pgb_liv\php_ms\Reader\FastaEntry\PeffFastaEntry
FASTA entry parser to map generic PEFF headers to protein elements
- Author: Andrew Collins
Synopsis
- // methods
- public static void parseIdentifier()
- public void getProtein()
- private void parseAttributes()
- private static array parseModifications()
Hierarchy
Coverage
| Methods | 0% | 0 / 4 |
| Lines | 0% | 0 / 86 |
Violations
PHPMessDetector
| Line | Rule | Message |
|---|---|---|
| 60 | StaticAccess | Avoid using static access to class '\pgb_liv\php_ms\Core\Database\DatabaseFactory' in method 'getProtein'. |
| 89 - 146 | CyclomaticComplexity | The method parseAttributes() has a Cyclomatic Complexity of 20. The configured cyclomatic complexity threshold is 10. |
| 92 | StaticAccess | Avoid using static access to class '\pgb_liv\php_ms\Core\Organism' in method 'parseAttributes'. |
| 110 | StaticAccess | Avoid using static access to class '\pgb_liv\php_ms\Core\Gene' in method 'parseAttributes'. |
Methods
private
- parseAttributes() — Parses the attribute array and inputs the data into the protein
- parseModifications() — Parses ModResPsi/ModResUnimod element and returns the parsed modifications
public
- getProtein() — {@inheritdoc}
- parseIdentifier()
History
-
2019-04-04T12:35:18+01:00 (commit #2da71d6)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Redundancy tidy
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2019-04-04T12:15:00+01:00 (commit #984f154)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Clean up
-
2019-04-04T11:42:00+01:00 (commit #26a21ad)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Refined database support model Updated PEFF support to be compliant
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2019-04-02T13:48:22+01:00 (commit #f90fad3)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Code tidy
-
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Fixed IonSort using outdated methods Fixed digest performing NME on single AA sequences Changed handling of database data, allows for a single sequence to map to multiple formats.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
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2018-03-23T16:39:58+00:00 (commit #f7704be)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added support for PEFF unimod modifications
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2017-10-25T09:20:00+01:00 (commit #57f57a0)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Minor code tidy
-
2017-07-26T17:11:10+01:00 (commit #02a75db)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Fixed PEFF parser not parsing if keyword case is not exact Added support for calculating ppm delta from da tolerance
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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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2017-07-10T14:02:20+01:00 (commit #7f8830c)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Fixed PEFF writer using incorrect slash Refactored fasta reader/writers Added PEFF testing
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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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2017-05-09T17:19:06+01:00 (commit #cfe67d8)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed Unimod fasta regex Added Fasta/PEFF writer support
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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
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2017-05-08T17:36:37+01:00 (commit #7de6913)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added PEFF support Added support for modifications on proteins