public class IonFactory extends Object
Modifier and Type | Method and Description |
---|---|
void |
addDefaultNeutralLoss(NeutralLoss newNeutralLoss)
Adds a default neutral loss to the default neutral losses if the
corresponding loss was not here already.
|
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.
|
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.
|
public static IonFactory getInstance()
public void addDefaultNeutralLoss(NeutralLoss newNeutralLoss)
newNeutralLoss
- the new neutral losspublic ArrayList<NeutralLoss> getDefaultNeutralLosses()
public 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 © 2015. All rights reserved.