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
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Nested Class Summary
Nested classes/interfaces inherited from class com.compomics.util.experiment.biology.ions.Ion
Ion.IonType
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Field Summary
Fields Modifier and Type Field Description static ReporterIon
ACE_K_126
Standard reporter ion for lysine acetylation (PMID: 18338905).static ReporterIon
ACE_K_143
Standard reporter ion for lysine acetylation (PMID: 18338905).static ReporterIon
DI_METHYL_R_112
Standard reporter ion for di-methylation of R (PMID: 16335983).static ReporterIon
DI_METHYL_R_115
Standard reporter ion for di-methylation of R (PMID: 16335983).static ReporterIon
DI_METHYL_R_157
Standard reporter ion for di-methylation of R (PMID: 16335983).static ReporterIon
FORMYL_K
Standard reporter ion for formylation of K (PMID: 24895383).static ReporterIon
iodoTMT_126
Standard reporter ion iodoTMT 126.static ReporterIon
iodoTMT_126_ETD
Standard reporter ion iodoTMT 126 with ETD fragmentation.static ReporterIon
iodoTMT_127
Standard reporter ion iodoTMT 127.static ReporterIon
iodoTMT_127_ETD
Standard reporter ion iodoTMT 127 with ETD fragmentation.static ReporterIon
iodoTMT_128
Standard reporter ion iodoTMT 128.static ReporterIon
iodoTMT_128_ETD
Standard reporter ion iodoTMT 128 with ETD fragmentation.static ReporterIon
iodoTMT_129
Standard reporter ion iodoTMT 128.static ReporterIon
iodoTMT_129_ETD
Standard reporter ion iodoTMT 128 with ETD fragmentation.static ReporterIon
iodoTMT_130
Standard reporter ion iodoTMT 130.static ReporterIon
iodoTMT_130_ETD
Standard reporter ion iodoTMT 130 with ETD fragmentation.static ReporterIon
iodoTMT_131
Standard reporter ion iodoTMT 131.static ReporterIon
iodoTMT_131_ETD
Standard reporter ion iodoTMT 131 with ETD fragmentation.static ReporterIon
iodoTMT_zero
Standard reporter ion iodoTMT zero.static ReporterIon
iodoTMT_zero_ETD
Standard reporter ion iodoTMT zero with ETD fragmentation.static ReporterIon
iTRAQ_145
Standard reporter ion iTRAQ (reporter + balancer).static ReporterIon
iTRAQ_305
Standard reporter ion iTRAQ (reporter + balancer).static ReporterIon
iTRAQ4Plex_114
Standard reporter ion iTRAQ 4Plex 114.static ReporterIon
iTRAQ4Plex_115
Standard reporter ion iTRAQ 4Plex 115.static ReporterIon
iTRAQ4Plex_116
Standard reporter ion iTRAQ 4Plex 116.static ReporterIon
iTRAQ4Plex_117
Standard reporter ion iTRAQ 4Plex 117.static ReporterIon
iTRAQ8Plex_113
Standard reporter ion iTRAQ 8Plex 113.static ReporterIon
iTRAQ8Plex_114
Standard reporter ion iTRAQ 8Plex 114.static ReporterIon
iTRAQ8Plex_115
Standard reporter ion iTRAQ 8Plex 115.static ReporterIon
iTRAQ8Plex_116
Standard reporter ion iTRAQ 8Plex 116.static ReporterIon
iTRAQ8Plex_117
Standard reporter ion iTRAQ 8Plex 117.static ReporterIon
iTRAQ8Plex_118
Standard reporter ion iTRAQ 8Plex 118.static ReporterIon
iTRAQ8Plex_119
Standard reporter ion iTRAQ 8Plex 119.static ReporterIon
iTRAQ8Plex_121
Standard reporter ion iTRAQ 8Plex 121.static ReporterIon
METHYL_R_112
Standard reporter ion for methylation of R (PMID: 16335983).static ReporterIon
METHYL_R_115
Standard reporter ion for methylation of R (PMID: 16335983).static ReporterIon
METHYL_R_143
Standard reporter ion for methylation of R (PMID: 16335983).static ReporterIon
METHYL_R_70
Standard reporter ion for methylation of R (PMID: 16335983).static ReporterIon
METHYL_R_87
Standard reporter ion for methylation of R.static ReporterIon
PHOSPHO_Y
Standard reporter ion for phosphorylation of tyrosine (PMID: 11473401).static ReporterIon
QQ
Standard reporter ion for SUMO-2/3 Q87R.static ReporterIon
QQ_H2O
Standard reporter ion for SUMO-2/3 Q87R.static ReporterIon
QQT
Standard reporter ion for SUMO-2/3 Q87R.static ReporterIon
QQT_H2O
Standard reporter ion for SUMO-2/3 Q87R.static ReporterIon
QQTG
Standard reporter ion for SUMO-2/3 Q87R.static ReporterIon
QQTG_H2O
Standard reporter ion for SUMO-2/3 Q87R.static ReporterIon
QQTGG
Standard reporter ion for SUMO-2/3 Q87R.static ReporterIon
QQTGG_H2O
Standard reporter ion for SUMO-2/3 Q87R.static ReporterIon
TMT_126
Standard reporter ion TMT 126.static ReporterIon
TMT_126_ETD
Standard reporter ion TMT 126 with ETD fragmentation.static ReporterIon
TMT_127C
Standard reporter ion TMT 127C.static ReporterIon
TMT_127C_ETD
Standard reporter ion TMT 127C with ETD fragmentation.static ReporterIon
TMT_127N
Standard reporter ion TMT 127N.static ReporterIon
TMT_127N_ETD
Standard reporter ion TMT 127N with ETD fragmentation.static ReporterIon
TMT_128C
Standard reporter ion TMT 128C.static ReporterIon
TMT_128C_ETD
Standard reporter ion TMT 128C with ETD fragmentation.static ReporterIon
TMT_128N
Standard reporter ion TMT 128N.static ReporterIon
TMT_128N_ETD
Standard reporter ion TMT 128N with ETD fragmentation.static ReporterIon
TMT_129C
Standard reporter ion TMT 129C.static ReporterIon
TMT_129C_ETD
Standard reporter ion TMT 129C with ETD fragmentation.static ReporterIon
TMT_129N
Standard reporter ion TMT 129N.static ReporterIon
TMT_129N_ETD
Standard reporter ion TMT 129N with ETD fragmentation.static ReporterIon
TMT_130C
Standard reporter ion TMT 130C.static ReporterIon
TMT_130C_ETD
Standard reporter ion TMT 130C with ETD fragmentation.static ReporterIon
TMT_130N
Standard reporter ion TMT 130N.static ReporterIon
TMT_130N_ETD
Standard reporter ion TMT 130N with ETD fragmentation.static ReporterIon
TMT_131
Standard reporter ion TMT 131.static ReporterIon
TMT_131_ETD
Standard reporter ion TMT 131 with ETD fragmentation.static ReporterIon
TMT_131C
Standard reporter ion TMT 131C.static ReporterIon
TMT_131C_ETD
Standard reporter ion TMT 131C with ETD fragmentation.static ReporterIon
TMT_226
Standard reporter ion TMT (reporter + balancer).static ReporterIon
TMT_230
Standard reporter ion TMT (reporter + balancer).static ReporterIon
TMTpro_126
Standard reporter ion TMTpro-126.static ReporterIon
TMTpro_127C
Standard reporter ion TMTpro-127C.static ReporterIon
TMTpro_127N
Standard reporter ion TMTpro-127N.static ReporterIon
TMTpro_128C
Standard reporter ion TMTpro-128C.static ReporterIon
TMTpro_128N
Standard reporter ion TMTpro-128N.static ReporterIon
TMTpro_129C
Standard reporter ion TMTpro-129C.static ReporterIon
TMTpro_129N
Standard reporter ion TMTpro-129N.static ReporterIon
TMTpro_130C
Standard reporter ion TMTpro-130C.static ReporterIon
TMTpro_130N
Standard reporter ion TMTpro-130N.static ReporterIon
TMTpro_131C
Standard reporter ion TMTpro-131C.static ReporterIon
TMTpro_131N
Standard reporter ion TMTpro-131N.static ReporterIon
TMTpro_132C
Standard reporter ion TMTpro-132C.static ReporterIon
TMTpro_132N
Standard reporter ion TMTpro-132N.static ReporterIon
TMTpro_133C
Standard reporter ion TMTpro-133C.static ReporterIon
TMTpro_133N
Standard reporter ion TMTpro-133N.static ReporterIon
TMTpro_134N
Standard reporter ion TMTpro-134N.Fields inherited from class com.compomics.util.experiment.biology.ions.Ion
atomChain, theoreticMass, theoreticMass1, type
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Constructor Summary
Constructors Constructor Description ReporterIon()
Empty default constructorReporterIon(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
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Field Details
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iTRAQ4Plex_114
Standard reporter ion iTRAQ 4Plex 114. -
iTRAQ4Plex_115
Standard reporter ion iTRAQ 4Plex 115. -
iTRAQ4Plex_116
Standard reporter ion iTRAQ 4Plex 116. -
iTRAQ4Plex_117
Standard reporter ion iTRAQ 4Plex 117. -
iTRAQ8Plex_113
Standard reporter ion iTRAQ 8Plex 113. -
iTRAQ8Plex_114
Standard reporter ion iTRAQ 8Plex 114. -
iTRAQ8Plex_115
Standard reporter ion iTRAQ 8Plex 115. -
iTRAQ8Plex_116
Standard reporter ion iTRAQ 8Plex 116. -
iTRAQ8Plex_117
Standard reporter ion iTRAQ 8Plex 117. -
iTRAQ8Plex_118
Standard reporter ion iTRAQ 8Plex 118. -
iTRAQ8Plex_119
Standard reporter ion iTRAQ 8Plex 119. -
iTRAQ8Plex_121
Standard reporter ion iTRAQ 8Plex 121. -
iTRAQ_145
Standard reporter ion iTRAQ (reporter + balancer). -
iTRAQ_305
Standard reporter ion iTRAQ (reporter + balancer). -
TMT_126
Standard reporter ion TMT 126. -
TMT_127N
Standard reporter ion TMT 127N. -
TMT_127C
Standard reporter ion TMT 127C. -
TMT_128N
Standard reporter ion TMT 128N. -
TMT_128C
Standard reporter ion TMT 128C. -
TMT_129N
Standard reporter ion TMT 129N. -
TMT_129C
Standard reporter ion TMT 129C. -
TMT_130N
Standard reporter ion TMT 130N. -
TMT_130C
Standard reporter ion TMT 130C. -
TMT_131
Standard reporter ion TMT 131. -
TMT_131C
Standard reporter ion TMT 131C. -
TMT_126_ETD
Standard reporter ion TMT 126 with ETD fragmentation. -
TMT_127N_ETD
Standard reporter ion TMT 127N with ETD fragmentation. -
TMT_127C_ETD
Standard reporter ion TMT 127C with ETD fragmentation. -
TMT_128N_ETD
Standard reporter ion TMT 128N with ETD fragmentation. -
TMT_128C_ETD
Standard reporter ion TMT 128C with ETD fragmentation. -
TMT_129N_ETD
Standard reporter ion TMT 129N with ETD fragmentation. -
TMT_129C_ETD
Standard reporter ion TMT 129C with ETD fragmentation. -
TMT_130N_ETD
Standard reporter ion TMT 130N with ETD fragmentation. -
TMT_130C_ETD
Standard reporter ion TMT 130C with ETD fragmentation. -
TMT_131_ETD
Standard reporter ion TMT 131 with ETD fragmentation. -
TMT_131C_ETD
Standard reporter ion TMT 131C with ETD fragmentation. -
TMT_230
Standard reporter ion TMT (reporter + balancer). -
TMT_226
Standard reporter ion TMT (reporter + balancer). -
TMTpro_126
Standard reporter ion TMTpro-126. -
TMTpro_127N
Standard reporter ion TMTpro-127N. -
TMTpro_127C
Standard reporter ion TMTpro-127C. -
TMTpro_128N
Standard reporter ion TMTpro-128N. -
TMTpro_128C
Standard reporter ion TMTpro-128C. -
TMTpro_129N
Standard reporter ion TMTpro-129N. -
TMTpro_129C
Standard reporter ion TMTpro-129C. -
TMTpro_130N
Standard reporter ion TMTpro-130N. -
TMTpro_130C
Standard reporter ion TMTpro-130C. -
TMTpro_131N
Standard reporter ion TMTpro-131N. -
TMTpro_131C
Standard reporter ion TMTpro-131C. -
TMTpro_132N
Standard reporter ion TMTpro-132N. -
TMTpro_132C
Standard reporter ion TMTpro-132C. -
TMTpro_133N
Standard reporter ion TMTpro-133N. -
TMTpro_133C
Standard reporter ion TMTpro-133C. -
TMTpro_134N
Standard reporter ion TMTpro-134N. -
iodoTMT_zero
Standard reporter ion iodoTMT zero. -
iodoTMT_126
Standard reporter ion iodoTMT 126. -
iodoTMT_127
Standard reporter ion iodoTMT 127. -
iodoTMT_128
Standard reporter ion iodoTMT 128. -
iodoTMT_129
Standard reporter ion iodoTMT 128. -
iodoTMT_130
Standard reporter ion iodoTMT 130. -
iodoTMT_131
Standard reporter ion iodoTMT 131. -
iodoTMT_zero_ETD
Standard reporter ion iodoTMT zero with ETD fragmentation. -
iodoTMT_126_ETD
Standard reporter ion iodoTMT 126 with ETD fragmentation. -
iodoTMT_127_ETD
Standard reporter ion iodoTMT 127 with ETD fragmentation. -
iodoTMT_128_ETD
Standard reporter ion iodoTMT 128 with ETD fragmentation. -
iodoTMT_129_ETD
Standard reporter ion iodoTMT 128 with ETD fragmentation. -
iodoTMT_130_ETD
Standard reporter ion iodoTMT 130 with ETD fragmentation. -
iodoTMT_131_ETD
Standard reporter ion iodoTMT 131 with ETD fragmentation. -
ACE_K_126
Standard reporter ion for lysine acetylation (PMID: 18338905). -
ACE_K_143
Standard reporter ion for lysine acetylation (PMID: 18338905). -
PHOSPHO_Y
Standard reporter ion for phosphorylation of tyrosine (PMID: 11473401). -
FORMYL_K
Standard reporter ion for formylation of K (PMID: 24895383). -
METHYL_R_87
Standard reporter ion for methylation of R. -
METHYL_R_112
Standard reporter ion for methylation of R (PMID: 16335983). -
METHYL_R_115
Standard reporter ion for methylation of R (PMID: 16335983). -
METHYL_R_143
Standard reporter ion for methylation of R (PMID: 16335983). -
METHYL_R_70
Standard reporter ion for methylation of R (PMID: 16335983). -
DI_METHYL_R_112
Standard reporter ion for di-methylation of R (PMID: 16335983). -
DI_METHYL_R_115
Standard reporter ion for di-methylation of R (PMID: 16335983). -
DI_METHYL_R_157
Standard reporter ion for di-methylation of R (PMID: 16335983). -
QQ
Standard reporter ion for SUMO-2/3 Q87R. -
QQ_H2O
Standard reporter ion for SUMO-2/3 Q87R. -
QQT
Standard reporter ion for SUMO-2/3 Q87R. -
QQT_H2O
Standard reporter ion for SUMO-2/3 Q87R. -
QQTG
Standard reporter ion for SUMO-2/3 Q87R. -
QQTG_H2O
Standard reporter ion for SUMO-2/3 Q87R. -
QQTGG
Standard reporter ion for SUMO-2/3 Q87R. -
QQTGG_H2O
Standard reporter ion for SUMO-2/3 Q87R.
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Constructor Details
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ReporterIon
public ReporterIon()Empty default constructor -
ReporterIon
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
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ReporterIon
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 ionsave
- if true the reporter ion will be saved in the static map for later reuse
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ReporterIon
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 ionatomChain
- the atomic composition of this ion
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ReporterIon
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 ionsave
- if true the reporter ion will be saved in the static map for later reuse
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Method Details
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addReporterIon
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
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getName
This method returns the name of the reporter ion. -
setName
Setter for the ion name.- Parameters:
name
- the new ion name
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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
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getPrideCvTerm
Description copied from class:Ion
Returns the CV term adapted to the fragment ion. Null if none corresponding.- Specified by:
getPrideCvTerm
in classIon
- Returns:
- the CV term adapted to the fragment ion. Null if none corresponding
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getPsiMsCvTerm
Description copied from class:Ion
Returns the CV term adapted to the fragment ion. Null if none corresponding.- Specified by:
getPsiMsCvTerm
in classIon
- Returns:
- the CV term adapted to the fragment ion. Null if none corresponding
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isSameAs
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
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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.
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getSubType
public int getSubType()Description copied from class:Ion
Returns the ion subtype.- Specified by:
getSubType
in classIon
- Returns:
- the ion subtype as integer
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getSubTypeAsString
Description copied from class:Ion
Returns the subtype as string.- Specified by:
getSubTypeAsString
in classIon
- Returns:
- the subtype as string
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getReporterIon
Returns the reporter ion indexed by the given index.- Parameters:
subType
- the index of interest- Returns:
- the corresponding reporter ion
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getReporterIon
Returns the reporter ion corresponding to the given name.- Parameters:
name
- the name of the reporter ion- Returns:
- the corresponding reporter ion
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getImplementedIons
Returns a set of possible subtypes.- Returns:
- a set of possible subtypes
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getSortedImplementedIons
Returns an ordered list of possible subtypes.- Returns:
- an ordered list of possible subtypes
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getPossibleSubtypes
public static int[] getPossibleSubtypes()Returns the possible subtypes.- Returns:
- the possible subtypes
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getNeutralLosses
Description copied from class:Ion
Returns the possible neutral losses of this ion type. An empty list if none.- Specified by:
getNeutralLosses
in classIon
- Returns:
- the possible neutral losses of this ion type
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isSameAs
Description copied from class:Ion
Returns a boolean indicating whether the ion is the same as another ion. -
clone
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