ReporterIon (computational omics utilities 4.5.7 API)

java.lang.Object
- com.compomics.util.experiment.personalization.ExperimentObject
- - com.compomics.util.experiment.biology.Ion
  - - com.compomics.util.experiment.biology.ions.ReporterIon

All Implemented Interfaces:

Serializable, Cloneable
```
public class ReporterIon
extends Ion
```
This class models a reporter ion and is its own factory.

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 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`	`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_226` Standard reporter ion TMT (reporter + balancer).
`static ReporterIon`	`TMT_230` Standard reporter ion TMT (reporter + balancer).

Fields inherited from class com.compomics.util.experiment.biology.Ion
atomChain, theoreticMass, type

Constructor Summary

Constructors
Constructor and Description
`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.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
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 an arraylist of possible subtypes.
`int`	`getIndex()` Returns the index of a reporter ion.
`String`	`getName()` This method returns the name of the reporter ion.
`ArrayList<NeutralLoss>`	`getNeutralLosses()` Returns the possible neutral losses of this ion type.
`static ArrayList<Integer>`	`getPossibleSubtypes()` Returns an arraylist of possible subtypes.
`CvTerm`	`getPrideCvTerm()` Returns the pride 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.
`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.

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

- Field Detail
  - 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_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_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).
  - 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 Detail
  - 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 Detail
  - 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 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
  - 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 an arraylist of possible subtypes.
    
    Returns:
    
    an arraylist of possible subtypes
  - getPossibleSubtypes
```
public static ArrayList<Integer> getPossibleSubtypes()
```
    Returns an arraylist of possible subtypes.
    
    Returns:
    
    an arraylist of possible subtypes
  - 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
  - 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

Class ReporterIon

Nested Class Summary

Nested classes/interfaces inherited from class com.compomics.util.experiment.biology.Ion

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject

Methods inherited from class java.lang.Object

Field Detail

iTRAQ4Plex_114

iTRAQ4Plex_115

iTRAQ4Plex_116

iTRAQ4Plex_117

iTRAQ8Plex_113

iTRAQ8Plex_114

iTRAQ8Plex_115

iTRAQ8Plex_116

iTRAQ8Plex_117

iTRAQ8Plex_118

iTRAQ8Plex_119

iTRAQ8Plex_121

iTRAQ_145

iTRAQ_305

TMT_126

TMT_127N

TMT_127C

TMT_128N

TMT_128C

TMT_129N

TMT_129C

TMT_130N

TMT_130C

TMT_131

TMT_126_ETD

TMT_127N_ETD

TMT_127C_ETD

TMT_128N_ETD

TMT_128C_ETD

TMT_129N_ETD

TMT_129C_ETD

TMT_130N_ETD

TMT_130C_ETD

TMT_131_ETD

TMT_230

TMT_226

ACE_K_126

ACE_K_143

PHOSPHO_Y

FORMYL_K

METHYL_R_87

METHYL_R_112

METHYL_R_115

METHYL_R_143

METHYL_R_70

DI_METHYL_R_112

DI_METHYL_R_115

DI_METHYL_R_157

QQ

QQ_H2O

QQT

QQT_H2O

QQTG

QQTG_H2O

QQTGG

QQTGG_H2O

Constructor Detail

ReporterIon

ReporterIon

ReporterIon

ReporterIon

Method Detail

addReporterIon

getName

setName

setMass

getPrideCvTerm

isSameAs

getIndex