public class IonFactory extends Object
Modifier and Type | Method and Description |
---|---|
static ArrayList<ArrayList<NeutralLoss>> |
getAccountedNeutralLosses(ArrayList<NeutralLoss> possibleNeutralLosses)
Convenience method returning the possible neutral losses combination as
accounted by the factory, i.e., for now up to two neutral losses per
peak.
|
static ArrayList<NeutralLoss> |
getDefaultNeutralLosses()
Returns the default neutral losses.
|
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> |
getFragmentIons(Peptide peptide)
This method returns all the theoretic ions expected from a peptide.
|
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> |
getFragmentIons(Peptide peptide,
SpecificAnnotationSettings specificAnnotationSettings)
This method returns the theoretic ions expected from a peptide.
|
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> |
getFragmentIons(Tag tag)
This method returns the theoretic ions expected from a tag.
|
static IonFactory |
getInstance()
Static method which returns the instance of the factory.
|
static double |
getLossesMass(ArrayList<NeutralLoss> neutralLosses)
Convenience summing the masses of various neutral losses.
|
static ArrayList<NeutralLoss> |
getNeutralLosses(PtmSettings ptmSettings)
Returns a list containing the default neutral losses and the losses found
in the given modifications.
|
static HashSet<Integer> |
getReporterIons(PtmSettings ptmSettings)
Returns the reporter ions to annotate with the given PTM settings.
|
public static IonFactory getInstance()
public static ArrayList<NeutralLoss> getDefaultNeutralLosses()
public static ArrayList<NeutralLoss> getNeutralLosses(PtmSettings ptmSettings)
ptmSettings
- the PTM settingspublic static HashSet<Integer> getReporterIons(PtmSettings ptmSettings)
ptmSettings
- the PTMs to annotatepublic HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> getFragmentIons(Peptide peptide)
peptide
- The considered peptidepublic HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> getFragmentIons(Peptide peptide, SpecificAnnotationSettings specificAnnotationSettings)
peptide
- The considered peptidespecificAnnotationSettings
- if provided, only the ions detectable
using these settings will be selectedpublic HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> getFragmentIons(Tag tag)
tag
- The considered tagpublic static ArrayList<ArrayList<NeutralLoss>> getAccountedNeutralLosses(ArrayList<NeutralLoss> possibleNeutralLosses)
possibleNeutralLosses
- the possible neutral lossespublic static double getLossesMass(ArrayList<NeutralLoss> neutralLosses)
neutralLosses
- list of neutral lossesCopyright © 2016. All rights reserved.