pgb_liv\php_ms\Utility\Digest\DigestRegularExpression
A base digestion class that can be used to perform digestion with a valid regular expression.
- Author: Andrew Collins
Synopsis
- // members
- private $cleavageRule;
- // methods
- public void __construct()
- protected void performDigestion()
- // Inherited methods from AbstractDigest
- public void setMaxMissedCleavage()
- public int getMaxMissedCleavage()
- public void setNmeEnabled()
- public boolean isNmeEnabled()
- public array digest()
- protected abstract void performDigestion()
- protected void setName()
- public void getName()
Hierarchy
Extends
Implements
Coverage
| Methods | 50% | 1 / 2 |
| Lines | 97.06% | 33 / 34 |
Violations
Checkstyle
| Line | Column | Severity | Message |
|---|---|---|---|
| 95 | 27 | error | Opening parenthesis of a multi-line function call must be the last content on the line |
| 95 | 67 | error | Only one argument is allowed per line in a multi-line function call |
| 96 | 1 | error | Multi-line function call not indented correctly; expected 16 spaces but found 20 |
| 96 | 80 | error | Closing parenthesis of a multi-line function call must be on a line by itself |
Members
private
- $cleavageRule
—
string
Cleavage rule regular expresion.
Methods
protected
- performDigestion() — Digest the protein and produce peptides matching the enzyme rules.
Inherited from pgb_liv\php_ms\Utility\Digest\AbstractDigest
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
-
2019-04-02T11:54:45+01:00 (commit #c7d351b)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Code tidy
-
2017-10-12T11:54:29+01:00 (commit #c1a6d58)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added support for multiple proteins on peptide identifications Added support for Chromosome objects on proteins Added support for writing proBedFiles
-
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
-
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
-
2017-03-14T17:02:52+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
-
2017-01-17T16:17:26+00:00 (commit #a805feb)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed Digest generating empty peptide if peptide terminated with R or K
-
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
-
2017-01-10T17:57:46+00:00 (commit #acca036)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed compile error due to multiple constructors
-
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