Source of file ModifiableSequenceTrait.php
Size: 7,700 Bytes - Last Modified: 2019-05-10T12:24:09+01:00
src/Core/ModifiableSequenceTrait.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\Core; use pgb_liv\php_ms\Constant\PhysicalConstants; use pgb_liv\php_ms\Constant\ChemicalConstants; /** * Trait for providing access to a sequence and set of modifications * * @author Andrew Collins */trait ModifiableSequenceTrait {/** * The amino-acid sequence that can be modified * * @var string */private $sequence; /** * Array of modifications on this protein sequence * * @var Modification[] */private $modifications = array(); /** * Sets whether this sequence is a decoy or not * * @var bool */private $isDecoy; /** * Sets the sequence for this object * * @param string $sequence * The amino-acid sequence to set */public function setSequence($sequence) { if (preg_match('/^[A-Z]+$/', $sequence) !== 1) { throw new \InvalidArgumentException('Argument 1 must be a valid peptide sequence.'); } $this->sequence = $sequence; } /** * Gets the sequence for this object * * @return string */public function getSequence() { return $this->sequence; } /** * Adds the specified modification to this protein * * @param Modification $modification * Modification object to apply */public function addModification(Modification $modification) { $this->modifications[] = $modification; } /** * Adds the specified modifications to this protein * * @param array $modifications * Modifications to apply */public function addModifications(array $modifications) { foreach ($modifications as $modification) { $this->addModification($modification); } } /** * Gets the modifications * * @return Modification[] */public function getModifications() { return $this->modifications; } /** * Clears the modifications */public function clearModifications() { $this->modifications = array(); } /** * Remove a modification */public function removeModification(Modification $searchModification) { foreach ($this->modifications as $key => $modification) { if ($modification !== $searchModification) { continue; } unset($this->modifications[$key]); } } /** * Returns whether this protein contains modifications or not * * @return boolean True if the object contains modifications */public function isModified() { return count($this->modifications) != 0; } /** * Sets whether this sequence is a decoy sequence * * @param bool $bool * Value to set to */public function setIsDecoy($bool) { if (! is_bool($bool)) { throw new \InvalidArgumentException('Argument 1 must be a boolean value'); } $this->isDecoy = $bool; } /** * Gets whether this sequence is a decoy sequence * * @return boolean */public function isDecoy() { return $this->isDecoy; } /** * Gets the length of the sequence in this object * * @return int */public function getLength() { return strlen($this->getSequence()); } /** * Gets the theoretical monoisotopic neutral mass for this sequence and it's modifications * * @return float The neutral mass of the sequence * @deprecated Use getMonoisotopicMass() directly */public function getMass() { return $this->getMonoisotopicMass(); } /** * Gets the theoretical monoisotopic neutral mass for this sequence and it's modifications * * @return float The neutral mass of the sequence */public function getMonoisotopicMass() { $acids = str_split($this->getSequence(), 1); $mass = ChemicalConstants::HYDROGEN_MASS + ChemicalConstants::HYDROGEN_MASS + ChemicalConstants::OXYGEN_MASS; foreach ($acids as $acid) { switch ($acid) { case 'X': case 'B': case 'Z': continue; default: $mass += AminoAcidMono::getMonoisotopicMass($acid); break; } } // Add modification mass // Catch modification on position, residue or terminus foreach ($this->getModifications() as $modification) { if (! is_null($modification->getLocation())) { $mass += $modification->getMonoisotopicMass(); continue; } switch ($modification->getPosition()) { case Modification::POSITION_NTERM: case Modification::POSITION_PROTEIN_NTERM: // TODO: Handle protein level safely // A peptide can be both at protein n-term and not since multiple proteins supported $nTerm = $this->sequence[0]; if (in_array($nTerm, $modification->getResidues())) { $mass += $modification->getMonoisotopicMass(); } break; case Modification::POSITION_CTERM: case Modification::POSITION_PROTEIN_CTERM: // TODO: Handle protein level safely // A peptide can be both at protein n-term and not since multiple proteins supported $cTerm = $this->sequence[strlen($this->sequence) - 1]; if (in_array($cTerm, $modification->getResidues())) { $mass += $modification->getMonoisotopicMass(); } break; default: foreach ($acids as $acid) { if (in_array($acid, $modification->getResidues())) { $mass += $modification->getMonoisotopicMass(); } } break; } } return $mass; } /** * Calculates the theoretical mass/charge value for this sequence. * Note: To get the experimental value, check the PrecursorIon data that this peptide might be a child of. * * @param int $charge * The charge value to use for the calculation */public function getMonoisotopicMassCharge($charge) { $massCharge = $this->getMonoisotopicMass(); $massCharge += PhysicalConstants::PROTON_MASS * $charge; return $massCharge / $charge; } /** * Reverses the current sequence. * Suitable for creating decoy sequences * * @todo This method does not yet respect modification absolute location data */public function reverseSequence() { $this->sequence = strrev($this->sequence); } } |