com.compomics.util.experiment.biology
Class FragmentFactory

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

public class FragmentFactory
extends java.lang.Object

This factory generates the expected fragment ions from a peptide sequence.

Author:
Marc Vaudel, Harald Barsnes

Method Summary
 java.util.ArrayList<PeptideFragmentIon> getFragmentIons(Peptide peptide)
          This method returns the theoretic fragment ions expected from a peptide sequence.
static FragmentFactory getInstance()
          Static method which returns the instance of the factory
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Method Detail

getInstance

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

Returns:
the instance of the factory

getFragmentIons

public java.util.ArrayList<PeptideFragmentIon> getFragmentIons(Peptide peptide)
This method returns the theoretic fragment ions expected from a peptide sequence. /!\ this method will work only if the ptm found in the peptide are in the PTMFactory

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


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