pgb_liv\php_ms\Utility\Digest\DigestTrypsin
Trypsin digestion for generated trypsinated peptides.
- Author: Andrew Collins
Synopsis
- // constants
- const CLEAVAGE_RULE = '/(?<=[KR])(?!P|$)/';
- // methods
- public void __construct()
- // Inherited methods from DigestRegularExpression
- public void __construct()
- protected void performDigestion()
- // Inherited methods from AbstractDigest
- public void setMaxMissedCleavage()
- public int getMaxMissedCleavage()
- public void setNmeEnabled()
- public boolean isNmeEnabled()
- public array digest()
- protected abstract void performDigestion()
- protected void setName()
- public void getName()
Hierarchy
Extends
Implements
Coverage
| Methods | 100% | 1 / 1 |
| Lines | 100% | 3 / 3 |
Constants
| Name | Value |
|---|---|
| CLEAVAGE_RULE | '/(?<=[KR])(?!P|$)/' |
Methods
Inherited from pgb_liv\php_ms\Utility\Digest\DigestRegularExpression
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
-
2017-03-31T18:19:53+01:00 (commit #3085645)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Tweaked Trypsin regexp to not split on line terminator Added Peptide support to mass filter Added additional methods to DigestInterface Added initial MS-GF+ code
-
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
-
2017-01-13T13:24:39+00:00 (commit #09d6bb9)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed incorrect constant usage
-
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