pgb_liv\php_ms\Writer\ProBedWriter
A file writer class for creating proBed files.
- Author: Andrew Collins
Synopsis
- // members
- private $fileHandle = null;
- private $name;
- private integer $uniqueId = 0;
- // methods
- public void __construct()
- public void write()
- public void close()
- public void __destruct()
- private void writeHeader()
- private void writeIdentification()
- private void getModificationString()
- private void isValid()
Coverage
| Methods | 0% | 0 / 8 |
| Lines | 0% | 0 / 99 |
Violations
PHPMessDetector
| Line | Rule | Message |
|---|---|---|
| 86 - 189 | ExcessiveMethodLength | The method writeIdentification() has 104 lines of code. Current threshold is set to 100. Avoid really long methods. |
| 199 - 201 | ElseExpression | The method getModificationString uses an else expression. Else is never necessary and you can simplify the code to work without else. |
Checkstyle
| Line | Column | Severity | Message |
|---|---|---|---|
| 156 | 13 | error | Opening parenthesis of a multi-line function call must be the last content on the line |
| 157 | 146 | warning | Line exceeds 120 characters; contains 146 characters |
| 158 | 1 | error | Multi-line function call not indented correctly; expected 12 spaces but found 16 |
| 158 | 21 | error | Closing parenthesis of a multi-line function call must be on a line by itself |
Tasks
| Line | Task |
|---|---|
| 219 | Correct handling missing version. Required by spec? |
Members
private
- $fileHandle
- $name
- $uniqueId
Methods
private
public
- __construct() — Creates a new instance of a ProBed Writer.
- __destruct()
- close()
- write()
History
-
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Fixed IonSort using outdated methods Fixed digest performing NME on single AA sequences Changed handling of database data, allows for a single sequence to map to multiple formats.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
-
2017-12-06T17:10:05+00:00 (commit #d5b69a2)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed Peptide Exon Nucleotide Sizes not being read as an array Fixed proBed blockSizes not writing an array
-
2017-12-04T14:07:51+00:00 (commit #a5cf8e1)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Disabled requirement that GenomeReferenceVersion must exist (for novel data)
-
2017-10-25T11:32:31+01:00 (commit #ccae3f8)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed various documentation and import issues
-
2017-10-25T09:20:00+01:00 (commit #57f57a0)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Minor code tidy
-
2017-10-18T14:41:27+01:00 (commit #9d9cb35)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added ability to set custom headers to proBed writer Added test skipping if proteome exchange is offline
-
2017-10-17T13:36:22+01:00 (commit #2610601)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed Sonar issues
-
2017-10-12T11:54:29+01:00 (commit #c1a6d58)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added support for multiple proteins on peptide identifications Added support for Chromosome objects on proteins Added support for writing proBedFiles