mass < $this->minMass) {

            return false;

        }

        if (! is_null($this->maxMass) && $mass > $this->maxMass) {

            return false;

        }

        return true;

    }

}