pgb_liv\php_ms\Utility\Digest\AbstractDigest
Abstract class for digestion algorithms.
- Author: Andrew Collins
Synopsis
- // members
- private bool $isNmeEnabled = true;
- private integer $maxMissedCleavage = 0;
- private string $name = 'Unknown';
- // methods
- public void setMaxMissedCleavage()
- public int getMaxMissedCleavage()
- public void setNmeEnabled()
- public boolean isNmeEnabled()
- public array digest()
- private array performMethionineExcision()
- protected abstract void performDigestion()
- protected void setName()
- public void getName()
Coverage
| Methods | 88.89% | 8 / 9 |
| Lines | 97.3% | 36 / 37 |
Violations
Checkstyle
| Line | Column | Severity | Message |
|---|---|---|---|
| 62 | 1 | error | Multi-line function call not indented correctly; expected 12 spaces but found 16 |
| 62 | 99 | error | Closing parenthesis of a multi-line function call must be on a line by itself |
| 91 | 1 | error | Multi-line function call not indented correctly; expected 12 spaces but found 16 |
| 91 | 91 | error | Closing parenthesis of a multi-line function call must be on a line by itself |
Members
private
- $isNmeEnabled
—
pgb_liv\php_ms\Utility\Digest\bool
Whether to perform n-terminus methionine excision when generating peptides - $maxMissedCleavage
—
integer
Maximum number of missed cleavages a peptide may contain - $name
—
string
The name for this enzyme
Methods
private
- performMethionineExcision() — Performs methionine excision on an array of peptides
protected
public
- digest() — Digest the protein and produce peptides matching the enzyme rules.
- getMaxMissedCleavage() — Gets the maximum missed cleavage count value
- getName()
- isNmeEnabled() — Returns whether n-terminal methionine excision will be performed or not.
- setMaxMissedCleavage() — Set the maximum number of missed cleavages the algorithm should produce.
- setNmeEnabled() — Sets whether n-terminal methionine excision should be performed.
History
-
2019-04-01T14:53:41+01:00 (commit #cc91234)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed IonSort using outdated methods Fixed digest performing NME on single AA sequences Changed handling of database data, allows for a single sequence to map to multiple formats. Should be better suited for PEFF
-
2017-12-19T15:28:53+00:00 (commit #218cf30)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added methods to Tolerance for comparing two values
-
2017-10-12T12:20:52+01:00 (commit #178ea94)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed AbstractDigest not reflecting protein changes Fixed unit tests
-
2017-05-31T14:38:50+01:00 (commit #68bb326)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed MzML merge not updating precursor references Fixed FastaReader failing if protein did not have a description text after the identifier
-
2017-04-19T18:15:41+01:00 (commit #856a8a6)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Updated Peptide/Modification to use methods from CrowdSourcing
-
2017-03-30T17:42:57+01:00 (commit #5842bc4)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added all PSI-MS specified enzymes
-
2017-03-14T17:02:52+00:00 (commit #49ccdc6)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added addition Digest test coverage
-
2017-02-07T12:08:27+00:00 (commit #df5ea29)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
* Added support for n-terminus methionine excision to digestion
-
2017-01-19T17:19:34+00:00 (commit #8517fc8)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added validation to SpectraEntry->setCharge Added validation to AbstractDigest->setMaxMissedCleavage Added additional test to DigestTrypsin to validate an empty peptide is not created Added Spectra charge filtering
-
2017-01-13T13:17:36+00:00 (commit #3c2d727)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed warnings generated by XML missing doctype Added DigestRegularExpression as boiler plate code for all regular expression suitable enzyme
-
2017-01-11T15:23:51+00:00 (commit #2a88d63)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added Trpysin digestion unit test
-
2017-01-11T13:56:23+00:00 (commit #91a55ef)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Improved filtering and digestion documentation
-
2017-01-11T13:40:21+00:00 (commit #9d6bc95)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added peptide filtering by length
-
2017-01-10T17:59:54+00:00 (commit #b31d27a)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed AbstractDigest extending itself
-
2017-01-10T17:51:30+00:00 (commit #b3dacff)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added initial Protein code Added initial Peptide code Added initial digestion code Improved Fasta and MGF tests
-
2017-01-09T16:16:46+00:00 (commit #e51fa74)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added Uniprot Fasta parsing