pgb_liv\php_ms\Utility\Fragment\AbstractFragment
Abstract class containing generic filtering methods
- Author: Andrew Collins
Synopsis
- // members
- private bool $isReversed = false;
- protected $sequence;
- // methods
- 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
Coverage
| Methods | 100% | 10 / 10 |
| Lines | 100% | 51 / 51 |
Violations
PHPMessDetector
| Line | Rule | Message |
|---|---|---|
| 72 | StaticAccess | Avoid using static access to class '\pgb_liv\php_ms\Core\AminoAcidMono' in method 'getIons'. |
Members
private
- $isReversed
—
pgb_liv\php_ms\Utility\Fragment\bool
Whether the fragments should be read right-left or left-right
protected
- $sequence
Methods
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
- __construct() — Creates a new instance of this fragmenter using the specified peptide
- getIons() — {@inheritdoc}
- isReversed() — {@inheritdoc}
History
-
2019-04-02T13:48:22+01:00 (commit #f90fad3)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Code tidy
-
2019-04-02T11:54:45+01:00 (commit #c7d351b)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Code tidy
-
2018-05-24T12:07:12+01:00 (commit #24d745d)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Moved average and monoisotopic mass methods to trait to provide consistency to objects
-
2018-05-23T12:14:08+01:00 (commit #cb13f8c)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Addition of Chemical and Physical constants file. Currently only contains constants used internally. Deprecated original constant sites and updated internal usages.
-
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
-
2017-10-25T11:32:31+01:00 (commit #ccae3f8)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed various documentation and import issues
-
2017-10-24T16:05:10+01:00 (commit #b2240f0)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Tweaked PHPMD rules
-
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
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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
-
2017-09-27T11:47:41+01:00 (commit #617b2e0)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Minor code style fixes
-
2017-09-27T10:29:58+01:00 (commit #acbeb8a)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed missing property in Abstract Fragment
-
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
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2017-08-08T18:42:00+01:00 (commit #2b783b9)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Added modification support to fragmenters Fixed null pointer if residues was not set before a get residues call
-
2017-07-12T14:53:50+01:00 (commit #b6bd42a)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Added search tests
-
2017-07-10T16:56:51+01:00 (commit #e81ad50)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Simplified fragmentation mass additive