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

Class PeptideFragmentIon

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

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

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

All Implemented Interfaces:

Serializable

public class PeptideFragmentIon
extends Ion

This class models a peptide fragment 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
static final int	A_ION	Identifier for an a-ion.
static final int	B_ION	Identifier for a b-ion.
static final int	C_ION	Identifier for a c-ion.
static final int	X_ION	Identifier for an x-ion.
static final int	Y_ION	Identifier for a y-ion.
static final int	Z_ION	Identifier for a z-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
PeptideFragmentIon()	Empty default constructor.
PeptideFragmentIon(int fragmentType)	Constructor for a generic ion without neutral losses.
PeptideFragmentIon(int fragmentType, int number, double mass, NeutralLoss[] neutralLosses)	Constructor.
PeptideFragmentIon(int fragmentType, NeutralLoss[] neutralLosses)	Constructor for a generic ion.

Method Summary

Modifier and Type	Method	Description
int	getAaNumber(int peptideLength)	Returns the 1 based index of the amino acid which generated this ion.
static Integer	getIonType(String ionSymbol)	Returns the ion index corresponding to the given symbol in the drop down menu.
String	getName()	Returns the name of the ion.
String	getNameWithNumber()	Returns the name with number.
NeutralLoss[]	getNeutralLosses()	Returns the possible neutral losses of this ion type.
int	getNumber()	Returns the number of the fragment in the sequence.
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.
static String	getSubTypeAsString(int subType)	Returns the type of fragment ion as a letter.
static boolean	isForward(int subType)	Indicates whether the given subtype refers to a forward or a rewind ion.
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

A_ION

public static final int A_ION

Identifier for an a-ion.

See Also:

• Constant Field Values

B_ION

public static final int B_ION

Identifier for a b-ion.

See Also:

• Constant Field Values

C_ION

public static final int C_ION

Identifier for a c-ion.

See Also:

• Constant Field Values

X_ION

public static final int X_ION

Identifier for an x-ion.

See Also:

• Constant Field Values

Y_ION

public static final int Y_ION

Identifier for a y-ion.

See Also:

• Constant Field Values

Z_ION

public static final int Z_ION

Identifier for a z-ion.

See Also:

• Constant Field Values

Constructor Details

PeptideFragmentIon

public PeptideFragmentIon()

Empty default constructor.

PeptideFragmentIon

public PeptideFragmentIon(int fragmentType,
 int number,
 double mass,
 NeutralLoss[] neutralLosses)

Constructor.

Parameters:

fragmentType - the type of peptide fragment ion as indexed by the static fields

number - the number of the fragment ion

mass - the mass of the fragment ion

neutralLosses - the neutral losses of the ion

PeptideFragmentIon

public PeptideFragmentIon(int fragmentType,
 NeutralLoss[] neutralLosses)

Constructor for a generic ion.

Parameters:

fragmentType - the type of peptide fragment ion as indexed by the static fields

neutralLosses - the neutral losses of the ion

PeptideFragmentIon

public PeptideFragmentIon(int fragmentType)

Constructor for a generic ion without neutral losses.

Parameters:

fragmentType - the type of peptide fragment ion as indexed by the static fields

Method Details

getNumber

public int getNumber()

Returns the number of the fragment in the sequence.

Returns:

the number of the fragment in the sequence

getAaNumber

public int getAaNumber(int peptideLength)

Returns the 1 based index of the amino acid which generated this ion.

Parameters:

peptideLength - the length of the peptide

Returns:

the 1 based index of the amino acid which generated this ion

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

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

getNameWithNumber

public String getNameWithNumber()

Returns the name with number. For example b5-H2O.

Returns:

the name with number

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

getSubTypeAsString

public static String getSubTypeAsString(int subType)

Returns the type of fragment ion as a letter. e.g. 'a' for an a-ion.

Parameters:

subType - the subtype

Returns:

the type of fragment ion as a letter

getIonType

public static Integer getIonType(String ionSymbol)

Returns the ion index corresponding to the given symbol in the drop down menu.

Parameters:

ionSymbol - the ion symbol

Returns:

the ion index corresponding to the given symbol in the drop down menu

getPossibleSubtypes

public static int[] getPossibleSubtypes()

Returns the possible subtypes.

Returns:

the possible subtypes

isForward

public static boolean isForward(int subType)

Indicates whether the given subtype refers to a forward or a rewind ion.

Parameters:

subType - the subtype as integer.

Returns:

true for forward ions

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