Code Coverage |
||||||||||
Classes and Traits |
Functions and Methods |
Lines |
||||||||
| Total | |
100.00% |
1 / 1 |
|
100.00% |
9 / 9 |
CRAP | |
100.00% |
51 / 51 |
| AbstractFragment | |
100.00% |
1 / 1 |
|
100.00% |
10 / 10 |
25 | |
100.00% |
51 / 51 |
| __construct | |
100.00% |
1 / 1 |
3 | |
100.00% |
4 / 4 |
|||
| getIons | |
100.00% |
1 / 1 |
8 | |
100.00% |
25 / 25 |
|||
| getNTerminalMass | |
100.00% |
1 / 1 |
4 | |
100.00% |
7 / 7 |
|||
| getCTerminalMass | |
100.00% |
1 / 1 |
4 | |
100.00% |
8 / 8 |
|||
| getEnd | |
100.00% |
1 / 1 |
1 | |
100.00% |
1 / 1 |
|||
| getStart | |
100.00% |
1 / 1 |
1 | |
100.00% |
1 / 1 |
|||
| getAdditiveMass | |
100.00% |
1 / 1 |
1 | |
100.00% |
0 / 0 |
|||
| setIsReversed | |
100.00% |
1 / 1 |
1 | |
100.00% |
2 / 2 |
|||
| isReversed | |
100.00% |
1 / 1 |
1 | |
100.00% |
1 / 1 |
|||
| getChargedIon | |
100.00% |
1 / 1 |
1 | |
100.00% |
2 / 2 |
|||
| <?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; | |
| } | |
| } |