com.compomics.util.experiment.biology
Class IonFactory

java.lang.Object
  extended by com.compomics.util.experiment.biology.IonFactory

public class IonFactory
extends Object

This factory generates the expected ions from a peptide.

Author:
Marc Vaudel, Harald Barsnes

Method Summary
 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.
 ArrayList<Ion> getFragmentIons(Peptide peptide)
          This method returns the theoretic ions expected from a peptide.
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.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Method Detail

getInstance

public static IonFactory getInstance()
Static method which returns the instance of the factory.

Returns:
the instance of the factory

addDefaultNeutralLoss

public void addDefaultNeutralLoss(NeutralLoss newNeutralLoss)
Adds a default neutral loss to the default neutral losses if the corresponding loss was not here already.

Parameters:
newNeutralLoss - the new neutral loss

getDefaultNeutralLosses

public ArrayList<NeutralLoss> getDefaultNeutralLosses()
Returns the default neutral losses.

Returns:
the default neutral losses

getFragmentIons

public ArrayList<Ion> getFragmentIons(Peptide peptide)
This method returns the theoretic ions expected from a peptide. /!\ this method will work only if the ptms found in the peptide are in the PTMFactory.

Parameters:
peptide - The considered peptide
Returns:
the expected fragment ions

getAccountedNeutralLosses

public 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.

Parameters:
possibleNeutralLosses - the possible neutral losses
Returns:
the possible combinations

getLossesMass

public static double getLossesMass(ArrayList<NeutralLoss> neutralLosses)
Convenience summing the masses of various neutral losses.

Parameters:
neutralLosses - list of neutral losses
Returns:
the summ of the masses


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