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

Class Ion

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.biology.ions.Ion
All Implemented Interfaces:
Serializable
Direct Known Subclasses:
ElementaryIon, Glycan, ImmoniumIon, PeptideFragmentIon, PrecursorIon, RelatedIon, ReporterIon, TagFragmentIon
public abstract class Ion extends ExperimentObject
This class models an ion.
Author:
Marc Vaudel
See Also:

  • Field Details

    • type

      protected Ion.IonType type
      Type of ion.

    • theoreticMass1

      protected double theoreticMass1
      The theoretic mass.

    • atomChain

      protected AtomChain atomChain
      The atomic composition of the ion.

  • Constructor Details

    • Ion

      public Ion()
      Empty default constructor

  • Method Details

    • getName

      public abstract String getName()
      Returns the name of the ion. The name should be short enough to be displayed on a spectrum.
      Returns:
      the name of the ion

    • getPrideCvTerm

      public abstract CvTerm getPrideCvTerm()
      Returns the CV term adapted to the fragment ion. Null if none corresponding.
      Returns:
      the CV term adapted to the fragment ion. Null if none corresponding

    • getPsiMsCvTerm

      public abstract CvTerm getPsiMsCvTerm()
      Returns the CV term adapted to the fragment ion. Null if none corresponding.
      Returns:
      the CV term adapted to the fragment ion. Null if none corresponding

    • getSubType

      public abstract int getSubType()
      Returns the ion subtype.
      Returns:
      the ion subtype as integer

    • getSubTypeAsString

      public abstract String getSubTypeAsString()
      Returns the subtype as string.
      Returns:
      the subtype as string

    • getPossibleSubtypes

      public static int[] getPossibleSubtypes(Ion.IonType ionType)
      Returns an array of possible subtypes.
      Parameters:
      ionType - an array of possible subtypes
      Returns:
      an array of possible subtypes

    • getPossibleSubtypesAsSet

      public static HashSet<Integer> getPossibleSubtypesAsSet(Ion.IonType ionType)
      Returns a hashset of possible subtypes.
      Parameters:
      ionType - a hashset of possible subtypes
      Returns:
      a hashset of possible subtypes

    • getNeutralLosses

      public abstract NeutralLoss[] getNeutralLosses()
      Returns the possible neutral losses of this ion type. An empty list if none.
      Returns:
      the possible neutral losses of this ion type

    • hasNeutralLosses

      public boolean hasNeutralLosses()
      Indicates whether the ion has a neutral loss.
      Returns:
      a boolean indicating whether the ion has a neutral loss

    • isSameAs

      public abstract boolean isSameAs(Ion anotherIon)
      Returns a boolean indicating whether the ion is the same as another ion.
      Parameters:
      anotherIon - the other ion
      Returns:
      a boolean indicating whether the ion is the same as another ion

    • getNeutralLossesAsString

      public String getNeutralLossesAsString()
      Returns the neutral loss (if any), the empty string if no loss.
      Returns:
      the neutral loss

    • getNeutralLossesAsString

      public static String getNeutralLossesAsString(NeutralLoss[] neutralLosses)
      Returns the neutral loss (if any), the empty string if no loss.
      Parameters:
      neutralLosses - the neutral loss (if any)
      Returns:
      the neutral loss

    • getTheoreticMass

      public double getTheoreticMass()
      Returns the theoretic mass, from the atomic composition if available, from the theoreticMass field otherwise.
      Returns:
      the theoretic mass

    • getTheoreticMz

      public double getTheoreticMz(Integer charge)
      Returns the m/z expected for this ion at the given charge.
      Parameters:
      charge - the charge of interest
      Returns:
      the m/z expected for this ion

    • getAtomicComposition

      public AtomChain getAtomicComposition()
      Returns the atomic composition.
      Returns:
      the atomic composition

    • setAtomicComposition

      public void setAtomicComposition(AtomChain atomChain)
      Returns the atomic composition.
      Parameters:
      atomChain - the atomic composition

    • setTheoreticMass

      public void setTheoreticMass(double theoreticMass)
      Sets a new theoretic mass.
      Parameters:
      theoreticMass - a new theoretic mass

    • getType

      public Ion.IonType getType()
      Returns the ion type.
      Returns:
      the ion type

    • getImplementedIonTypes

      public static ArrayList<Ion.IonType> getImplementedIonTypes()
      Returns the implemented ion types.
      Returns:
      the implemented ion types

    • getTypeAsString

      public String getTypeAsString()
      Returns the type of ion as string.
      Returns:
      the type of ion as string

    • getTypeAsString

      public static String getTypeAsString(Ion.IonType type)
      Returns the type of ion as string.
      Parameters:
      type - the type of ion as string
      Returns:
      the type of ion as string

    • getGenericIon

      public static Ion getGenericIon(Ion.IonType ionType, int subType, NeutralLoss[] neutralLosses)
      Convenience method returning a generic ion based on the given ion type.
      Parameters:
      ionType - the ion type
      subType - the ion subtype
      neutralLosses - the neutral losses. Null list if none.
      Returns:
      a generic ion

    • getGenericIon

      public static Ion getGenericIon(Ion.IonType ionType, int subType)
      Convenience method returning a generic ion based on the given ion type without neutral losses.
      Parameters:
      ionType - the ion type
      subType - the ion subtype
      Returns:
      a generic ion