pgb_liv\php_ms\Utility\Fragment\XFragment
Generates the X ions from a peptide
- Author: Andrew Collins
Synopsis
- // Inherited members from AbstractFragment
- protected $sequence;
- // methods
- protected void getAdditiveMass()
- protected void getStart()
- // Inherited methods from AbstractFragmentReverse
- 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% | 2 / 2 |
Violations
Checkstyle
| Line | Column | Severity | Message |
|---|---|---|---|
| 38 | 184 | warning | Line exceeds 120 characters; contains 184 characters |
Members
protected
- $sequence
Methods
protected
- getAdditiveMass() — {@inheritdoc}
- getStart() — {@inheritdoc}
Inherited from pgb_liv\php_ms\Utility\Fragment\AbstractFragmentReverse
public
- 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
-
2019-01-29T15:58:13+00:00 (commit #f1ad344)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Tidied up mass additives
-
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
-
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
-
2017-07-10T16:56:51+01:00 (commit #e81ad50)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Simplified fragmentation mass additive
-
2017-07-10T16:30:42+01:00 (commit #86d6efb)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Fixed C ions gaining an extra ion Fixed Z ions gaining extra mass Add fragmentation tests
-
2017-06-30T19:52:10+01:00 (commit #3c20d79)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Added additional testing Moved sequence mass calculation to trait from peptide. Allows protein mass to be calculated.
-
2017-06-30T12:56:00+01:00 (commit #60f1a8b)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Fixed protein name not returning a value Allowed peptide sequence to be set in constructor Moved fragmentation code to separate classes
-
2017-06-30T11:36:28+01:00 (commit #f8926bd)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fragmentation placeholder code