Package com.compomics.util.experiment.biology.ions

Class NeutralLoss

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.biology.ions.NeutralLoss
All Implemented Interfaces:
Serializable
public class NeutralLoss extends ExperimentObject
This class represents a neutral loss.
Author:
Marc Vaudel
See Also:

  • Field Details

    • H2O

      public static final NeutralLoss H2O
      H2O loss.

    • NH3

      public static final NeutralLoss NH3
      NH3 loss.

    • H3PO4

      public static final NeutralLoss H3PO4
      H3PO4 loss.

    • HPO3

      public static final NeutralLoss HPO3
      H3PO3 loss.

    • CH4OS

      public static final NeutralLoss CH4OS
      CH4OS loss.

    • C3H9N

      public static final NeutralLoss C3H9N
      C3H9N loss.

    • HCNO

      public static final NeutralLoss HCNO
      HCNO loss.

    • name

      public final String name
      The name of the neutral loss.

    • aminoAcids

      public final char[] aminoAcids
      Amino acids that are likely to induce this loss. Null if not a loss originating from amino acids.

  • Constructor Details

    • NeutralLoss

      public NeutralLoss(String name, AtomChain composition, boolean fixed, char[] aminoAcids)
      Constructor for a user defined neutral loss. The neutral loss is added to the factory.
      Parameters:
      name - name of the neutral loss
      composition - the atomic composition of the neutral loss
      fixed - is the neutral loss fixed or not
      aminoAcids - the amino acids that are likely to induce this loss

    • NeutralLoss

      public NeutralLoss()
      Default construtor

    • NeutralLoss

      public NeutralLoss(String name, AtomChain composition, boolean fixed)
      Constructor for a user defined neutral loss. The neutral loss is added to the factory.
      Parameters:
      name - name of the neutral loss
      composition - the atomic composition of the neutral loss
      fixed - is the neutral loss fixed or not

    • NeutralLoss

      public NeutralLoss(String name, AtomChain composition, boolean fixed, char[] aminoAcids, boolean save)
      Constructor for a user defined neutral loss.
      Parameters:
      name - name of the neutral loss
      composition - the atomic composition of the neutral loss
      fixed - is the neutral loss fixed or not
      aminoAcids - the amino acids that are likely to induce this loss
      save - if true, the neutral loss will be added to the factory

  • Method Details

    • addNeutralLoss

      public static void addNeutralLoss(NeutralLoss neutralLoss)
      Adds a neutral loss to the class static map. Neutral losses with the same name will be overwritten.
      Parameters:
      neutralLoss - the neutral loss to add

    • getNeutralLoss

      public static NeutralLoss getNeutralLoss(String name)
      Returns the neutral loss associated to the given name in the static map of the class. Null if not found.
      Parameters:
      name - the name of the neutral loss of interest
      Returns:
      the neutral loss

    • removeNeutralLoss

      public static void removeNeutralLoss(String name)
      Removes the neutral loss associated to the given name in the static map of the class.
      Parameters:
      name - the name of the neutral loss to remove

    • getPsiMsCvTerm

      public CvTerm getPsiMsCvTerm()
      Returns the CV term for the neutral loss. Null if none corresponding.
      Returns:
      the CV term for the neutral loss.

    • isFixed

      public boolean isFixed()
      Returns a boolean indicating whether the neutral loss is fixed or not.
      Returns:
      a boolean indicating whether the neutral loss is fixed or not

    • setFixed

      public void setFixed(boolean fixed)
      Sets whether the loss is fixed or not.
      Parameters:
      fixed - a boolean indicating whether the loss is fixed or not

    • getComposition

      public AtomChain getComposition()
      The composition of the loss.
      Returns:
      The composition of the loss

    • setComposition

      public void setComposition(AtomChain composition)
      Sets the composition of the neutral loss.
      Parameters:
      composition - the composition of the neutral loss

    • getMass

      public double getMass()
      Returns the mass of the neutral loss, from the atomic composition if available, from the mass field otherwise.
      Returns:
      the mass of the neutral loss

    • isSameAs

      public boolean isSameAs(NeutralLoss anotherNeutralLoss)
      Method indicating whether another neutral loss is the same as the one considered.
      Parameters:
      anotherNeutralLoss - another neutral loss
      Returns:
      boolean indicating whether the other neutral loss is the same as the one considered

    • clone

      public NeutralLoss clone()
      Overrides:
      clone in class Object