pgb_liv\php_ms\Writer\MgfWriter
A file writer class for creating Mascot Generic Format (MGF) files.
- Author: Andrew Collins
Synopsis
- // members
- private $fileHandle = null;
- // methods
- public void __construct()
- public void write()
- public void close()
- public void __destruct()
Coverage
| Methods | 75% | 3 / 4 |
| Lines | 90% | 36 / 40 |
Violations
PHPMessDetector
| Line | Rule | Message |
|---|---|---|
| 79 - 81 | ElseExpression | The method write uses an else expression. Else is never necessary and you can simplify the code to work without else. |
Checkstyle
| Line | Column | Severity | Message |
|---|---|---|---|
| 78 | 121 | warning | Line exceeds 120 characters; contains 121 characters |
Tasks
| Line | Task |
|---|---|
| 61 | Validate mandatory/optional fields |
Members
private
- $fileHandle
Methods
public
- __construct() — Creates a new instance of an MGF file writer.
- __destruct() — Finalise method to ensure the instance is correctly closed.
- close() — Closes the file handle for this instance and releases resources.
- write() — Writes the precursor ion and it's associated fragments to the file associated with this instance
History
-
2019-04-02T13:52:52+01:00 (commit #6f46afa)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed test
-
2018-06-25T13:27:30+01:00 (commit #41c132a)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added ChargedMassTrait to provide consistent support for mz values. Note breaking charges to setMassCharge
-
2018-03-02T11:23:12+00:00 (commit #18615e6)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added support for fragmenting protein sequences Added support for reading/writing MGF precursor intensities
-
2018-02-26T13:03:05+00:00 (commit #55786e2)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added support for RT Avg/RT Window in Precursor/Fragment ions
-
2017-08-07T15:16:42+01:00 (commit #f494d2a)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Fixed MgfReader parsing empty fragment lines Fixed MgfWriter writing empty scans/rt elements
-
2017-07-19T11:06:06+01:00 (commit #3cfd460)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Fixed MzIdentML reader using incorrect method name Fixed MGFWriter appending whitespace if charge is missing
-
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
-
2017-07-06T15:20:49+01:00 (commit #15dc11d)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Added additional test coverage
-
2017-07-06T14:31:15+01:00 (commit #299112b)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Fixed MgfWriter using wrong class for input Add MgfWriter tests
-
2017-04-11T17:03:38+01:00 (commit #d65dbda)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added RT filter Added MGF Writer
-
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