com.compomics.util.experiment.biology.ions

Class Glycon

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.biology.Ion

com.compomics.util.experiment.biology.ions.Glycon

All Implemented Interfaces:

Serializable, Cloneable

public class Glycon
extends Ion

This class will models a glycon fragment.

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	DEUTEROACETYLATED_MASS Final index for deuteroacetylated masses.
static int	DEUTEROMETHYLATED_MASS Final index for deuteromethylated masses.
static int	PERACETYLATED_MASS Final index for peracetylated masses.
static int	PERMETHYLATED_MASS Final index for permethylated masses.
static int	UNDERIVATED_MASS Final index for underivated masses.

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

theoreticMass, type

Constructor Summary

Constructors

Constructor and Description
Glycon(String name, String longName) Constructor for a glycon.

Method Summary

Methods

Modifier and Type	Method and Description
void	addMass(int massType, double value) Add a mass for this glycon.
double	getMass(int aType) Get the glycon mass.
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

UNDERIVATED_MASS

public static final int UNDERIVATED_MASS

Final index for underivated masses.

See Also:

Constant Field Values

PERMETHYLATED_MASS

public static final int PERMETHYLATED_MASS

Final index for permethylated masses.

See Also:

Constant Field Values

DEUTEROMETHYLATED_MASS

public static final int DEUTEROMETHYLATED_MASS

Final index for deuteromethylated masses.

See Also:

Constant Field Values

PERACETYLATED_MASS

public static final int PERACETYLATED_MASS

Final index for peracetylated masses.

See Also:

Constant Field Values

DEUTEROACETYLATED_MASS

public static final int DEUTEROACETYLATED_MASS

Final index for deuteroacetylated masses.

See Also:

Constant Field Values

Constructor Detail

Glycon

public Glycon(String name,
      String longName)

Constructor for a glycon.

Parameters:

name - The name of the glycon

longName - A shortened name for the glycon

Method Detail

addMass

public void addMass(int massType,
           double value)

Add a mass for this glycon.

Parameters:

massType - mass type indexed according to the static field

value - Value of the mass

getMass

public double getMass(int aType)

Get the glycon mass.

Parameters:

aType - Type of mass requested indexed according to static int.

Returns:

the requested mass

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