public class ReporterIon extends Ion
Ion.IonType
Modifier and Type | Field and 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).
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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.
|
atomChain, theoreticMass, theoreticMass1, type
NO_KEY
Constructor and Description |
---|
ReporterIon()
Empty default constructor
|
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.
|
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.
|
Modifier and Type | Method and 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(Ion anotherIon)
Returns a boolean indicating whether the ion is the same as another ion.
|
boolean |
isSameAs(ReporterIon anotherReporterIon)
Compares the current reporter ion with another one based on their masses.
|
void |
setMass(double referenceMass)
Method to set the mass of the reporter ion.
|
void |
setName(String name)
Setter for the ion name.
|
getAtomicComposition, getGenericIon, getGenericIon, getImplementedIonTypes, getNeutralLossesAsString, getNeutralLossesAsString, getPossibleSubtypes, getPossibleSubtypesAsSet, getTheoreticMass, getTheoreticMz, getType, getTypeAsString, getTypeAsString, hasNeutralLosses, setAtomicComposition, setTheoreticMass
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
public static final ReporterIon iTRAQ4Plex_114
public static final ReporterIon iTRAQ4Plex_115
public static final ReporterIon iTRAQ4Plex_116
public static final ReporterIon iTRAQ4Plex_117
public static final ReporterIon iTRAQ8Plex_113
public static final ReporterIon iTRAQ8Plex_114
public static final ReporterIon iTRAQ8Plex_115
public static final ReporterIon iTRAQ8Plex_116
public static final ReporterIon iTRAQ8Plex_117
public static final ReporterIon iTRAQ8Plex_118
public static final ReporterIon iTRAQ8Plex_119
public static final ReporterIon iTRAQ8Plex_121
public static final ReporterIon iTRAQ_145
public static final ReporterIon iTRAQ_305
public static final ReporterIon TMT_126
public static final ReporterIon TMT_127N
public static final ReporterIon TMT_127C
public static final ReporterIon TMT_128N
public static final ReporterIon TMT_128C
public static final ReporterIon TMT_129N
public static final ReporterIon TMT_129C
public static final ReporterIon TMT_130N
public static final ReporterIon TMT_130C
public static final ReporterIon TMT_131
public static final ReporterIon TMT_131C
public static final ReporterIon TMT_126_ETD
public static final ReporterIon TMT_127N_ETD
public static final ReporterIon TMT_127C_ETD
public static final ReporterIon TMT_128N_ETD
public static final ReporterIon TMT_128C_ETD
public static final ReporterIon TMT_129N_ETD
public static final ReporterIon TMT_129C_ETD
public static final ReporterIon TMT_130N_ETD
public static final ReporterIon TMT_130C_ETD
public static final ReporterIon TMT_131_ETD
public static final ReporterIon TMT_131C_ETD
public static final ReporterIon TMT_230
public static final ReporterIon TMT_226
public static final ReporterIon TMTpro_126
public static final ReporterIon TMTpro_127N
public static final ReporterIon TMTpro_127C
public static final ReporterIon TMTpro_128N
public static final ReporterIon TMTpro_128C
public static final ReporterIon TMTpro_129N
public static final ReporterIon TMTpro_129C
public static final ReporterIon TMTpro_130N
public static final ReporterIon TMTpro_130C
public static final ReporterIon TMTpro_131N
public static final ReporterIon TMTpro_131C
public static final ReporterIon TMTpro_132N
public static final ReporterIon TMTpro_132C
public static final ReporterIon TMTpro_133N
public static final ReporterIon TMTpro_133C
public static final ReporterIon TMTpro_134N
public static final ReporterIon iodoTMT_zero
public static final ReporterIon iodoTMT_126
public static final ReporterIon iodoTMT_127
public static final ReporterIon iodoTMT_128
public static final ReporterIon iodoTMT_129
public static final ReporterIon iodoTMT_130
public static final ReporterIon iodoTMT_131
public static final ReporterIon iodoTMT_zero_ETD
public static final ReporterIon iodoTMT_126_ETD
public static final ReporterIon iodoTMT_127_ETD
public static final ReporterIon iodoTMT_128_ETD
public static final ReporterIon iodoTMT_129_ETD
public static final ReporterIon iodoTMT_130_ETD
public static final ReporterIon iodoTMT_131_ETD
public static final ReporterIon ACE_K_126
public static final ReporterIon ACE_K_143
public static final ReporterIon PHOSPHO_Y
public static final ReporterIon FORMYL_K
public static final ReporterIon METHYL_R_87
public static final ReporterIon METHYL_R_112
public static final ReporterIon METHYL_R_115
public static final ReporterIon METHYL_R_143
public static final ReporterIon METHYL_R_70
public static final ReporterIon DI_METHYL_R_112
public static final ReporterIon DI_METHYL_R_115
public static final ReporterIon DI_METHYL_R_157
public static final ReporterIon QQ
public static final ReporterIon QQ_H2O
public static final ReporterIon QQT
public static final ReporterIon QQT_H2O
public static final ReporterIon QQTG
public static final ReporterIon QQTG_H2O
public static final ReporterIon QQTGG
public static final ReporterIon QQTGG_H2O
public ReporterIon()
public ReporterIon(String name, double mass)
name
- name of the reporter ion. Should be unique to the ion.mass
- theoretic mass of the reporter ionpublic ReporterIon(String name, double mass, boolean save)
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 reusepublic ReporterIon(String name, AtomChain atomChain)
name
- name of the reporter ion. Should be unique to the ionatomChain
- the atomic composition of this ionpublic ReporterIon(String name, AtomChain atomChain, boolean save)
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 reusepublic static void addReporterIon(ReporterIon reporterIon)
reporterIon
- the reporter ion to addpublic String getName()
public void setName(String name)
name
- the new ion namepublic void setMass(double referenceMass)
referenceMass
- the mass where the reporter ions should be foundpublic CvTerm getPrideCvTerm()
Ion
getPrideCvTerm
in class Ion
public CvTerm getPsiMsCvTerm()
Ion
getPsiMsCvTerm
in class Ion
public boolean isSameAs(ReporterIon anotherReporterIon)
anotherReporterIon
- the other reporter ionpublic int getIndex()
public int getSubType()
Ion
getSubType
in class Ion
public String getSubTypeAsString()
Ion
getSubTypeAsString
in class Ion
public static ReporterIon getReporterIon(int subType)
subType
- the index of interestpublic static ReporterIon getReporterIon(String name)
name
- the name of the reporter ionpublic static Set<String> getImplementedIons()
public static ArrayList<String> getSortedImplementedIons()
public static int[] getPossibleSubtypes()
public NeutralLoss[] getNeutralLosses()
Ion
getNeutralLosses
in class Ion
public boolean isSameAs(Ion anotherIon)
Ion
public ReporterIon clone()
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