com.compomics.util.experiment.biology.ions
Class ReporterIon

java.lang.Object
  extended by com.compomics.util.experiment.personalization.ExperimentObject
      extended by com.compomics.util.experiment.biology.Ion
          extended by com.compomics.util.experiment.biology.ions.ReporterIon
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable

public class ReporterIon
extends Ion

This class models a reporter ion. Ion indexes should be the rounded mass. User: Marc Date: Sep 1, 2010 Time: 1:44:59 PM

See Also:
Serialized Form

Field Summary
static ReporterIon iTRAQ113
          Standard reporter ion iTRAQ 113
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
static ReporterIon TMT3
          Standard reporter ion TMT3
static ReporterIon TMT4
          Standard reporter ion TMT4
static ReporterIon TMT5
          Standard reporter ion TMT5
 
Fields inherited from class com.compomics.util.experiment.biology.Ion
ELEMENTARY_ION, familyType, GLYCON_FRAGMENT, PEPTIDE_FRAGMENT, REPORTER_ION, theoreticMass
 
Constructor Summary
ReporterIon(java.lang.String name, double mass)
          Constructor for a user-defined reporter ion
 
Method Summary
 java.lang.String getName()
          This method returns the name of the reporter ion
 void setMass(double referenceMass)
          Method to set the mass of the reporter ion
 
Methods inherited from class com.compomics.util.experiment.biology.Ion
getIonFamilyType, proton
 
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, getParameterKey, getUrParam
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

iTRAQ113

public static final ReporterIon iTRAQ113
Standard reporter ion iTRAQ 113


iTRAQ114

public static final ReporterIon iTRAQ114
Standard reporter ion iTRAQ 114


iTRAQ115

public static final ReporterIon iTRAQ115
Standard reporter ion iTRAQ 115


iTRAQ116

public static final ReporterIon iTRAQ116
Standard reporter ion iTRAQ 116


iTRAQ117

public static final ReporterIon iTRAQ117
Standard reporter ion iTRAQ 117


iTRAQ118

public static final ReporterIon iTRAQ118
Standard reporter ion iTRAQ 118


iTRAQ119

public static final ReporterIon iTRAQ119
Standard reporter ion iTRAQ 119


iTRAQ121

public static final ReporterIon iTRAQ121
Standard reporter ion iTRAQ 121


TMT0

public static final ReporterIon TMT0
Standard reporter ion TMT0


TMT1

public static final ReporterIon TMT1
Standard reporter ion TMT1


TMT2

public static final ReporterIon TMT2
Standard reporter ion TMT2


TMT3

public static final ReporterIon TMT3
Standard reporter ion TMT3


TMT4

public static final ReporterIon TMT4
Standard reporter ion TMT4


TMT5

public static final ReporterIon TMT5
Standard reporter ion TMT5

Constructor Detail

ReporterIon

public ReporterIon(java.lang.String name,
                   double mass)
Constructor for a user-defined reporter ion

Parameters:
name - name of the reporter ion
mass - theoretic mass of the reporter ion
Method Detail

getName

public java.lang.String getName()
This method returns the name of the reporter ion

Returns:
name of the reporter ion

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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