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 |
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.
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static ReporterIon |
iTRAQ8Plex_115
Standard reporter ion iTRAQ 8Plex 115.
|
static ReporterIon |
iTRAQ8Plex_116
Standard reporter ion iTRAQ 8Plex 116.
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static ReporterIon |
iTRAQ8Plex_117
Standard reporter ion iTRAQ 8Plex 117.
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static ReporterIon |
iTRAQ8Plex_118
Standard reporter ion iTRAQ 8Plex 118.
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static ReporterIon |
iTRAQ8Plex_119
Standard reporter ion iTRAQ 8Plex 119.
|
static ReporterIon |
iTRAQ8Plex_121
Standard reporter ion iTRAQ 8Plex 121.
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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.
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static ReporterIon |
QQ_H2O
Standard reporter ion for SUMO-2/3 Q87R.
|
static ReporterIon |
QQT
Standard reporter ion for SUMO-2/3 Q87R.
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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.
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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.
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static ReporterIon |
TMT_127N_ETD
Standard reporter ion TMT 127N with ETD fragmentation.
|
static ReporterIon |
TMT_128C
Standard reporter ion TMT 128C.
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static ReporterIon |
TMT_128C_ETD
Standard reporter ion TMT 128C with ETD fragmentation.
|
static ReporterIon |
TMT_128N
Standard reporter ion TMT 128N.
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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_226
Standard reporter ion TMT (reporter + balancer).
|
static ReporterIon |
TMT_230
Standard reporter ion TMT (reporter + balancer).
|
atomChain, theoreticMass, theoreticMass1, type
Constructor and Description |
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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, getUrParam, getUrParams, removeUrParam, setUrParams
getFirstLevel, getId, setFirstLevel, setId
jdoZooEvict, jdoZooGetBackup, jdoZooGetClassDef, jdoZooGetContext, jdoZooGetNode, jdoZooGetOid, jdoZooGetTimestamp, jdoZooHasState, jdoZooInit, jdoZooIsDeleted, jdoZooIsDetached, jdoZooIsDirty, jdoZooIsNew, jdoZooIsPersistent, jdoZooIsStateHollow, jdoZooIsTransactional, jdoZooMarkClean, jdoZooMarkDeleted, jdoZooMarkDetached, jdoZooMarkDirty, jdoZooMarkHollow, jdoZooMarkTransient, jdoZooSetOid, jdoZooSetTimestamp, toString, zooActivateRead, zooActivateWrite, zooActivateWrite
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_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_230
public static final ReporterIon TMT_226
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(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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