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:
Serializable, 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

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Serialized Form

Field Summary
static int ITRAQ_113
          Reporter ion index iTRAQ 113
static int ITRAQ_114
          Reporter ion index iTRAQ 114
static int ITRAQ_115
          Reporter ion index iTRAQ 115
static int ITRAQ_116
          Reporter ion index iTRAQ 116
static int ITRAQ_117
          Reporter ion index iTRAQ 117
static int ITRAQ_118
          Reporter ion index iTRAQ 118
static int ITRAQ_119
          Reporter ion index iTRAQ 119
static int ITRAQ_121
          Reporter ion index iTRAQ 121
static int TMT0
          Reporter ion index TMT 0
static int TMT1
          Reporter ion index TMT 1
static int TMT2
          Reporter ion index TMT 2
static int TMT3
          Reporter ion index TMT 3
static int TMT4
          Reporter ion index TMT 4
static int TMT5
          Reporter ion index TMT 5
 
Fields inherited from class com.compomics.util.experiment.biology.Ion
ELEMENTARY_ION, familyType, GLYCON_FRAGMENT, PEPTIDE_FRAGMENT, REPORTER_ION, theoreticMass
 
Constructor Summary
ReporterIon(int index)
          Constructor for a reporter ion
ReporterIon(int index, String name, double mass)
          Constructor for a user-defined reporter ion
 
Method Summary
 int getIndex()
          Getter for the ion type
 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

ITRAQ_113

public static final int ITRAQ_113
Reporter ion index iTRAQ 113

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Constant Field Values

ITRAQ_114

public static final int ITRAQ_114
Reporter ion index iTRAQ 114

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Constant Field Values

ITRAQ_115

public static final int ITRAQ_115
Reporter ion index iTRAQ 115

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Constant Field Values

ITRAQ_116

public static final int ITRAQ_116
Reporter ion index iTRAQ 116

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Constant Field Values

ITRAQ_117

public static final int ITRAQ_117
Reporter ion index iTRAQ 117

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Constant Field Values

ITRAQ_118

public static final int ITRAQ_118
Reporter ion index iTRAQ 118

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Constant Field Values

ITRAQ_119

public static final int ITRAQ_119
Reporter ion index iTRAQ 119

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Constant Field Values

ITRAQ_121

public static final int ITRAQ_121
Reporter ion index iTRAQ 121

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Constant Field Values

TMT0

public static final int TMT0
Reporter ion index TMT 0

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Constant Field Values

TMT1

public static final int TMT1
Reporter ion index TMT 1

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Constant Field Values

TMT2

public static final int TMT2
Reporter ion index TMT 2

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Constant Field Values

TMT3

public static final int TMT3
Reporter ion index TMT 3

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Constant Field Values

TMT4

public static final int TMT4
Reporter ion index TMT 4

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Constant Field Values

TMT5

public static final int TMT5
Reporter ion index TMT 5

See Also:
Constant Field Values
Constructor Detail

ReporterIon

public ReporterIon(int index)
Constructor for a reporter ion

Parameters:
index - reporter ion index according to the static fields

ReporterIon

public ReporterIon(int index,
                   String name,
                   double mass)
Constructor for a user-defined reporter ion

Parameters:
index - index of the reporter ion (for user-defined ions avoid static fields index)
name - name of the reporter ion
mass - theoretic mass of the reporter ion
Method Detail

getIndex

public int getIndex()
Getter for the ion type

Returns:
the ion index according to the static fields

getName

public 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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