All Implemented Interfaces:
Serializable

public class RelatedIon
extends Ion
Represents a related ion, i.e., an ion that is related to a given amino acid, and is its own factory.
Author:
Harald Barsnes, Marc Vaudel
See Also:
Serialized Form
  • Field Details

    • RELATED_R_1

      public static final RelatedIon RELATED_R_1
      Related ion for R. Cyanamid and ammonia loss from immonium ion (C4H7N).
    • RELATED_R_2

      public static final RelatedIon RELATED_R_2
      Related ion for R. Cyanamid loss from immonium ion (C4H10N2).
    • RELATED_R_3

      public static final RelatedIon RELATED_R_3
      Related ion for R. Ammonia loss from immonium ion (C5H9N3).
    • RELATED_R_4

      public static final RelatedIon RELATED_R_4
      Related ion for R (C5H10N2O).
    • RELATED_N_1

      public static final RelatedIon RELATED_N_1
      Related ion for N. Ammonia loss from immonium ion (C3H3NO).
    • RELATED_D_1

      public static final RelatedIon RELATED_D_1
      Related ion for D. water loss from immonium ion (C3H3NO).
    • RELATED_C_1

      public static final RelatedIon RELATED_C_1
      Related ion for C. Carbamidomethylated immonium ion (C4H8N2SO).
    • RELATED_C_2

      public static final RelatedIon RELATED_C_2
      Related ion for C. Carbamidomethylated and ammonia loss from immonium ion (C4H5NSO).
    • RELATED_E_1

      public static final RelatedIon RELATED_E_1
      Related ion for E. Water loss from immonium ion (C4H5NO).
    • RELATED_Q_1

      public static final RelatedIon RELATED_Q_1
      Related ion for Q. Ammonia loss from immonium ion (C4H5NO).
    • RELATED_Q_2

      public static final RelatedIon RELATED_Q_2
      Related ion for Q. Internal b-ion (C5H8N2O2).
    • RELATED_H_1

      public static final RelatedIon RELATED_H_1
      Related ion for H (C4H5N2).
    • RELATED_H_2

      public static final RelatedIon RELATED_H_2
      Related ion for H. Internal b-ion (C6H7N3O).
    • RELATED_K_1

      public static final RelatedIon RELATED_K_1
      Related ion for K. Ammonia loss from immonium ion (C5H9N).
    • RELATED_K_2

      public static final RelatedIon RELATED_K_2
      Related ion for K. Ammonia loss from internal b-ion (C6H9NO).
    • RELATED_K_3

      public static final RelatedIon RELATED_K_3
      Related ion for K. Internal b-ion (C6H12N2O).
    • RELATED_M_1

      public static final RelatedIon RELATED_M_1
      Related ion for M (C2H4S).
    • RELATED_F_1

      public static final RelatedIon RELATED_F_1
      Related ion for F. Tropylium ion (C7H6).
    • RELATED_W_1

      public static final RelatedIon RELATED_W_1
      Related ion for W (C9H7N).
    • RELATED_Y_1

      public static final RelatedIon RELATED_Y_1
      Related ion for Y (C7H7O).
  • Constructor Details

    • RelatedIon

      public RelatedIon()
      Empty default constructor
    • RelatedIon

      public RelatedIon​(AminoAcid aminoAcidTarget, AtomChain atomChain, int subType)
      Constructor for a related ion.
      Parameters:
      aminoAcidTarget - the amino acid target
      atomChain - the atomic composition of this ion
      subType - the ion subtype
    • RelatedIon

      public RelatedIon​(AminoAcid aminoAcidTarget, AtomChain atomChain, int subType, boolean save)
      Constructor for a related ion.
      Parameters:
      aminoAcidTarget - the amino acid target
      atomChain - the atomic composition of this ion
      subType - the ion subtype
      save - if true the related ion will be saved in the static map for later reuse
  • Method Details

    • getRelatedIons

      public static ArrayList<RelatedIon> getRelatedIons​(char aa)
      Returns the list of related ions for the given amino acid.
      Parameters:
      aa - the amino acid target single letter code
      Returns:
      the list of related ions for the given amino acid
    • getRelatedIons

      public static ArrayList<RelatedIon> getRelatedIons​(AminoAcid aminoAcidTarget)
      Returns the list of related ions for the given amino acid.
      Parameters:
      aminoAcidTarget - the amino acid target
      Returns:
      the list of related ions for the given amino acid
    • 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
    • isSameAs

      public boolean isSameAs​(RelatedIon anotherRelatedIon)
      Compares the current related ion with another one based on their composition.
      Parameters:
      anotherRelatedIon - the other related ion
      Returns:
      a boolean indicating whether compositions are equal
    • 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