pgb_liv\php_ms\Core\Spectra\IonTrait
Generic trait for providing ion properties such as mass, charge and intensity
- Author: Andrew Collins
Synopsis
- // members
- private $intensity;
- private $retentionTimeWindow;
- // methods
- public void setMass()
- public float getMass()
- public void setIntensity()
- public float getIntensity()
- public void setRetentionTime()
- public void setRetentionTimeWindow()
- public float getRetentionTime()
- public array getRetentionTimeWindow()
- public boolean hasRetentionTimeWindow()
- // Inherited methods from ChargedMassTrait
- public void setMonoisotopicMassCharge()
- public void setAverageMassCharge()
- public float getMonoisotopicMassCharge()
- public float getAverageMassCharge()
- public void setCharge()
- public int getCharge()
- public static float getMassCharge()
- public static float getNeutralMass()
- // Inherited methods from MassTrait
- public void setMonoisotopicMass()
- public float getMonoisotopicMass()
- public void setAverageMass()
- public float getAverageMass()
Hierarchy
Uses
Used by
Coverage
| Methods | 0% | 0 / 9 | 
| Lines | 0% | / | 
Violations
Checkstyle
| Line | Column | Severity | Message | 
|---|---|---|---|
| 80 | 1 | error | Multi-line function call not indented correctly; expected 12 spaces but found 16 | 
| 80 | 99 | error | Closing parenthesis of a multi-line function call must be on a line by itself | 
| 106 | 1 | error | Multi-line function call not indented correctly; expected 12 spaces but found 16 | 
| 106 | 103 | error | Closing parenthesis of a multi-line function call must be on a line by itself | 
| 124 | 1 | error | Multi-line function call not indented correctly; expected 12 spaces but found 16 | 
| 124 | 108 | error | Closing parenthesis of a multi-line function call must be on a line by itself | 
| 129 | 1 | error | Multi-line function call not indented correctly; expected 12 spaces but found 16 | 
| 129 | 106 | error | Closing parenthesis of a multi-line function call must be on a line by itself | 
Tasks
| Line | Task | 
|---|---|
| 27+ | Add support for Scan/Scan Range | 
Members
private
- $intensity
                —
                float
 The intensity value of this ion
- $retentionTimeWindow
                —
                array
 The retention time window for this object
Methods
public
- getIntensity() — Gets the intensity value for this object
- getMass() — Gets the monoisotopic neutral mass value for this ion
- getRetentionTime() — Gets the retention time in seconds, or the average if a window has been set
- getRetentionTimeWindow() — Gets the retention time window in seconds
- hasRetentionTimeWindow() — Returns true if the retention time is a window
- setIntensity() — Sets the intensity value for this ion
- setMass() — Sets the monoisotopic neutral mass value for this ion
- setRetentionTime() — Sets the spectra elements retention time
- setRetentionTimeWindow() — Sets the spectra elements retention time or retention time window
Inherited from pgb_liv\php_ms\Core\ChargedMassTrait
public
- getAverageMassCharge() — Gets the average mass-to-charge ratio for this ion
- getCharge() — Gets the charge value associated with this instance
- getMassCharge() — Gets the mass-to-charge value for the specified mass and charge
- getMonoisotopicMassCharge() — Gets the monoisotopic mass-to-charge ratio for this instance
- getNeutralMass() — gets the neutral mass for the specified mass-to-charge ratio and charge
- setAverageMassCharge() — Sets the average mass-to-charge ratio for this instance
- setCharge() — Sets the charge of this instance
- setMonoisotopicMassCharge() — Sets the monoisotopic mass-to-charge ratio for this instance.
Inherited from pgb_liv\php_ms\Core\MassTrait
public
- getAverageMass() — Gets the average mass of this object
- getMonoisotopicMass() — Gets the monoisotopic mass of this object
- setAverageMass() — Sets the average mass for this object
- setMonoisotopicMass() — Sets the monoisotopic mass for this object
History
- 
            2018-06-25T13:27:30+01:00 (commit #41c132a)Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk) Added ChargedMassTrait to provide consistent support for mz values. Note breaking charges to setMassCharge 
- 
            2018-06-22T17:07:30+01:00 (commit #52ba8f6)Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk) Added planning notes 
- 
            2018-05-24T12:42:49+01:00 (commit #a0ce09e)Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk) no message 
- 
            2018-05-24T12:16:52+01:00 (commit #314ea98)Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk) Updated ion trait to factor in missing mass values 
- 
            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. 
- 
            2018-02-26T13:03:05+00:00 (commit #55786e2)Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk) Added support for RT Avg/RT Window in Precursor/Fragment ions 
- 
            2017-10-24T16:05:10+01:00 (commit #b2240f0)Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk) Tweaked PHPMD rules 
- 
            2017-05-10T16:39:50+01:00 (commit #1c94e76)Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk) Replaced SpectraEntry with PrecursorIon and FragmentIon Added internal support for complete decoy proteins 
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            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 
- 
            2017-04-20T17:30:58+01:00 (commit #75121a4)Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk) Fixed peptide mods Added support for SpecificityRules 
- 
            2017-04-20T14:02:21+01:00 (commit #de04a20)Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk) Fixed identification not saving to correct array 
- 
            2017-04-20T12:36:41+01:00 (commit #b221f61)Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk) Fixed setModification being used rather than addModification 
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            2017-04-12T18:00:04+01:00 (commit #7965bf5)Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk) Added first pass of MzIdentML reader 
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            2017-02-08T17:47:48+00:00 (commit #65575b9)Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk) Added additional unit tests to SpectraEntry 
- 
            2017-02-03T14:07:00+00:00 (commit #2cecba2)Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk) Fixed incorrect proton mass