Source of file Modification.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\Core;

/**

 * A modification object which may be applied to a peptide or protein

 *

 * @author Andrew Collins

 */

class Modification

{

    const TYPE_FIXED = 0;

    const TYPE_VARIABLE = 1;

    const POSITION_ANY = 'any';

    const POSITION_NTERM = 'N-term';

    const POSITION_CTERM = 'C-term';

    const POSITION_PROTEIN_NTERM = 'Prot-N-term';

    const POSITION_PROTEIN_CTERM = 'Prot-C-term';

    private $location;

    private $monoisotopicMass;

    private $averageMass;

    private $name;

    private $residues;

    private $type = Modification::TYPE_VARIABLE;

    private $position = Modification::POSITION_ANY;

    /**

     * Accession (HUPO-PSI format) for this modification

     *

     * @var string

     */

    private $accession;

    /**

     * Sets the location for this modification

     *

     * @param int $location

     *            The location to set this modification at

     * @throws \InvalidArgumentException If argument 1 is not of type int

     */

    public function setLocation($location)

    {

        if (! is_int($location)) {

            throw new \InvalidArgumentException(

                'Argument 1 must be an int value. Valued passed is of type ' . gettype($location));

        }

        $this->location = $location;

    }

    /**

     * Gets the location of this modification

     *

     * @return int

     */

    public function getLocation()

    {

        return $this->location;

    }

    /**

     * Sets the monoisotopic mass for this modification

     *

     * @param float $mass

     *            The monoisotopic mass to set

     * @throws \InvalidArgumentException If argument 1 is not of type float

     */

    public function setMonoisotopicMass($mass)

    {

        if (! is_float($mass) && ! is_int($mass)) {

            throw new \InvalidArgumentException(

                'Argument 1 must be a float or integer value. Valued passed is of type ' . gettype($mass));

        }

        $this->monoisotopicMass = $mass;

    }

    /**

     * Gets the monoisotopic mass

     *

     * @return float

     */

    public function getMonoisotopicMass()

    {

        return $this->monoisotopicMass;

    }

    public function setAverageMass($mass)

    {

        if (! is_float($mass) && ! is_int($mass)) {

            throw new \InvalidArgumentException(

                'Argument 1 must be a float or integer value. Valued passed is of type ' . gettype($mass));

        }

        $this->averageMass = $mass;

    }

    public function getAverageMass()

    {

        return $this->averageMass;

    }

    public function setName($name)

    {

        $this->name = $name;

    }

    /**

     * Gets this name of this instance

     *

     * @return string

     */

    public function getName()

    {

        return $this->name;

    }

    /**

     * Set residues for this modification

     *

     * @param array $residues

     *            Array of residues this modification may occur on

     * @throws \InvalidArgumentException If argument 1 is not of type float

     */

    public function setResidues(array $residues)

    {

        if (empty($residues)) {

            throw new \InvalidArgumentException('Argument 1 must not be empty.');

        }

        foreach ($residues as $residue) {

            if (!preg_match('/^[A-Z]$/', $residue)) {

                throw new \InvalidArgumentException('Argument 1 must be an array of single char values (A-Z). Value passed is ' . $residue);

            }

        }

        // Force sort order

        sort($residues);

        // Force unique residue positions

        $this->residues = array_combine($residues, $residues);

    }

    /**

     * Gets the residues the modification is assosciated with

     *

     * @return array

     */

    public function getResidues()

    {

        if (is_null($this->residues)) {

            return array();

        }

        return array_values($this->residues);

    }

    public function setType($type)

    {

        $this->type = $type;

    }

    public function getType()

    {

        return $this->type;

    }

    public function isFixed()

    {

        return $this->type == Modification::TYPE_FIXED;

    }

    public function isVariable()

    {

        return $this->type == Modification::TYPE_VARIABLE;

    }

    /**

     * Sets the position this modification can occur on within the peptide or protein.

     * Default is 'Any'.

     *

     * @param int $position

     *            Position the modification can occur, see POSITION_ for list of options.

     * @throws \InvalidArgumentException If unknown position specified

     */

    public function setPosition($position)

    {

        switch ($position) {

            case Modification::POSITION_ANY:

            case Modification::POSITION_NTERM:

            case Modification::POSITION_CTERM:

            case Modification::POSITION_PROTEIN_NTERM:

            case Modification::POSITION_PROTEIN_CTERM:

                $this->position = $position;

                break;

            default:

                throw new \InvalidArgumentException('Postion must be any or terminus (see POSITION_XXXX)');

        }

    }

    public function getPosition()

    {

        return $this->position;

    }

    /**

     * Sets the accession for this modification.

     * Recommended for use when interacting with HUPO-PSI formats.

     *

     * @param string $accession

     *            The accession value to set

     */

    public function setAccession($accession)

    {

        $this->accession = $accession;

    }

    /**

     * Gets the accession for this modification if present

     *

     * @return string

     */

    public function getAccession()

    {

        return $this->accession;

    }

}