pgb_liv\php_ms\Search\Parameters\AbstractSearchParameters
Abstract class containing generic filtering methods
- Author: Andrew Collins
Synopsis
- // members
- private $databases;
- private $spectraPath;
- private $precursorTolerance;
- private $fragmentTolerance;
- private $enzyme;
- private boolean $isDecoyEnabled = false;
- private $missedCleavageCount;
- private array $modifications = ;
- // methods
- public void setDatabases()
- public string getDatabases()
- public void setEnzyme()
- public void getEnzyme()
- public void setMissedCleavageCount()
- public void getMissedCleavageCount()
- public void getPrecursorTolerance()
- public void setPrecursorTolerance()
- public void setFragmentTolerance()
- public Tolerance getFragmentTolerance()
- public void setSpectraPath()
- public void getSpectraPath()
- public void setDecoyEnabled()
- public void isDecoyEnabled()
- public void addModification()
- public array getModifications()
- public void clearModifications()
- public void addFixedModification()
- public void getFixedModifications()
- public void addVariableModification()
- public void getVariableModifications()
Coverage
| Methods | 100% | 21 / 21 |
| Lines | 100% | 52 / 52 |
Violations
PHPMessDetector
| Line | Rule | Message |
|---|---|---|
| 119 | BooleanArgumentFlag | The method setSpectraPath has a boolean flag argument $ignoreValidation, which is a certain sign of a Single Responsibility Principle violation. |
Members
private
- $databases
- $enzyme
- $fragmentTolerance
- $isDecoyEnabled
- $missedCleavageCount
- $modifications
- $precursorTolerance
- $spectraPath
Methods
public
- addFixedModification()
- addModification()
- addVariableModification()
- clearModifications()
- getDatabases() — The sequence database(s) to be searched.
- getEnzyme()
- getFixedModifications()
- getFragmentTolerance() — Gets the Fragment Tolerance object
- getMissedCleavageCount()
- getModifications()
- getPrecursorTolerance()
- getSpectraPath()
- getVariableModifications()
- isDecoyEnabled()
- setDatabases()
- setDecoyEnabled()
- setEnzyme()
- setFragmentTolerance()
- setMissedCleavageCount()
- setPrecursorTolerance()
- setSpectraPath() — Sets the spectra file location
History
-
2017-07-12T14:22:04+01:00 (commit #b6b32a2)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Added search params test coverage
-
2017-04-19T16:43:03+01:00 (commit #ba22061)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed unit tests
-
2017-04-18T17:01:19+01:00 (commit #6727a89)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added additional MzIdentML parser support Partitioned code to allow branching between 1.1/1.2
-
2017-04-13T15:55:22+01:00 (commit #02f8b48)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Addded adapter code to translate between MzIdentML and MSGF params
-
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