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java.lang.Objectcom.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.identification.matches.IonMatch
public class IonMatch
This class will model the assignment of a peak to a theoretical ion.
Field Summary | |
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Charge |
charge
The supposed charge of the ion |
Ion |
ion
The matching ion |
Peak |
peak
The matched peak |
Constructor Summary | |
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IonMatch(Peak aPeak,
Ion anIon,
Charge aCharge)
Constructor for an ion peak. |
Method Summary | |
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double |
getAbsoluteError()
Get the absolute matching error in Da. |
CvTerm |
getChargePrideCvTerm()
Returns the pride CV term for the ion match charge |
double |
getError()
Deprecated. replaced by getAbsoluteError() and getRelativeError() |
CvTerm |
getIntensityPrideCvTerm()
Returns the pride CV term for the ion match intensity |
CvTerm |
getIonMassErrorPrideCvTerm()
Returns the pride CV term for the ion match error |
CvTerm |
getMZPrideCvTerm()
Returns the pride CV term for the ion match m/z |
java.lang.String |
getPeakAnnotation()
Returns the annotation to use for the given ion match as a String. |
java.lang.String |
getPeakAnnotation(boolean html)
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 |
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addUrParam, getParameterKey, getUrParam |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public Peak peak
public Ion ion
public Charge charge
Constructor Detail |
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public IonMatch(Peak aPeak, Ion anIon, Charge aCharge)
aPeak
- the matched peakanIon
- the corresponding type of ionaCharge
- the charge of the ionMethod Detail |
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public double getError()
public double getAbsoluteError()
public double getRelativeError()
public java.lang.String getPeakAnnotation()
public java.lang.String getPeakAnnotation(boolean html)
html
- if true, returns the annotation as HTML with subscripts tags
public CvTerm getMZPrideCvTerm()
public CvTerm getIntensityPrideCvTerm()
public CvTerm getIonMassErrorPrideCvTerm()
public CvTerm getChargePrideCvTerm()
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