pgb_liv\php_ms\Core\Spectra\FragmentIon
Fragment Ion Class.
- Author: Andrew Collins
Synopsis
- // Inherited methods from IonTrait
- 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
Coverage
| Methods | 0% | 0 / 0 |
| Lines | 0% | 0 / 0 |
Constants
| Name | Value |
|---|---|
| RETENTION_TIME_START | 0 |
| RETENTION_TIME_END | 1 |
Methods
Inherited from pgb_liv\php_ms\Core\Spectra\IonTrait
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
-
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
-
2017-04-19T17:02:35+01:00 (commit #81c98fa)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed Sonar issues
-
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
-
2017-03-31T18:19:53+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
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2017-03-30T17:42:57+01:00 (commit #5842bc4)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added all PSI-MS specified enzymes
-
2017-01-13T13:24:39+00:00 (commit #09d6bb9)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed incorrect constant usage
-
2017-01-13T13:17:36+00:00 (commit #3c2d727)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed warnings generated by XML missing doctype Added DigestRegularExpression as boiler plate code for all regular expression suitable enzyme
-
2017-01-11T15:23:51+00:00 (commit #2a88d63)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added Trpysin digestion unit test
-
2017-01-11T13:56:23+00:00 (commit #91a55ef)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Improved filtering and digestion documentation
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2017-01-11T13:40:21+00:00 (commit #9d6bc95)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added peptide filtering by length
-
2017-01-10T17:57:46+00:00 (commit #acca036)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed compile error due to multiple constructors
-
2017-01-10T17:51:30+00:00 (commit #b3dacff)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added initial Protein code Added initial Peptide code Added initial digestion code Improved Fasta and MGF tests