Source of file AbstractFragment.php
Size: 5,057 Bytes - Last Modified: 2019-05-10T12:24:09+01:00
src/Utility/Fragment/AbstractFragment.php
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| <?php/** * Copyright 2018 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\AminoAcidMono; use pgb_liv\php_ms\Core\ModifiableSequenceInterface; use pgb_liv\php_ms\Constant\PhysicalConstants; /** * Abstract class containing generic filtering methods * * @author Andrew Collins */abstract class AbstractFragment implements FragmentInterface {/** * Whether the fragments should be read right-left or left-right * * @var bool */private $isReversed = false; protected $sequence; /** * Creates a new instance of this fragmenter using the specified peptide * * @param ModifiableSequenceInterface $sequence * Peptide object which must contain a sequence * @throws \InvalidArgumentException If the peptide object does not contain a sequence */public function __construct(ModifiableSequenceInterface $sequence) { if (is_null($sequence->getSequence()) || strlen($sequence->getSequence()) == 0) { throw new \InvalidArgumentException('Null or empty sequence received.'); } $this->sequence = $sequence; } /** * * {@inheritdoc} */public function getIons($charge = 1) { $ions = array(); $sequenceString = $this->sequence->getSequence(); $sum = 0; $cTermMass = $this->getCTerminalMass(); $nTermMass = $this->getNTerminalMass(); for ($i = $this->getStart(); $i < $this->getEnd(); $i ++) { $residue = $sequenceString[$i]; $mass = AminoAcidMono::getMonoisotopicMass($residue); // Add mass if ($i == 0) { $mass += $this->getAdditiveMass(); $mass += $nTermMass; } // Add modification mass // Catch modification on position or residue foreach ($this->sequence->getModifications() as $modification) { // Check every position or residue if ($modification->getLocation() === $i + 1 || (is_null($modification->getLocation()) && in_array($residue, $modification->getResidues()))) { // Residue is modified $mass += $modification->getMonoisotopicMass(); } } if ($i + 1 == $this->sequence->getLength()) { $mass += $cTermMass; } $sum += $mass; $ions[$i + 1] = $this->getChargedIon($sum, $charge); } return $ions; } protected function getNTerminalMass() { $mass = 0; foreach ($this->sequence->getModifications() as $modification) { if ($modification->getLocation() === 0 || in_array('[', $modification->getResidues())) { $mass += $modification->getMonoisotopicMass(); } } return $mass; } protected function getCTerminalMass() { $mass = 0; foreach ($this->sequence->getModifications() as $modification) { if ($modification->getLocation() === $this->sequence->getLength() + 1 || in_array(']', $modification->getResidues())) { $mass += $modification->getMonoisotopicMass(); } } return $mass; } /** * Gets the end position of the detectable fragments * * @return int */protected function getEnd() { return $this->sequence->getLength(); } /** * Gets the start position of the detectable fragments * * @return int */protected function getStart() { return 0; } /** * Gets the additional mass gained in fragmentation * * @return double */abstract protected function getAdditiveMass(); protected function setIsReversed($bool) { $this->isReversed = $bool; } /** * * {@inheritdoc} */public function isReversed() { return $this->isReversed; } /** * Charges the mass to the specified charge * * @param double $mass * The neutral mass to charge * @param int $charge * The integer charge value to charge too * @return double */protected function getChargedIon($mass, $charge) { $chargedMass = $mass + (PhysicalConstants::PROTON_MASS * $charge); return $chargedMass / $charge; } } |