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

Class ImmoniumIon

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

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

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

All Implemented Interfaces:

Serializable

public class ImmoniumIon
extends Ion

Represents an immonium ion.

Author:

Marc Vaudel, Harald Barsnes

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
final char	aa	The amino acid that can generate this ion as single letter code.
static final ImmoniumIon	ALANINE	Alanine immonium ion.
static final ImmoniumIon	ARGININE	Arginine immonium ion.
static final ImmoniumIon	ASPARAGINE	Asparagine immonium ion.
static final ImmoniumIon	ASPARTIC_ACID	Aspartic acid immonium ion.
static final ImmoniumIon	CYSTEINE	Cysteine immonium ion.
static final ImmoniumIon	GLUTAMIC_ACID	Glutamic acid immonium ion.
static final ImmoniumIon	GLUTAMINE	Glutamine immonium ion.
static final ImmoniumIon	GLYCINE	Glycine immonium ion.
static final ImmoniumIon	HISTIDINE	Histidine immonium ion.
static final ImmoniumIon	ISOLEUCINE	Isoleucine immonium ion.
static final ImmoniumIon	LEUCINE	Leucine immonium ion.
static final ImmoniumIon	LYSINE	Lysine immonium ion.
static final ImmoniumIon	METHIONINE	Methionine immonium ion.
static final ImmoniumIon	PHENYLALANINE	Phenylananine immonium ion.
static final ImmoniumIon	PROLINE	Proline immonium ion.
static final ImmoniumIon	PYRROLYSINE	Pyrrolysine immonium ion.
static final ImmoniumIon	SELENOCYSTEINE	Selenocysteine immonium ion.
static final ImmoniumIon	SERINE	Serine immonium ion.
static final ImmoniumIon	THREONINE	Threonine immonium ion.
static final ImmoniumIon	TRYPTOPHAN	Tryptophan immonium ion.
static final ImmoniumIon	TYROSINE	Tyrosine immonium ion.
static final ImmoniumIon	VALINE	Valine immonium ion.

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
ImmoniumIon()	Empty default constructor

Method Summary

Modifier and Type	Method	Description
static ImmoniumIon	getImmoniumIon(char residue)	Returns the immonium ion produced by the given amino acid.
static ImmoniumIon	getImmoniumIon(int subType)	Returns the immonium ion corresponding to the given subtype.
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.
int	getSubType()	Returns the ion subtype.
String	getSubTypeAsString()	Returns the subtype as string.
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

ALANINE

public static final ImmoniumIon ALANINE

Alanine immonium ion.

ARGININE

public static final ImmoniumIon ARGININE

Arginine immonium ion.

ASPARAGINE

public static final ImmoniumIon ASPARAGINE

Asparagine immonium ion.

ASPARTIC_ACID

public static final ImmoniumIon ASPARTIC_ACID

Aspartic acid immonium ion.

CYSTEINE

public static final ImmoniumIon CYSTEINE

Cysteine immonium ion.

GLUTAMIC_ACID

public static final ImmoniumIon GLUTAMIC_ACID

Glutamic acid immonium ion.

GLUTAMINE

public static final ImmoniumIon GLUTAMINE

Glutamine immonium ion.

GLYCINE

public static final ImmoniumIon GLYCINE

Glycine immonium ion.

HISTIDINE

public static final ImmoniumIon HISTIDINE

Histidine immonium ion.

ISOLEUCINE

public static final ImmoniumIon ISOLEUCINE

Isoleucine immonium ion.

LEUCINE

public static final ImmoniumIon LEUCINE

Leucine immonium ion.

LYSINE

public static final ImmoniumIon LYSINE

Lysine immonium ion.

METHIONINE

public static final ImmoniumIon METHIONINE

Methionine immonium ion.

PHENYLALANINE

public static final ImmoniumIon PHENYLALANINE

Phenylananine immonium ion.

PROLINE

public static final ImmoniumIon PROLINE

Proline immonium ion.

SELENOCYSTEINE

public static final ImmoniumIon SELENOCYSTEINE

Selenocysteine immonium ion.

SERINE

public static final ImmoniumIon SERINE

Serine immonium ion.

THREONINE

public static final ImmoniumIon THREONINE

Threonine immonium ion.

TRYPTOPHAN

public static final ImmoniumIon TRYPTOPHAN

Tryptophan immonium ion.

TYROSINE

public static final ImmoniumIon TYROSINE

Tyrosine immonium ion.

VALINE

public static final ImmoniumIon VALINE

Valine immonium ion.

PYRROLYSINE

public static final ImmoniumIon PYRROLYSINE

Pyrrolysine immonium ion.

aa

public final char aa

The amino acid that can generate this ion as single letter code.

Constructor Details

ImmoniumIon

public ImmoniumIon()

Empty default constructor

Method Details

getImmoniumIon

public static ImmoniumIon getImmoniumIon(int subType)

Returns the immonium ion corresponding to the given subtype.

Parameters:

subType - the subtype

Returns:

the immonium ion

getImmoniumIon

public static ImmoniumIon getImmoniumIon(char residue)

Returns the immonium ion produced by the given amino acid.

Parameters:

residue - the amino acid as char

Returns:

the immonium ion

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