pgb_liv\php_ms\Writer\FastaWriter
A file writer class for creating FASTA files.
Generates data in PEFF only.
- Author: Andrew Collins
Synopsis
- // constants
- const DECOY_COUNT = '_DecoyCount';
- const UNKNOWN_PLACEHOLDER = 'Unknown';
- // members
- private $tmpHandle = null;
- private $outputHandle = null;
- private array $databases = ;
- private $conversion = null;
- // methods
- public void __construct()
- public void write()
- public void close()
- public void __destruct()
- private void writeHeader()
- private void writeDescription()
- private void writeSequence()
- private void recordDatabase()
- private void initialiseDatabase()
- public void setHeader()
- public void setConversionSource()
- public void isConversion()
Coverage
| Methods | 41.67% | 5 / 12 |
| Lines | 51.79% | 58 / 112 |
Violations
PHPMessDetector
| Line | Rule | Message |
|---|---|---|
| 125 - 171 | CyclomaticComplexity | The method writeDescription() has a Cyclomatic Complexity of 10. The configured cyclomatic complexity threshold is 10. |
| 125 - 171 | NPathComplexity | The method writeDescription() has an NPath complexity of 240. The configured NPath complexity threshold is 200. |
Checkstyle
| Line | Column | Severity | Message |
|---|---|---|---|
| 185 | 122 | warning | Line exceeds 120 characters; contains 122 characters |
Constants
| Name | Value |
|---|---|
| DECOY_COUNT | '_DecoyCount' |
| UNKNOWN_PLACEHOLDER | 'Unknown' |
Members
private
- $conversion
- $databases
- $outputHandle
- $tmpHandle
Methods
private
public
- __construct() — Creates a new instance of a Fasta Writer.
- __destruct()
- close()
- isConversion()
- setConversionSource()
- setHeader()
- write()
History
-
2019-04-04T12:35:18+01:00 (commit #2da71d6)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Redundancy tidy
-
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
-
2019-04-02T11:54:45+01:00 (commit #c7d351b)
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Fixed IonSort using outdated methods Fixed digest performing NME on single AA sequences Changed handling of database data, allows for a single sequence to map to multiple formats.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
-
2018-01-03T14:41:00+00:00 (commit #3adbebd)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added support for null lengths on FilterLength
-
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
-
2017-07-07T15:33:52+01:00 (commit #164b80b)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Added fasta writer testing Improved fasta parser auto-detect Added uniprot fasta writer
-
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
-
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
-
2017-04-07T17:51:31+01:00 (commit #9252412)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
* Added fragment generation code * Added FastaWriter class