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

Class ElementaryIon

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

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

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

All Implemented Interfaces:

Serializable

public class ElementaryIon
extends Ion

This class represents an elementary ion.

Author:

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 ElementaryIon	proton	A proton.
static final int	PROTON	Subtype int for a proton.
static double[]	protonMassMultiples	Cache for the multiples of the proton mass.

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
ElementaryIon()	Empty default constructor
ElementaryIon(String name, double theoreticMass, int subType)	Constructor.

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.
static double	getProtonMassMultiple(int i)	Returns the mass of the proton multiplied by i.
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

PROTON

public static final int PROTON

Subtype int for a proton.

See Also:

• Constant Field Values

proton

public static final ElementaryIon proton

A proton.

protonMassMultiples

public static double[] protonMassMultiples

Cache for the multiples of the proton mass.

Constructor Details

ElementaryIon

public ElementaryIon()

Empty default constructor

ElementaryIon

public ElementaryIon(String name,
 double theoreticMass,
 int subType)

Constructor.

Parameters:

name - the name of the ion

theoreticMass - the theoretic mass of the ion

subType - the subtype index

Method Details

getProtonMassMultiple

public static double getProtonMassMultiple(int i)

Returns the mass of the proton multiplied by i. if i is smaller or equal to ten a value in cache is used. It is calculated otherwise. Throws an exception for negative i without sanity check.

Parameters:

i - i

Returns:

the mass of the proton multiplied by i

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