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

Class RelatedIon

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.biology.ions.Ion

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

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

Nested Class Summary

Nested classes/interfaces inherited from class com.compomics.util.experiment.biology.ions.Ion

Ion.IonType

Field Summary

Fields

Modifier and Type	Field	Description
static final RelatedIon	RELATED_C_1	Related ion for C.
static final RelatedIon	RELATED_C_2	Related ion for C.
static final RelatedIon	RELATED_D_1	Related ion for D.
static final RelatedIon	RELATED_E_1	Related ion for E.
static final RelatedIon	RELATED_F_1	Related ion for F.
static final RelatedIon	RELATED_H_1	Related ion for H (C4H5N2).
static final RelatedIon	RELATED_H_2	Related ion for H.
static final RelatedIon	RELATED_K_1	Related ion for K.
static final RelatedIon	RELATED_K_2	Related ion for K.
static final RelatedIon	RELATED_K_3	Related ion for K.
static final RelatedIon	RELATED_M_1	Related ion for M (C2H4S).
static final RelatedIon	RELATED_N_1	Related ion for N.
static final RelatedIon	RELATED_Q_1	Related ion for Q.
static final RelatedIon	RELATED_Q_2	Related ion for Q.
static final RelatedIon	RELATED_R_1	Related ion for R.
static final RelatedIon	RELATED_R_2	Related ion for R.
static final RelatedIon	RELATED_R_3	Related ion for R.
static final RelatedIon	RELATED_R_4	Related ion for R (C5H10N2O).
static final RelatedIon	RELATED_W_1	Related ion for W (C9H7N).
static final RelatedIon	RELATED_Y_1	Related ion for Y (C7H7O).

Fields inherited from class com.compomics.util.experiment.biology.ions.Ion

atomChain, theoreticMass1, type

Fields inherited from class com.compomics.util.experiment.personalization.ExperimentObject

NO_KEY

Constructor Summary

Constructors

Constructor	Description
RelatedIon()	Empty default constructor
RelatedIon(AminoAcid aminoAcidTarget, AtomChain atomChain, int subType)	Constructor for a related ion.
RelatedIon(AminoAcid aminoAcidTarget, AtomChain atomChain, int subType, boolean save)	Constructor for a related ion.

Method Summary

Modifier and Type	Method	Description
String	getName()	Returns the name of the ion.
NeutralLoss[]	getNeutralLosses()	Returns the possible neutral losses of this ion type.
static int[]	getPossibleSubtypes()	Returns the possible subtypes.
CvTerm	getPrideCvTerm()	Returns the CV term adapted to the fragment ion.
CvTerm	getPsiMsCvTerm()	Returns the CV term adapted to the fragment ion.
static ArrayList<RelatedIon>	getRelatedIons(char aa)	Returns the list of related ions for the given amino acid.
static ArrayList<RelatedIon>	getRelatedIons(AminoAcid aminoAcidTarget)	Returns the list of related ions for the given amino acid.
int	getSubType()	Returns the ion subtype.
String	getSubTypeAsString()	Returns the subtype as string.
boolean	isSameAs(RelatedIon anotherRelatedIon)	Compares the current related ion with another one based on their composition.
boolean	isSameAs(Ion anotherIon)	Returns a boolean indicating whether the ion is the same as another ion.

Methods inherited from class com.compomics.util.experiment.biology.ions.Ion

getAtomicComposition, getGenericIon, getGenericIon, getImplementedIonTypes, getNeutralLossesAsString, getNeutralLossesAsString, getPossibleSubtypes, getPossibleSubtypesAsSet, getTheoreticMass, getTheoreticMz, getType, getTypeAsString, getTypeAsString, hasNeutralLosses, setAtomicComposition, setTheoreticMass

Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject

addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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