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 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
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
theoreticMass, type
 
Constructor Summary
ReporterIon(int subType)
          Constructor for a user-defined reporter ion.
ReporterIon(String name, double mass)
          Constructor for a user-defined reporter ion.
 
Method Summary
 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.
 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
getGenericIon, getGenericIon, getImplementedIonTypes, getNeutralLossesAsString, getNeutralLossesAsString, getPossibleSubtypes, getTheoreticMass, getType, getTypeAsString, getTypeAsString, setTheoreticMass
 
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(String name,
                   double mass)
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

ReporterIon

public ReporterIon(int subType)
Constructor for a user-defined reporter ion.

Parameters:
subType - the reporter ion type
Method Detail

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

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


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