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

Class ReporterIon

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

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

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

All Implemented Interfaces:

Serializable

public class ReporterIon
extends Ion

This class models a reporter ion and is its own factory.

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 ReporterIon	ACE_K_126	Standard reporter ion for lysine acetylation (PMID: 18338905).
static final ReporterIon	ACE_K_143	Standard reporter ion for lysine acetylation (PMID: 18338905).
static final ReporterIon	DI_METHYL_R_112	Standard reporter ion for di-methylation of R (PMID: 16335983).
static final ReporterIon	DI_METHYL_R_115	Standard reporter ion for di-methylation of R (PMID: 16335983).
static final ReporterIon	DI_METHYL_R_157	Standard reporter ion for di-methylation of R (PMID: 16335983).
static final ReporterIon	FORMYL_K	Standard reporter ion for formylation of K (PMID: 24895383).
static final ReporterIon	iodoTMT_126	Standard reporter ion iodoTMT 126.
static final ReporterIon	iodoTMT_126_ETD	Standard reporter ion iodoTMT 126 with ETD fragmentation.
static final ReporterIon	iodoTMT_127	Standard reporter ion iodoTMT 127.
static final ReporterIon	iodoTMT_127_ETD	Standard reporter ion iodoTMT 127 with ETD fragmentation.
static final ReporterIon	iodoTMT_128	Standard reporter ion iodoTMT 128.
static final ReporterIon	iodoTMT_128_ETD	Standard reporter ion iodoTMT 128 with ETD fragmentation.
static final ReporterIon	iodoTMT_129	Standard reporter ion iodoTMT 128.
static final ReporterIon	iodoTMT_129_ETD	Standard reporter ion iodoTMT 128 with ETD fragmentation.
static final ReporterIon	iodoTMT_130	Standard reporter ion iodoTMT 130.
static final ReporterIon	iodoTMT_130_ETD	Standard reporter ion iodoTMT 130 with ETD fragmentation.
static final ReporterIon	iodoTMT_131	Standard reporter ion iodoTMT 131.
static final ReporterIon	iodoTMT_131_ETD	Standard reporter ion iodoTMT 131 with ETD fragmentation.
static final ReporterIon	iodoTMT_zero	Standard reporter ion iodoTMT zero.
static final ReporterIon	iodoTMT_zero_ETD	Standard reporter ion iodoTMT zero with ETD fragmentation.
static final ReporterIon	iTRAQ_145	Standard reporter ion iTRAQ (reporter + balancer).
static final ReporterIon	iTRAQ_305	Standard reporter ion iTRAQ (reporter + balancer).
static final ReporterIon	iTRAQ4Plex_114	Standard reporter ion iTRAQ 4Plex 114.
static final ReporterIon	iTRAQ4Plex_115	Standard reporter ion iTRAQ 4Plex 115.
static final ReporterIon	iTRAQ4Plex_116	Standard reporter ion iTRAQ 4Plex 116.
static final ReporterIon	iTRAQ4Plex_117	Standard reporter ion iTRAQ 4Plex 117.
static final ReporterIon	iTRAQ8Plex_113	Standard reporter ion iTRAQ 8Plex 113.
static final ReporterIon	iTRAQ8Plex_114	Standard reporter ion iTRAQ 8Plex 114.
static final ReporterIon	iTRAQ8Plex_115	Standard reporter ion iTRAQ 8Plex 115.
static final ReporterIon	iTRAQ8Plex_116	Standard reporter ion iTRAQ 8Plex 116.
static final ReporterIon	iTRAQ8Plex_117	Standard reporter ion iTRAQ 8Plex 117.
static final ReporterIon	iTRAQ8Plex_118	Standard reporter ion iTRAQ 8Plex 118.
static final ReporterIon	iTRAQ8Plex_119	Standard reporter ion iTRAQ 8Plex 119.
static final ReporterIon	iTRAQ8Plex_121	Standard reporter ion iTRAQ 8Plex 121.
static final ReporterIon	METHYL_R_112	Standard reporter ion for methylation of R (PMID: 16335983).
static final ReporterIon	METHYL_R_115	Standard reporter ion for methylation of R (PMID: 16335983).
static final ReporterIon	METHYL_R_143	Standard reporter ion for methylation of R (PMID: 16335983).
static final ReporterIon	METHYL_R_70	Standard reporter ion for methylation of R (PMID: 16335983).
static final ReporterIon	METHYL_R_87	Standard reporter ion for methylation of R.
static final ReporterIon	PHOSPHO_Y	Standard reporter ion for phosphorylation of tyrosine (PMID: 11473401).
static final ReporterIon	QQ	Standard reporter ion for SUMO-2/3 Q87R.
static final ReporterIon	QQ_H2O	Standard reporter ion for SUMO-2/3 Q87R.
static final ReporterIon	QQT	Standard reporter ion for SUMO-2/3 Q87R.
static final ReporterIon	QQT_H2O	Standard reporter ion for SUMO-2/3 Q87R.
static final ReporterIon	QQTG	Standard reporter ion for SUMO-2/3 Q87R.
static final ReporterIon	QQTG_H2O	Standard reporter ion for SUMO-2/3 Q87R.
static final ReporterIon	QQTGG	Standard reporter ion for SUMO-2/3 Q87R.
static final ReporterIon	QQTGG_H2O	Standard reporter ion for SUMO-2/3 Q87R.
static final ReporterIon	TMT_126	Standard reporter ion TMT 126.
static final ReporterIon	TMT_126_ETD	Standard reporter ion TMT 126 with ETD fragmentation.
static final ReporterIon	TMT_127C	Standard reporter ion TMT 127C.
static final ReporterIon	TMT_127C_ETD	Standard reporter ion TMT 127C with ETD fragmentation.
static final ReporterIon	TMT_127N	Standard reporter ion TMT 127N.
static final ReporterIon	TMT_127N_ETD	Standard reporter ion TMT 127N with ETD fragmentation.
static final ReporterIon	TMT_128C	Standard reporter ion TMT 128C.
static final ReporterIon	TMT_128C_ETD	Standard reporter ion TMT 128C with ETD fragmentation.
static final ReporterIon	TMT_128N	Standard reporter ion TMT 128N.
static final ReporterIon	TMT_128N_ETD	Standard reporter ion TMT 128N with ETD fragmentation.
static final ReporterIon	TMT_129C	Standard reporter ion TMT 129C.
static final ReporterIon	TMT_129C_ETD	Standard reporter ion TMT 129C with ETD fragmentation.
static final ReporterIon	TMT_129N	Standard reporter ion TMT 129N.
static final ReporterIon	TMT_129N_ETD	Standard reporter ion TMT 129N with ETD fragmentation.
static final ReporterIon	TMT_130C	Standard reporter ion TMT 130C.
static final ReporterIon	TMT_130C_ETD	Standard reporter ion TMT 130C with ETD fragmentation.
static final ReporterIon	TMT_130N	Standard reporter ion TMT 130N.
static final ReporterIon	TMT_130N_ETD	Standard reporter ion TMT 130N with ETD fragmentation.
static final ReporterIon	TMT_131	Standard reporter ion TMT 131.
static final ReporterIon	TMT_131_ETD	Standard reporter ion TMT 131 with ETD fragmentation.
static final ReporterIon	TMT_131C	Standard reporter ion TMT 131C.
static final ReporterIon	TMT_131C_ETD	Standard reporter ion TMT 131C with ETD fragmentation.
static final ReporterIon	TMT_226	Standard reporter ion TMT (reporter + balancer).
static final ReporterIon	TMT_230	Standard reporter ion TMT (reporter + balancer).
static final ReporterIon	TMTpro_126	Standard reporter ion TMTpro-126.
static final ReporterIon	TMTpro_127C	Standard reporter ion TMTpro-127C.
static final ReporterIon	TMTpro_127N	Standard reporter ion TMTpro-127N.
static final ReporterIon	TMTpro_128C	Standard reporter ion TMTpro-128C.
static final ReporterIon	TMTpro_128N	Standard reporter ion TMTpro-128N.
static final ReporterIon	TMTpro_129C	Standard reporter ion TMTpro-129C.
static final ReporterIon	TMTpro_129N	Standard reporter ion TMTpro-129N.
static final ReporterIon	TMTpro_130C	Standard reporter ion TMTpro-130C.
static final ReporterIon	TMTpro_130N	Standard reporter ion TMTpro-130N.
static final ReporterIon	TMTpro_131C	Standard reporter ion TMTpro-131C.
static final ReporterIon	TMTpro_131N	Standard reporter ion TMTpro-131N.
static final ReporterIon	TMTpro_132C	Standard reporter ion TMTpro-132C.
static final ReporterIon	TMTpro_132N	Standard reporter ion TMTpro-132N.
static final ReporterIon	TMTpro_133C	Standard reporter ion TMTpro-133C.
static final ReporterIon	TMTpro_133N	Standard reporter ion TMTpro-133N.
static final ReporterIon	TMTpro_134C	Standard reporter ion TMTpro-134C.
static final ReporterIon	TMTpro_134N	Standard reporter ion TMTpro-134N.
static final ReporterIon	TMTpro_135N	Standard reporter ion TMTpro-135N.

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
ReporterIon()	Empty default constructor
ReporterIon(String name, double mass)	Constructor for a user-defined reporter ion.
ReporterIon(String name, double mass, boolean save)	Constructor for a user-defined reporter ion.
ReporterIon(String name, AtomChain atomChain)	Constructor for a user-defined reporter ion.
ReporterIon(String name, AtomChain atomChain, boolean save)	Constructor for a user-defined reporter ion.

Method Summary

Modifier and Type	Method	Description
static void	addReporterIon(ReporterIon reporterIon)	Adds a reporter ion to the class static map.
ReporterIon	clone()
static Set<String>	getImplementedIons()	Returns a set of possible subtypes.
int	getIndex()	Returns the index of a reporter ion.
String	getName()	This method returns the name of the reporter ion.
NeutralLoss[]	getNeutralLosses()	Returns the possible neutral losses of this ion type.
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.
static ReporterIon	getReporterIon(int subType)	Returns the reporter ion indexed by the given index.
static ReporterIon	getReporterIon(String name)	Returns the reporter ion corresponding to the given name.
static ArrayList<String>	getSortedImplementedIons()	Returns an ordered list of possible subtypes.
int	getSubType()	Returns the ion subtype.
String	getSubTypeAsString()	Returns the subtype as string.
boolean	isSameAs(ReporterIon anotherReporterIon)	Compares the current reporter ion with another one based on their masses.
boolean	isSameAs(Ion anotherIon)	Returns a boolean indicating whether the ion is the same as another ion.
void	setMass(double referenceMass)	Method to set the mass of the reporter ion.
void	setName(String name)	Setter for the ion name.

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

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

Field Details

iTRAQ4Plex_114

public static final ReporterIon iTRAQ4Plex_114

Standard reporter ion iTRAQ 4Plex 114.

iTRAQ4Plex_115

public static final ReporterIon iTRAQ4Plex_115

Standard reporter ion iTRAQ 4Plex 115.

iTRAQ4Plex_116

public static final ReporterIon iTRAQ4Plex_116

Standard reporter ion iTRAQ 4Plex 116.

iTRAQ4Plex_117

public static final ReporterIon iTRAQ4Plex_117

Standard reporter ion iTRAQ 4Plex 117.

iTRAQ8Plex_113

public static final ReporterIon iTRAQ8Plex_113

Standard reporter ion iTRAQ 8Plex 113.

iTRAQ8Plex_114

public static final ReporterIon iTRAQ8Plex_114

Standard reporter ion iTRAQ 8Plex 114.

iTRAQ8Plex_115

public static final ReporterIon iTRAQ8Plex_115

Standard reporter ion iTRAQ 8Plex 115.

iTRAQ8Plex_116

public static final ReporterIon iTRAQ8Plex_116

Standard reporter ion iTRAQ 8Plex 116.

iTRAQ8Plex_117

public static final ReporterIon iTRAQ8Plex_117

Standard reporter ion iTRAQ 8Plex 117.

iTRAQ8Plex_118

public static final ReporterIon iTRAQ8Plex_118

Standard reporter ion iTRAQ 8Plex 118.

iTRAQ8Plex_119

public static final ReporterIon iTRAQ8Plex_119

Standard reporter ion iTRAQ 8Plex 119.

iTRAQ8Plex_121

public static final ReporterIon iTRAQ8Plex_121

Standard reporter ion iTRAQ 8Plex 121.

iTRAQ_145

public static final ReporterIon iTRAQ_145

Standard reporter ion iTRAQ (reporter + balancer).

iTRAQ_305

public static final ReporterIon iTRAQ_305

Standard reporter ion iTRAQ (reporter + balancer).

TMT_126

public static final ReporterIon TMT_126

Standard reporter ion TMT 126.

TMT_127N

public static final ReporterIon TMT_127N

Standard reporter ion TMT 127N.

TMT_127C

public static final ReporterIon TMT_127C

Standard reporter ion TMT 127C.

TMT_128N

public static final ReporterIon TMT_128N

Standard reporter ion TMT 128N.

TMT_128C

public static final ReporterIon TMT_128C

Standard reporter ion TMT 128C.

TMT_129N

public static final ReporterIon TMT_129N

Standard reporter ion TMT 129N.

TMT_129C

public static final ReporterIon TMT_129C

Standard reporter ion TMT 129C.

TMT_130N

public static final ReporterIon TMT_130N

Standard reporter ion TMT 130N.

TMT_130C

public static final ReporterIon TMT_130C

Standard reporter ion TMT 130C.

TMT_131

public static final ReporterIon TMT_131

Standard reporter ion TMT 131.

TMT_131C

public static final ReporterIon TMT_131C

Standard reporter ion TMT 131C.

TMT_126_ETD

public static final ReporterIon TMT_126_ETD

Standard reporter ion TMT 126 with ETD fragmentation.

TMT_127N_ETD

public static final ReporterIon TMT_127N_ETD

Standard reporter ion TMT 127N with ETD fragmentation.

TMT_127C_ETD

public static final ReporterIon TMT_127C_ETD

Standard reporter ion TMT 127C with ETD fragmentation.

TMT_128N_ETD

public static final ReporterIon TMT_128N_ETD

Standard reporter ion TMT 128N with ETD fragmentation.

TMT_128C_ETD

public static final ReporterIon TMT_128C_ETD

Standard reporter ion TMT 128C with ETD fragmentation.

TMT_129N_ETD

public static final ReporterIon TMT_129N_ETD

Standard reporter ion TMT 129N with ETD fragmentation.

TMT_129C_ETD

public static final ReporterIon TMT_129C_ETD

Standard reporter ion TMT 129C with ETD fragmentation.

TMT_130N_ETD

public static final ReporterIon TMT_130N_ETD

Standard reporter ion TMT 130N with ETD fragmentation.

TMT_130C_ETD

public static final ReporterIon TMT_130C_ETD

Standard reporter ion TMT 130C with ETD fragmentation.

TMT_131_ETD

public static final ReporterIon TMT_131_ETD

Standard reporter ion TMT 131 with ETD fragmentation.

TMT_131C_ETD

public static final ReporterIon TMT_131C_ETD

Standard reporter ion TMT 131C with ETD fragmentation.

TMT_230

public static final ReporterIon TMT_230

Standard reporter ion TMT (reporter + balancer).

TMT_226

public static final ReporterIon TMT_226

Standard reporter ion TMT (reporter + balancer).

TMTpro_126

public static final ReporterIon TMTpro_126

Standard reporter ion TMTpro-126.

TMTpro_127N

public static final ReporterIon TMTpro_127N

Standard reporter ion TMTpro-127N.

TMTpro_127C

public static final ReporterIon TMTpro_127C

Standard reporter ion TMTpro-127C.

TMTpro_128N

public static final ReporterIon TMTpro_128N

Standard reporter ion TMTpro-128N.

TMTpro_128C

public static final ReporterIon TMTpro_128C

Standard reporter ion TMTpro-128C.

TMTpro_129N

public static final ReporterIon TMTpro_129N

Standard reporter ion TMTpro-129N.

TMTpro_129C

public static final ReporterIon TMTpro_129C

Standard reporter ion TMTpro-129C.

TMTpro_130N

public static final ReporterIon TMTpro_130N

Standard reporter ion TMTpro-130N.

TMTpro_130C

public static final ReporterIon TMTpro_130C

Standard reporter ion TMTpro-130C.

TMTpro_131N

public static final ReporterIon TMTpro_131N

Standard reporter ion TMTpro-131N.

TMTpro_131C

public static final ReporterIon TMTpro_131C

Standard reporter ion TMTpro-131C.

TMTpro_132N

public static final ReporterIon TMTpro_132N

Standard reporter ion TMTpro-132N.

TMTpro_132C

public static final ReporterIon TMTpro_132C

Standard reporter ion TMTpro-132C.

TMTpro_133N

public static final ReporterIon TMTpro_133N

Standard reporter ion TMTpro-133N.

TMTpro_133C

public static final ReporterIon TMTpro_133C

Standard reporter ion TMTpro-133C.

TMTpro_134N

public static final ReporterIon TMTpro_134N

Standard reporter ion TMTpro-134N.

TMTpro_134C

public static final ReporterIon TMTpro_134C

Standard reporter ion TMTpro-134C.

TMTpro_135N

public static final ReporterIon TMTpro_135N

Standard reporter ion TMTpro-135N.

iodoTMT_zero

public static final ReporterIon iodoTMT_zero

Standard reporter ion iodoTMT zero.

iodoTMT_126

public static final ReporterIon iodoTMT_126

Standard reporter ion iodoTMT 126.

iodoTMT_127

public static final ReporterIon iodoTMT_127

Standard reporter ion iodoTMT 127.

iodoTMT_128

public static final ReporterIon iodoTMT_128

Standard reporter ion iodoTMT 128.

iodoTMT_129

public static final ReporterIon iodoTMT_129

Standard reporter ion iodoTMT 128.

iodoTMT_130

public static final ReporterIon iodoTMT_130

Standard reporter ion iodoTMT 130.

iodoTMT_131

public static final ReporterIon iodoTMT_131

Standard reporter ion iodoTMT 131.

iodoTMT_zero_ETD

public static final ReporterIon iodoTMT_zero_ETD

Standard reporter ion iodoTMT zero with ETD fragmentation.

iodoTMT_126_ETD

public static final ReporterIon iodoTMT_126_ETD

Standard reporter ion iodoTMT 126 with ETD fragmentation.

iodoTMT_127_ETD

public static final ReporterIon iodoTMT_127_ETD

Standard reporter ion iodoTMT 127 with ETD fragmentation.

iodoTMT_128_ETD

public static final ReporterIon iodoTMT_128_ETD

Standard reporter ion iodoTMT 128 with ETD fragmentation.

iodoTMT_129_ETD

public static final ReporterIon iodoTMT_129_ETD

Standard reporter ion iodoTMT 128 with ETD fragmentation.

iodoTMT_130_ETD

public static final ReporterIon iodoTMT_130_ETD

Standard reporter ion iodoTMT 130 with ETD fragmentation.

iodoTMT_131_ETD

public static final ReporterIon iodoTMT_131_ETD

Standard reporter ion iodoTMT 131 with ETD fragmentation.

ACE_K_126

public static final ReporterIon ACE_K_126

Standard reporter ion for lysine acetylation (PMID: 18338905).

ACE_K_143

public static final ReporterIon ACE_K_143

Standard reporter ion for lysine acetylation (PMID: 18338905).

PHOSPHO_Y

public static final ReporterIon PHOSPHO_Y

Standard reporter ion for phosphorylation of tyrosine (PMID: 11473401).

FORMYL_K

public static final ReporterIon FORMYL_K

Standard reporter ion for formylation of K (PMID: 24895383).

METHYL_R_87

public static final ReporterIon METHYL_R_87

Standard reporter ion for methylation of R.

METHYL_R_112

public static final ReporterIon METHYL_R_112

Standard reporter ion for methylation of R (PMID: 16335983).

METHYL_R_115

public static final ReporterIon METHYL_R_115

Standard reporter ion for methylation of R (PMID: 16335983).

METHYL_R_143

public static final ReporterIon METHYL_R_143

Standard reporter ion for methylation of R (PMID: 16335983).

METHYL_R_70

public static final ReporterIon METHYL_R_70

Standard reporter ion for methylation of R (PMID: 16335983).

DI_METHYL_R_112

public static final ReporterIon DI_METHYL_R_112

Standard reporter ion for di-methylation of R (PMID: 16335983).

DI_METHYL_R_115

public static final ReporterIon DI_METHYL_R_115

Standard reporter ion for di-methylation of R (PMID: 16335983).

DI_METHYL_R_157

public static final ReporterIon DI_METHYL_R_157

Standard reporter ion for di-methylation of R (PMID: 16335983).

QQ

public static final ReporterIon QQ

Standard reporter ion for SUMO-2/3 Q87R.

QQ_H2O

public static final ReporterIon QQ_H2O

Standard reporter ion for SUMO-2/3 Q87R.

QQT

public static final ReporterIon QQT

Standard reporter ion for SUMO-2/3 Q87R.

QQT_H2O

public static final ReporterIon QQT_H2O

Standard reporter ion for SUMO-2/3 Q87R.

QQTG

public static final ReporterIon QQTG

Standard reporter ion for SUMO-2/3 Q87R.

QQTG_H2O

public static final ReporterIon QQTG_H2O

Standard reporter ion for SUMO-2/3 Q87R.

QQTGG

public static final ReporterIon QQTGG

Standard reporter ion for SUMO-2/3 Q87R.

QQTGG_H2O

public static final ReporterIon QQTGG_H2O

Standard reporter ion for SUMO-2/3 Q87R.

Constructor Details

ReporterIon

public ReporterIon()

Empty default constructor

ReporterIon

public ReporterIon(String name,
 double mass)

Constructor for a user-defined reporter ion. The reporter ion is saved in a static map by default and can be retrieved using the static methods. See getReporterIon(String name).

Parameters:

name - name of the reporter ion. Should be unique to the ion.

mass - theoretic mass of the reporter ion

ReporterIon

public ReporterIon(String name,
 double mass,
 boolean save)

Constructor for a user-defined reporter ion.

Parameters:

name - name of the reporter ion. Should be unique to the ion.

mass - theoretic mass of the reporter ion

save - if true the reporter ion will be saved in the static map for later reuse

ReporterIon

public ReporterIon(String name,
 AtomChain atomChain)

Constructor for a user-defined reporter ion. The reporter ion is saved in a static map by default and can be retrieved using the static methods. See getReporterIon(String name).

Parameters:

name - name of the reporter ion. Should be unique to the ion

atomChain - the atomic composition of this ion

ReporterIon

public ReporterIon(String name,
 AtomChain atomChain,
 boolean save)

Constructor for a user-defined reporter ion.

Parameters:

name - name of the reporter ion. Should be unique to the ion.

atomChain - the atomic composition of this ion

save - if true the reporter ion will be saved in the static map for later reuse

Method Details

addReporterIon

public static void addReporterIon(ReporterIon reporterIon)

Adds a reporter ion to the class static map. Reporter ions with the same name will be overwritten.

Parameters:

reporterIon - the reporter ion to add

getName

public String getName()

This method returns the name of the reporter ion.

Specified by:

getName in class Ion

Returns:

name of the reporter ion

setName

public void setName(String name)

Setter for the ion name.

Parameters:

name - the new ion name

setMass

public void setMass(double referenceMass)

Method to set the mass of the reporter ion.

Parameters:

referenceMass - the mass where the reporter ions should be found

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

isSameAs

public boolean isSameAs(ReporterIon anotherReporterIon)

Compares the current reporter ion with another one based on their masses.

Parameters:

anotherReporterIon - the other reporter ion

Returns:

a boolean indicating whether masses are equal

getIndex

public int getIndex()

Returns the index of a reporter ion. (i.e. its rounded m/z: 114 for iTRAQ 114).

Returns:

the index of a reporter ion.

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

getReporterIon

public static ReporterIon getReporterIon(int subType)

Returns the reporter ion indexed by the given index.

Parameters:

subType - the index of interest

Returns:

the corresponding reporter ion

getReporterIon

public static ReporterIon getReporterIon(String name)

Returns the reporter ion corresponding to the given name.

Parameters:

name - the name of the reporter ion

Returns:

the corresponding reporter ion

getImplementedIons

public static Set<String> getImplementedIons()

Returns a set of possible subtypes.

Returns:

a set of possible subtypes

getSortedImplementedIons

public static ArrayList<String> getSortedImplementedIons()

Returns an ordered list of possible subtypes.

Returns:

an ordered list of possible subtypes

getPossibleSubtypes

public static int[] getPossibleSubtypes()

Returns the possible subtypes.

Returns:

the possible subtypes

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

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

clone

public ReporterIon clone()

Overrides:

clone in class Object