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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 without isotope removal. |
double |
getAbsoluteError(boolean subtractIsotope)
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() |
double |
getError(boolean isPpm,
boolean subtractIsotope)
Returns the error. |
CvTerm |
getIntensityPrideCvTerm()
Returns the pride CV term for the ion match intensity. |
CvTerm |
getIonMassErrorPrideCvTerm()
Returns the pride CV term for the ion match error. |
int |
getIsotopeNumber()
Returns the distance in number of neutrons between the experimental mass and theoretic mass, image of the isotope number: 1 typically indicates C13 isotope. |
CvTerm |
getMZPrideCvTerm()
Returns the pride CV term for the ion match m/z. |
String |
getPeakAnnotation()
Returns the annotation to use for the ion match as a String. |
String |
getPeakAnnotation(boolean html)
Returns the annotation to use for the given ion match as a String. |
static String |
getPeakAnnotation(boolean html,
Ion ion,
Charge charge)
Returns the annotation to use for a given ion and charge as a String. |
static String |
getPeakAnnotation(Ion ion,
Charge charge)
Returns the annotation to use for a given ion and charge as a String. |
double |
getRelativeError()
Get the relative m/z matching error in ppm without isotope removal. |
double |
getRelativeError(boolean subtractIsotope)
Get the relative m/z 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(boolean subtractIsotope)
subtractIsotope
- indicates whether the isotope number shall be subtracted
public double getAbsoluteError()
public double getRelativeError(boolean subtractIsotope)
subtractIsotope
- indicates whether the isotope number shall be subtracted
public double getRelativeError()
public int getIsotopeNumber()
public double getError(boolean isPpm, boolean subtractIsotope)
isPpm
- a boolean indicating whether the error should be retrieved
in ppm (true) or in Dalton (false)
public String getPeakAnnotation()
public static String getPeakAnnotation(Ion ion, Charge charge)
ion
- the given ioncharge
- the given charge
public static String getPeakAnnotation(boolean html, Ion ion, Charge charge)
html
- if true, returns the annotation as HTML with subscripts tagsion
- the given ioncharge
- the given charge
public 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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