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

Class PrecursorIon

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.biology.ions.Ion
com.compomics.util.experiment.biology.ions.impl.PrecursorIon
All Implemented Interfaces:
Serializable
public class PrecursorIon extends Ion
A precursor ion.
Author:
Marc Vaudel
See Also:

  • Field Details

    • PRECURSOR

      public static final int PRECURSOR
      For now only one type of precursor implemented.
      See Also:

  • Constructor Details

    • PrecursorIon

      public PrecursorIon(double theoreticMass, NeutralLoss[] neutralLosses)
      Constructor.
      Parameters:
      theoreticMass - the theoretic mass
      neutralLosses - the neutral losses

    • PrecursorIon

      public PrecursorIon(NeutralLoss[] neutralLosses)
      Constructor for a generic ion.
      Parameters:
      neutralLosses - the neutral losses

    • PrecursorIon

      public PrecursorIon()
      Constructor for a generic ion without neutral losses.

    • PrecursorIon

      public PrecursorIon(double theoreticMass)
      Constructor for a generic ion without neutral losses.
      Parameters:
      theoreticMass - the theoretic mass of the precursor

  • Method Details

    • getName

      public String getName()
      Description copied from class: Ion
      Returns the name of the ion. The name should be short enough to be displayed on a spectrum.
      Specified by:
      getName in class Ion
      Returns:
      the name of the ion

    • getPrideCvTerm

      public CvTerm getPrideCvTerm()
      Description copied from class: Ion
      Returns the CV term adapted to the fragment ion. Null if none corresponding.
      Specified by:
      getPrideCvTerm in class Ion
      Returns:
      the CV term adapted to the fragment ion. Null if none corresponding

    • getPsiMsCvTerm

      public CvTerm getPsiMsCvTerm()
      Description copied from class: Ion
      Returns the CV term adapted to the fragment ion. Null if none corresponding.
      Specified by:
      getPsiMsCvTerm in class Ion
      Returns:
      the CV term adapted to the fragment ion. Null if none corresponding

    • getSubType

      public int getSubType()
      Description copied from class: Ion
      Returns the ion subtype.
      Specified by:
      getSubType in class Ion
      Returns:
      the ion subtype as integer

    • getSubTypeAsString

      public String getSubTypeAsString()
      Description copied from class: Ion
      Returns the subtype as string.
      Specified by:
      getSubTypeAsString in class Ion
      Returns:
      the subtype as string

    • getPossibleSubtypes

      public static int[] getPossibleSubtypes()
      Returns the possible subtypes.
      Returns:
      the possible subtypes

    • getNeutralLosses

      public NeutralLoss[] getNeutralLosses()
      Description copied from class: Ion
      Returns the possible neutral losses of this ion type. An empty list if none.
      Specified by:
      getNeutralLosses in class Ion
      Returns:
      the possible neutral losses of this ion type

    • isSameAs

      public boolean isSameAs(Ion anotherIon)
      Description copied from class: Ion
      Returns a boolean indicating whether the ion is the same as another ion.
      Specified by:
      isSameAs in class Ion
      Parameters:
      anotherIon - the other ion
      Returns:
      a boolean indicating whether the ion is the same as another ion