pgb_liv\php_ms\Core\ModifiableSequenceTrait
Trait for providing access to a sequence and set of modifications
- Author: Andrew Collins
Synopsis
- // members
- private $sequence;
- private array $modifications = ;
- private bool $isDecoy;
- // methods
- public void setSequence()
- public string getSequence()
- public void addModification()
- public void addModifications()
- public array getModifications()
- public void clearModifications()
- public void removeModification()
- public boolean isModified()
- public void setIsDecoy()
- public boolean isDecoy()
- public int getLength()
- public float getMass()
- public float getMonoisotopicMass()
- public void getMonoisotopicMassCharge()
- public void reverseSequence()
Hierarchy
Coverage
| Methods | 0% | 0 / 15 |
| Lines | 0% | / |
Violations
PHPMessDetector
| Line | Rule | Message |
|---|---|---|
| 193 - 253 | CyclomaticComplexity | The method getMonoisotopicMass() has a Cyclomatic Complexity of 15. The configured cyclomatic complexity threshold is 10. |
| 206 | StaticAccess | Avoid using static access to class 'pgb_liv\php_ms\Core\AminoAcidMono' in method 'getMonoisotopicMass'. |
Tasks
| Line | Task |
|---|---|
| 276+ | This method does not yet respect modification absolute location data |
Members
private
- $isDecoy
—
pgb_liv\php_ms\Core\bool
Sets whether this sequence is a decoy or not - $modifications
—
array
Array of modifications on this protein sequence - $sequence
—
string
The amino-acid sequence that can be modified
Methods
public
- addModification() — Adds the specified modification to this protein
- addModifications() — Adds the specified modifications to this protein
- clearModifications() — Clears the modifications
- getLength() — Gets the length of the sequence in this object
- getMass() — Gets the theoretical monoisotopic neutral mass for this sequence and it's modifications
- getModifications() — Gets the modifications
- getMonoisotopicMass() — Gets the theoretical monoisotopic neutral mass for this sequence and it's modifications
- getMonoisotopicMassCharge() — Calculates the theoretical mass/charge value for this sequence.
- getSequence() — Gets the sequence for this object
- isDecoy() — Gets whether this sequence is a decoy sequence
- isModified() — Returns whether this protein contains modifications or not
- removeModification() — Remove a modification
- reverseSequence() — Reverses the current sequence.
- setIsDecoy() — Sets whether this sequence is a decoy sequence
- setSequence() — Sets the sequence for this object
History
-
2019-04-04T15:43:11+01:00 (commit #091751e)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Removed redundant check
-
2019-04-04T15:00:11+01:00 (commit #0a24fdf)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Updated tests
-
2018-05-24T12:07:12+01:00 (commit #24d745d)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Moved average and monoisotopic mass methods to trait to provide consistency to objects
-
2018-05-23T12:14:08+01:00 (commit #cb13f8c)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Addition of Chemical and Physical constants file. Currently only contains constants used internally. Deprecated original constant sites and updated internal usages.
-
2018-03-08T12:22:15+00:00 (commit #fbf14fd)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added support for removing a modificiation
-
2018-03-02T11:23:12+00:00 (commit #18615e6)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added support for fragmenting protein sequences Added support for reading/writing MGF precursor intensities
-
2017-10-25T14:16:01+01:00 (commit #d497193)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Minor code tidy
-
2017-10-25T11:32:31+01:00 (commit #ccae3f8)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed various documentation and import issues
-
2017-10-24T16:05:10+01:00 (commit #b2240f0)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Tweaked PHPMD rules
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2017-10-12T12:30:54+01:00 (commit #9a5386a)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed Sonar issues
-
2017-10-11T16:30:22+01:00 (commit #445c0af)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added support for rank in Identification objects Added support for theoretical monoisotopic mass charge for peptide objects
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2017-09-12T13:45:55+01:00 (commit #bac2d5d)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Add modifications to sequence mass calculation
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2017-07-13T11:22:57+01:00 (commit #59351c4)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Removed deprecated methods Fixed comments Added further method validation
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2017-06-30T19:52:10+01:00 (commit #3c20d79)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Added additional testing Moved sequence mass calculation to trait from peptide. Allows protein mass to be calculated.
-
2017-05-10T16:39:50+01:00 (commit #1c94e76)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Replaced SpectraEntry with PrecursorIon and FragmentIon Added internal support for complete decoy proteins
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2017-05-09T15:17:48+01:00 (commit #b5944dd)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Updated to require PHP 5.4 / added traits