public class ReporterIon extends Ion
Ion.IonType
Modifier and Type | Field and Description |
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static ReporterIon |
iTRAQ113
Standard reporter ion iTRAQ 113.
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static ReporterIon |
iTRAQ114
Standard reporter ion iTRAQ 114.
|
static ReporterIon |
iTRAQ115
Standard reporter ion iTRAQ 115.
|
static ReporterIon |
iTRAQ116
Standard reporter ion iTRAQ 116.
|
static ReporterIon |
iTRAQ117
Standard reporter ion iTRAQ 117.
|
static ReporterIon |
iTRAQ118
Standard reporter ion iTRAQ 118.
|
static ReporterIon |
iTRAQ119
Standard reporter ion iTRAQ 119.
|
static ReporterIon |
iTRAQ121
Standard reporter ion iTRAQ 121.
|
static ReporterIon |
TMT0
Standard reporter ion TMT0.
|
static ReporterIon |
TMT1
Standard reporter ion TMT1.
|
static ReporterIon |
TMT2
Standard reporter ion TMT2.
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static ReporterIon |
TMT3
Standard reporter ion TMT3.
|
static ReporterIon |
TMT4
Standard reporter ion TMT4.
|
static ReporterIon |
TMT5
Standard reporter ion TMT5.
|
theoreticMass, type
Constructor and Description |
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ReporterIon(int subType)
Constructor for a user-defined reporter ion.
|
ReporterIon(java.lang.String name,
double mass)
Constructor for a user-defined reporter ion.
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Modifier and Type | Method and Description |
---|---|
int |
getIndex()
Returns the index of a reporter ion.
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java.lang.String |
getName()
This method returns the name of the reporter ion.
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java.util.ArrayList<NeutralLoss> |
getNeutralLosses()
Returns the possible neutral losses of this ion type.
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static java.util.ArrayList<java.lang.Integer> |
getPossibleSubtypes()
Returns an arraylist of possible subtypes.
|
CvTerm |
getPrideCvTerm()
Returns the pride cv term adapted to the fragment ion.
|
int |
getSubType()
Returns the ion subtype.
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java.lang.String |
getSubTypeAsString()
Returns the subtype as string.
|
boolean |
isSameAs(Ion anotherIon)
Returns a boolean indicating whether the ion is the same as another ion.
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boolean |
isSameAs(ReporterIon anotherReporterIon)
Compares the current reporter ion with another one based on their masses.
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void |
setMass(double referenceMass)
Method to set the mass of the reporter ion.
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void |
setName(java.lang.String name)
Setter for the ion name.
|
getGenericIon, getGenericIon, getImplementedIonTypes, getNeutralLossesAsString, getNeutralLossesAsString, getPossibleSubtypes, getTheoreticMass, getTheoreticMz, getType, getTypeAsString, getTypeAsString, setTheoreticMass
addUrParam, getParameterKey, getUrParam
public static final ReporterIon iTRAQ113
public static final ReporterIon iTRAQ114
public static final ReporterIon iTRAQ115
public static final ReporterIon iTRAQ116
public static final ReporterIon iTRAQ117
public static final ReporterIon iTRAQ118
public static final ReporterIon iTRAQ119
public static final ReporterIon iTRAQ121
public static final ReporterIon TMT0
public static final ReporterIon TMT1
public static final ReporterIon TMT2
public static final ReporterIon TMT3
public static final ReporterIon TMT4
public static final ReporterIon TMT5
public ReporterIon(java.lang.String name, double mass)
name
- name of the reporter ion. Should be unique to the ion.mass
- theoretic mass of the reporter ionpublic ReporterIon(int subType)
subType
- the reporter ion typepublic java.lang.String getName()
public void setName(java.lang.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 boolean isSameAs(ReporterIon anotherReporterIon)
anotherReporterIon
- the other reporter ionpublic int getIndex()
public int getSubType()
Ion
getSubType
in class Ion
public java.lang.String getSubTypeAsString()
Ion
getSubTypeAsString
in class Ion
public static java.util.ArrayList<java.lang.Integer> getPossibleSubtypes()
public java.util.ArrayList<NeutralLoss> getNeutralLosses()
Ion
getNeutralLosses
in class Ion
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