pgb_liv\php_ms\Search\MsgfPlusSearch
Client to perform MS-GF+ search and results retrieval
- Author: Andrew Collins
Synopsis
- // methods
- public void __construct()
- public void setHost()
- public string search()
- private void getCommand()
- private void appendArgument()
- private string executeCommand()
Coverage
| Methods | 16.67% | 1 / 6 |
| Lines | 4.17% | 3 / 72 |
Violations
PHPMessDetector
| Line | Rule | Message |
|---|---|---|
| 90 - 93 | ElseExpression | The method search uses an else expression. Else is never necessary and you can simplify the code to work without else. |
| 125 | StaticAccess | Avoid using static access to class '\pgb_liv\php_ms\Search\Parameters\MsgfPlusSearchParameters' in method 'getCommand'. |
| 184 | UnusedLocalVariable | Avoid unused local variables such as '$pipes'. |
Members
private
- $exePath
- $host
- $javaPath
Methods
private
- appendArgument()
- executeCommand() — Executes the MSGF+ Command.
- getCommand()
public
- __construct() — Create a new instance of this class.
- search() — Perform the MS-GF+ search using the specified parameters.
- setHost() — Execute the command on the target host via SSH
History
-
2019-07-10T11:49:55+01:00 (commit #4e2d0ff)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed bad method call in FDR calculator Added remote host usage to MS-GF+ search
-
2017-10-03T10:43:42+01:00 (commit #4c7c19e)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed Sonar issues
-
2017-09-29T13:16:59+01:00 (commit #95a27f9)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Add comments
-
2017-09-28T13:18:16+01:00 (commit #3acafbc)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed modification not allowing integer masses Fixed MS-GF+ Search not encapsulating file paths with quotes
-
2017-07-24T08:37:59+01:00 (commit #39f6125)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed MS-GF+ Search
-
2017-07-24T08:33:56+01:00 (commit #f930cd2)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed sonar issues
-
2017-04-21T17:55:07+01:00 (commit #b85fd81)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed MS-GF+ mod file creation using wrong method
-
2017-04-04T17:41:32+01:00 (commit #831a98c)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Required Search tolerances to use Tolerance class Added additional validation
-
2017-04-04T15:47:43+01:00 (commit #f1a1e63)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Add complete implementation of MS-GF+ search
-
2017-03-31T18:19:53+01:00 (commit #3085645)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Tweaked Trypsin regexp to not split on line terminator Added Peptide support to mass filter Added additional methods to DigestInterface Added initial MS-GF+ code