java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.identification.spectrum_annotation.NeutralLossesMap
All Implemented Interfaces:
Serializable

public class NeutralLossesMap
extends ExperimentObject
This class contains the informations relative to the accounting of neutral losses
Author:
Marc Vaudel
See Also:
Serialized Form
  • Constructor Details

  • Method Details

    • addNeutralLoss

      public void addNeutralLoss​(NeutralLoss neutralLoss, int bStart, int yStart)
      Adds a new neutral loss to the map.
      Parameters:
      neutralLoss - the new neutral loss
      bStart - the amino acid position where the neutral loss should start being accounted starting from the N-terminus (first is 1)
      yStart - the amino acid position where the neutral loss should start being accounted starting from the C-terminus (first is 1)
    • addNeutralLoss

      public void addNeutralLoss​(String neutralLossName, int bStart, int yStart)
      Adds a new neutral loss to the map.
      Parameters:
      neutralLossName - the new neutral loss name
      bStart - the amino acid position where the neutral loss should start being accounted starting from the N-terminus (first is 1)
      yStart - the amino acid position where the neutral loss should start being accounted starting from the C-terminus (first is 1)
    • clearNeutralLosses

      public void clearNeutralLosses()
      Clears the mapping.
    • makeSequenceIndependant

      public void makeSequenceIndependant()
      Makes the neutral losses sequence independent.
    • isEmpty

      public boolean isEmpty()
      Returns a boolean indicating if the mapping is empty.
      Returns:
      a boolean indicating if the mapping is empty
    • getAccountedNeutralLosses

      public ArrayList<String> getAccountedNeutralLosses()
      Returns an arraylist of the names of the implemented neutral losses.
      Returns:
      an arraylist of the names of the implemented neutral losses
    • getForwardStart

      public Integer getForwardStart​(String neutralLossName)
      Returns the amino acid where a neutral loss should start being accounted for when predicting b ions (counting from N-terminus, first aa is 1).
      Parameters:
      neutralLossName - the name of the neutral loss of interest
      Returns:
      the first amino acid where to account for the neutral loss
    • getRewindStart

      public int getRewindStart​(String neutralLossName)
      Returns the amino acid where a neutral loss should start being accounted for when predicting b ions (counting from N-terminus, first aa is 1).
      Parameters:
      neutralLossName - the name of the neutral loss of interest
      Returns:
      the first amino acid where to account for the neutral loss
    • containsLoss

      public boolean containsLoss​(String neutralLossName)
      Returns a boolean indicating whether a loss is implemented in the mapping.
      Parameters:
      neutralLossName - the name of the neutral loss of interest
      Returns:
      a boolean indicating whether a loss is implemented in the mapping
    • clone

      public NeutralLossesMap clone()
      Overrides:
      clone in class Object