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

Class Glycan

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

  • Field Details

    • UNDERIVATED_MASS

      public static final int UNDERIVATED_MASS
      Final index for underivated masses.
      See Also:

    • PERMETHYLATED_MASS

      public static final int PERMETHYLATED_MASS
      Final index for permethylated masses.
      See Also:

    • DEUTEROMETHYLATED_MASS

      public static final int DEUTEROMETHYLATED_MASS
      Final index for deuteromethylated masses.
      See Also:

    • PERACETYLATED_MASS

      public static final int PERACETYLATED_MASS
      Final index for peracetylated masses.
      See Also:

    • DEUTEROACETYLATED_MASS

      public static final int DEUTEROACETYLATED_MASS
      Final index for deuteroacetylated masses.
      See Also:

  • Constructor Details

    • Glycan

      public Glycan()
      Empty default constructor

    • Glycan

      public Glycan(String name, String longName)
      Constructor for a glycan.
      Parameters:
      name - The name of the glycan
      longName - A shortened name for the glycan

  • Method Details

    • addMass

      public void addMass(int massType, double value)
      Add a mass for this glycan.
      Parameters:
      massType - mass type indexed according to the static field
      value - Value of the mass

    • getMass

      public double getMass(int aType)
      Get the glycan mass.
      Parameters:
      aType - Type of mass requested indexed according to static int.
      Returns:
      the requested mass

    • 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