com.compomics.util.experiment.biology.ions

Class TagFragmentIon

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.biology.Ion

com.compomics.util.experiment.biology.ions.TagFragmentIon

All Implemented Interfaces:

Serializable, Cloneable

public class TagFragmentIon
extends Ion

A fragment ion obtained from a tag.

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	A_ION Identifier for an a ion.
static int	B_ION Identifier for a b ion.
static int	C_ION Identifier for a c ion.
static int	X_ION Identifier for an x ion.
static int	Y_ION Identifier for a y ion.
static int	Z_ION Identifier for a z ion.

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

atomChain, theoreticMass, type

Constructor Summary

Constructors

Constructor and Description
TagFragmentIon(int fragmentType) Constructor for a generic ion without neutral losses.
TagFragmentIon(int fragmentType, ArrayList<NeutralLoss> neutralLosses) Constructor for a generic ion.
TagFragmentIon(int fragmentType, int number, int subNumber, double mass, ArrayList<NeutralLoss> neutralLosses, double massGap) Constructor.

Method Summary

Modifier and Type	Method and Description
double	getMassGap() Returns the mass gap comprised in this ion.
String	getName() Returns the name of the ion.
String	getNameWithGapAndNumber() Returns the name with number and mass gap.
String	getNameWithNumber() Returns the name with number.
ArrayList<NeutralLoss>	getNeutralLosses() Returns the possible neutral losses of this ion type.
int	getNumber() Returns the number of the fragment in the tag.
static ArrayList<Integer>	getPossibleSubtypes() Returns an arraylist of possible subtypes.
CvTerm	getPrideCvTerm() Returns the pride cv term adapted to the fragment ion.
int	getSubNumber() Returns the number of the fragment in the current amino acid sequence.
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.
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

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 Detail

TagFragmentIon

public TagFragmentIon(int fragmentType,
                      int number,
                      int subNumber,
                      double mass,
                      ArrayList<NeutralLoss> neutralLosses,
                      double massGap)

Constructor.

Parameters:

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

number - the number of the fragment ion

subNumber - the number of the fragment ion in the current amino acid sequence

mass - the mass of the fragment ion

neutralLosses - the neutral losses of the ion

massGap - the mass gap before this tag fragment ions

TagFragmentIon

public TagFragmentIon(int fragmentType,
                      ArrayList<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

TagFragmentIon

public TagFragmentIon(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 Detail

getNumber

public int getNumber()

Returns the number of the fragment in the tag. 0 based.

Returns:

the number of the fragment in the tag

getSubNumber

public int getSubNumber()

Returns the number of the fragment in the current amino acid sequence. 0 based.

Returns:

the number of the fragment in the current amino acid sequence

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

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

getNameWithGapAndNumber

public String getNameWithGapAndNumber()

Returns the name with number and mass gap. For example 110.0...b5-H2O.

Returns:

the name with number

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

getSubTypeAsString

public static String getSubTypeAsString(int subType)

Returns the type of fragment ion as a letter.

Parameters:

subType - the subtype

Returns:

the type of fragment ion as a letter

getPossibleSubtypes

public static ArrayList<Integer> getPossibleSubtypes()

Returns an arraylist of possible subtypes.

Returns:

an arraylist of possible subtypes

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

getMassGap

public double getMassGap()

Returns the mass gap comprised in this ion.

Returns:

the mass gap