pgb_liv\php_ms\Reader\FastaEntry\UniProtFastaEntry
FASTA entry parser to map UniProt header to protein elements
- Author: Andrew Collins
Synopsis
class UniProtFastaEntry
implements
FastaInterface
{
- // methods
- public static void parseIdentifier()
- public void getProtein()
Hierarchy
Coverage
| Methods | 0% | 0 / 2 |
| Lines | 64.81% | 35 / 54 |
Violations
PHPMessDetector
| Line | Rule | Message |
|---|---|---|
| 54 - 121 | CyclomaticComplexity | The method getProtein() has a Cyclomatic Complexity of 14. The configured cyclomatic complexity threshold is 10. |
| 54 - 121 | NPathComplexity | The method getProtein() has an NPath complexity of 504. The configured NPath complexity threshold is 200. |
| 64 | StaticAccess | Avoid using static access to class '\pgb_liv\php_ms\Core\Database\UniProtSpDatabase' in method 'getProtein'. |
| 66 | StaticAccess | Avoid using static access to class '\pgb_liv\php_ms\Core\Database\UniProtTrDatabase' in method 'getProtein'. |
| 99 | StaticAccess | Avoid using static access to class '\pgb_liv\php_ms\Core\Organism' in method 'getProtein'. |
| 108 | StaticAccess | Avoid using static access to class '\pgb_liv\php_ms\Core\Gene' in method 'getProtein'. |
Methods
public
- getProtein() — {@inheritdoc}
- parseIdentifier()
History
-
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
-
2019-04-01T15:49:25+01:00 (commit #c1b6463)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
no message
-
2019-04-01T15:43:05+01:00 (commit #a852004)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed tests
-
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Fixed IonSort using outdated methods Fixed digest performing NME on single AA sequences Changed handling of database data, allows for a single sequence to map to multiple formats.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