com.compomics.util.experiment.identification.matches
Class IonMatch

java.lang.Object
  extended by com.compomics.util.experiment.personalization.ExperimentObject
      extended by com.compomics.util.experiment.identification.matches.IonMatch
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable

public class IonMatch
extends ExperimentObject

This class will model the assignment of a peak to a theoretical ion.

Author:
Marc Vaudel
See Also:
Serialized Form

Field Summary
 Charge charge
          The supposed charge of the ion
 Ion ion
          The matching ion
 Peak peak
          The matched peak
 
Constructor Summary
IonMatch(Peak aPeak, Ion anIon, Charge aCharge)
          Constructor for an ion peak.
 
Method Summary
 double getAbsoluteError()
          Get the absolute matching error in Da.
 double getError()
          Deprecated. replaced by getAbsoluteError() and getRelativeError()
 java.lang.String getPeakAnnotation()
          Returns the annotation to use for the given ion match as a String.
 double getRelativeError()
          Get the relative matching error in ppm.
 
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

peak

public Peak peak
The matched peak


ion

public Ion ion
The matching ion


charge

public Charge charge
The supposed charge of the ion

Constructor Detail

IonMatch

public IonMatch(Peak aPeak,
                Ion anIon,
                Charge aCharge)
Constructor for an ion peak.

Parameters:
aPeak - the matched peak
anIon - the corresponding type of ion
aCharge - the charge of the ion
Method Detail

getError

public double getError()
Deprecated. replaced by getAbsoluteError() and getRelativeError()

Get the matching error.

Returns:
the matching error

getAbsoluteError

public double getAbsoluteError()
Get the absolute matching error in Da.

Returns:
the absolute matching error

getRelativeError

public double getRelativeError()
Get the relative matching error in ppm.

Returns:
the relative matching error

getPeakAnnotation

public java.lang.String getPeakAnnotation()
Returns the annotation to use for the given ion match as a String. Format: ion type + [ion number] + [charge] + [neutral loss]

Returns:
the annotation to use for the given ion match


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