com.compomics.util.experiment.biology.ions

Class ImmoniumIon

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.biology.Ion

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

All Implemented Interfaces:

Serializable, Cloneable

public class ImmoniumIon
extends Ion

Represents an immonium 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	ALANINE Subtype int for an alanine immonium ion.
static int	ARGININE Subtype int for an arginine immonium ion.
static int	ASPARAGINE Subtype int for an asparagine immonium ion.
static int	ASPARTIC_ACID Subtype int for an aspartic acid immonium ion.
static int	CYSTEINE Subtype int for a cysteine immonium ion.
static int	GLUTAMIC_ACID Subtype int for a glutamic acid immonium ion.
static int	GLUTAMINE Subtype int for a glutamine immonium ion.
static int	GLYCINE Subtype int for a glycine immonium ion.
static int	HISTIDINE Subtype int for an histidine immonium ion.
static int	ISOLEUCINE Subtype int for an isoleucine immonium ion.
static int	LEUCINE Subtype int for a leucine immonium ion.
static int	LYSINE Subtype int for a lysine immonium ion.
static int	METHIONINE Subtype int for a methionine immonium ion.
static int	PHENYLALANINE Subtype int for a phenylananine immonium ion.
static int	PROLINE Subtype int for a proline immonium ion.
static int	SELENOCYSTEINE Subtype int for a selenocysteine immonium ion.
static int	SERINE Subtype int for a serine immonium ion.
static int	THREONINE Subtype int for a threonine immonium ion.
static int	TRYPTOPHAN Subtype int for a tryptophan immonium ion.
static int	TYROSINE Subtype int for a tyrosine immonium ion.
static int	VALINE Subtype int for a valine immonium ion.

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

atomChain, theoreticMass, type

Constructor Summary

Constructors

Constructor and Description
ImmoniumIon(char residue) Constructor for an immonium ion.
ImmoniumIon(int subType) Constructor for an immonium ion.

Method Summary

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.
static char	getResidue(int subtype) Returns the amino acid of the immonium ion based on the subtype index.
int	getSubType() Returns the ion subtype.
static int	getSubtype(char residue) Returns the subtype identifier based on the amino acid one letter symbol.
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

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

ALANINE

public static final int ALANINE

Subtype int for an alanine immonium ion.

See Also:

Constant Field Values

ARGININE

public static final int ARGININE

Subtype int for an arginine immonium ion.

See Also:

Constant Field Values

ASPARAGINE

public static final int ASPARAGINE

Subtype int for an asparagine immonium ion.

See Also:

Constant Field Values

ASPARTIC_ACID

public static final int ASPARTIC_ACID

Subtype int for an aspartic acid immonium ion.

See Also:

Constant Field Values

CYSTEINE

public static final int CYSTEINE

Subtype int for a cysteine immonium ion.

See Also:

Constant Field Values

GLUTAMIC_ACID

public static final int GLUTAMIC_ACID

Subtype int for a glutamic acid immonium ion.

See Also:

Constant Field Values

GLUTAMINE

public static final int GLUTAMINE

Subtype int for a glutamine immonium ion.

See Also:

Constant Field Values

GLYCINE

public static final int GLYCINE

Subtype int for a glycine immonium ion.

See Also:

Constant Field Values

HISTIDINE

public static final int HISTIDINE

Subtype int for an histidine immonium ion.

See Also:

Constant Field Values

ISOLEUCINE

public static final int ISOLEUCINE

Subtype int for an isoleucine immonium ion.

See Also:

Constant Field Values

LEUCINE

public static final int LEUCINE

Subtype int for a leucine immonium ion.

See Also:

Constant Field Values

LYSINE

public static final int LYSINE

Subtype int for a lysine immonium ion.

See Also:

Constant Field Values

METHIONINE

public static final int METHIONINE

Subtype int for a methionine immonium ion.

See Also:

Constant Field Values

PHENYLALANINE

public static final int PHENYLALANINE

Subtype int for a phenylananine immonium ion.

See Also:

Constant Field Values

PROLINE

public static final int PROLINE

Subtype int for a proline immonium ion.

See Also:

Constant Field Values

SELENOCYSTEINE

public static final int SELENOCYSTEINE

Subtype int for a selenocysteine immonium ion.

See Also:

Constant Field Values

SERINE

public static final int SERINE

Subtype int for a serine immonium ion.

See Also:

Constant Field Values

THREONINE

public static final int THREONINE

Subtype int for a threonine immonium ion.

See Also:

Constant Field Values

TRYPTOPHAN

public static final int TRYPTOPHAN

Subtype int for a tryptophan immonium ion.

See Also:

Constant Field Values

TYROSINE

public static final int TYROSINE

Subtype int for a tyrosine immonium ion.

See Also:

Constant Field Values

VALINE

public static final int VALINE

Subtype int for a valine immonium ion.

See Also:

Constant Field Values

Constructor Detail

ImmoniumIon

public ImmoniumIon(char residue)

Constructor for an immonium ion.

Parameters:

residue - the type of immonium ion as char

ImmoniumIon

public ImmoniumIon(int subType)

Constructor for an immonium ion.

Parameters:

subType - the type of immonium ion as integer as indexed by the static fields

Method Detail

getResidue

public static char getResidue(int subtype)

Returns the amino acid of the immonium ion based on the subtype index.

Parameters:

subtype - the subtype index from the static fields

Returns:

the one letter code of the amino acid

getSubtype

public static int getSubtype(char residue)

Returns the subtype identifier based on the amino acid one letter symbol.

Parameters:

residue - the amino acid as char

Returns:

the subtype as indexed by the static fields. -1 if not found.

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