pgb_liv\php_ms\Utility\Fragment\AbstractFragmentReverse
Abstract class containing generic filtering methods
- Author: Andrew Collins
Synopsis
- // Inherited members from AbstractFragment
- protected $sequence;
- // methods
- public void __construct()
- public void getIons()
- // Inherited methods from AbstractFragment
- public void __construct()
- public void getIons()
- protected void getNTerminalMass()
- protected void getCTerminalMass()
- protected int getEnd()
- protected int getStart()
- protected abstract double getAdditiveMass()
- protected void setIsReversed()
- public void isReversed()
- protected double getChargedIon()
Hierarchy
Extends
Implements
Coverage
| Methods | 100% | 2 / 2 |
| Lines | 100% | 28 / 28 |
Violations
PHPMessDetector
| Line | Rule | Message |
|---|---|---|
| 52 | StaticAccess | Avoid using static access to class '\pgb_liv\php_ms\Core\AminoAcidMono' in method 'getIons'. |
Members
protected
- $sequence
Methods
public
- __construct()
- getIons() — {@inheritdoc}
Inherited from pgb_liv\php_ms\Utility\Fragment\AbstractFragment
protected
- getAdditiveMass() — Gets the additional mass gained in fragmentation
- getCTerminalMass()
- getChargedIon() — Charges the mass to the specified charge
- getEnd() — Gets the end position of the detectable fragments
- getNTerminalMass()
- getStart() — Gets the start position of the detectable fragments
- setIsReversed()
public
- getIons() — {@inheritdoc}
- isReversed() — {@inheritdoc}
History
-
2019-04-04T15:18:47+01:00 (commit #b6402bf)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Updated tests
-
2018-05-22T15:21:51+01:00 (commit #447d714)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed unit test comparison failing on Fragment Ions B
-
2018-05-22T14:54:11+01:00 (commit #4b5ae80)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Updated Fragment Ion generators to support generating ions at specified charge values
-
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
-
2017-12-20T13:35:45+00:00 (commit #78f80e6)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed ordering of reversed fragmentation mehods
-
2017-10-24T16:05:10+01:00 (commit #b2240f0)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Tweaked PHPMD rules
-
2017-10-23T15:33:41+01:00 (commit #9c9c185)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed fragment unit tests
-
2017-10-19T17:26:09+01:00 (commit #8fb3113)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added fragment interface class Added fragment factory to get fragment types by a fragmentation method
-
2017-10-19T15:23:16+01:00 (commit #a2c1bc5)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added support for generating A and X ions
-
2017-09-27T10:28:21+01:00 (commit #a480057)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed fragmentation incorrectly handling terminal mods