|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectcom.compomics.util.experiment.biology.IonFactory
public class IonFactory
This factory generates the expected ions from a peptide.
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 java.util.ArrayList<java.util.ArrayList<NeutralLoss>> |
getAccountedNeutralLosses(java.util.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. |
java.util.ArrayList<NeutralLoss> |
getDefaultNeutralLosses()
Returns the default neutral losses. |
java.util.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(java.util.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 |
---|
public static IonFactory getInstance()
public void addDefaultNeutralLoss(NeutralLoss newNeutralLoss)
newNeutralLoss
- the new neutral losspublic java.util.ArrayList<NeutralLoss> getDefaultNeutralLosses()
public java.util.ArrayList<Ion> getFragmentIons(Peptide peptide)
peptide
- The considered peptide
public static java.util.ArrayList<java.util.ArrayList<NeutralLoss>> getAccountedNeutralLosses(java.util.ArrayList<NeutralLoss> possibleNeutralLosses)
possibleNeutralLosses
- the possible neutral losses
public static double getLossesMass(java.util.ArrayList<NeutralLoss> neutralLosses)
neutralLosses
- list of neutral losses
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |