com.compomics.util.experiment.biology.ions

Class PrecursorIon

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.biology.Ion

com.compomics.util.experiment.biology.ions.PrecursorIon

All Implemented Interfaces:

Serializable, Cloneable

public class PrecursorIon
extends Ion

A precursor ion.

Author:

Marc Vaudel

See Also:

Serialized Form

Nested Class Summary

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

Ion.IonType

Field Summary

Fields

Modifier and Type	Field and Description
static int	PRECURSOR For now only one type of precursor implemented.

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

theoreticMass, type

Constructor Summary

Constructors

Constructor and Description
PrecursorIon() Constructor for a generic ion without neutral losses.
PrecursorIon(ArrayList<NeutralLoss> neutralLosses) Constructor for a generic ion.
PrecursorIon(double theoreticMass) Constructor for a generic ion without neutral losses.
PrecursorIon(double theoreticMass, ArrayList<NeutralLoss> neutralLosses) Constructor.

Method Summary

Methods

Modifier and Type	Method and Description
String	getName() Returns the name of the ion.
ArrayList<NeutralLoss>	getNeutralLosses() Returns the possible neutral losses of this ion type.
static ArrayList<Integer>	getPossibleSubtypes() Returns an arraylist of possible subtypes.
CvTerm	getPrideCvTerm() Returns the pride 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.Ion

getGenericIon, getGenericIon, getImplementedIonTypes, getNeutralLossesAsString, getNeutralLossesAsString, getPossibleSubtypes, getTheoreticMass, getTheoreticMz, getType, getTypeAsString, getTypeAsString, setTheoreticMass

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

addUrParam, getParameterKey, getUrParam

Methods inherited from class java.lang.Object

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

Field Detail

PRECURSOR

public static final int PRECURSOR

For now only one type of precursor implemented.

See Also:

Constant Field Values

Constructor Detail

PrecursorIon

public PrecursorIon(double theoreticMass,
            ArrayList<NeutralLoss> neutralLosses)

Constructor.

Parameters:

theoreticMass - the theoretic mass

neutralLosses - the neutral losses

PrecursorIon

public PrecursorIon(ArrayList<NeutralLoss> neutralLosses)

Constructor for a generic ion.

Parameters:

neutralLosses - the neutral losses

PrecursorIon

public PrecursorIon()

Constructor for a generic ion without neutral losses.

PrecursorIon

public PrecursorIon(double theoreticMass)

Constructor for a generic ion without neutral losses.

Parameters:

theoreticMass - the theoretic mass of the precursor

Method Detail

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 pride cv term adapted to the fragment ion. null if none corresponding.

Specified by:

getPrideCvTerm in class Ion

Returns:

the pride 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 ArrayList<Integer> getPossibleSubtypes()

Returns an arraylist of possible subtypes.

Returns:

an arraylist of possible subtypes

getNeutralLosses

public ArrayList<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