public class IonMatch extends ExperimentObject
Modifier and Type | Class and Description |
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static class |
IonMatch.MzErrorType
Enum of the supported error types.
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Modifier and Type | Field and Description |
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Charge |
charge
The supposed charge of the ion.
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Ion |
ion
The matching ion.
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Peak |
peak
The matched peak.
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Constructor and Description |
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IonMatch(Peak aPeak,
Ion anIon,
Charge aCharge)
Constructor for an ion peak.
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Modifier and Type | Method and Description |
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double |
getAbsoluteError()
Get the absolute matching error in Da.
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double |
getAbsoluteError(int minIsotope,
int maxIsotope)
Get the absolute matching error in Da after isotope removal.
|
CvTerm |
getChargePrideCvTerm()
Returns the pride CV term for the ion match charge.
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double |
getError(boolean isPpm)
Returns the error.
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double |
getError(boolean isPpm,
int minIsotope,
int maxIsotope)
Returns the error.
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CvTerm |
getIntensityPrideCvTerm()
Returns the pride CV term for the ion match intensity.
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CvTerm |
getIonMassErrorPrideCvTerm(int minIsotope,
int maxIsotope)
Returns the pride CV term for the ion match error.
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int |
getIsotopeNumber(int minIsotope,
int maxIsotope)
Returns the distance in number of neutrons between the experimental mass
and theoretic mass, image of the isotope number: 1 typically indicates
C13 isotope.
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static String |
getMatchKey(int ionTypeIndex,
int ionSubType,
int fragmentIonNumber,
String neutralLossesAsString,
int charge)
Returns the key based on the different attributes of a match.
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static String |
getMatchKey(Ion ion,
int charge)
Returns the key for the ion match uniquely representing a peak annotation.
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static String |
getMatchKey(Ion ion,
int charge,
IonMatchKeysCache ionMatchKeysCache)
Returns the key for the ion match uniquely representing a peak annotation.
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CvTerm |
getMZPrideCvTerm()
Returns the pride CV term for the ion match m/z.
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String |
getPeakAnnotation()
Returns the annotation to use for the ion match as a String.
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String |
getPeakAnnotation(boolean html)
Returns the annotation to use for the given ion match as a String.
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static String |
getPeakAnnotation(boolean html,
Ion ion,
Charge charge)
Returns the annotation to use for a given ion and charge as a String.
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static String |
getPeakAnnotation(Ion ion,
Charge charge)
Returns the annotation to use for a given ion and charge as a String.
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double |
getRelativeError()
Get the relative m/z matching error in ppm.
|
double |
getRelativeError(int minIsotope,
int maxIsotope)
Get the relative m/z matching error in ppm after isotope removal.
|
addUrParam, getParameterKey, getUrParam
public Peak peak
public Ion ion
public Charge charge
public double getAbsoluteError()
public double getAbsoluteError(int minIsotope, int maxIsotope)
minIsotope
- the minimal isotopemaxIsotope
- the maximal isotopepublic double getRelativeError()
public double getRelativeError(int minIsotope, int maxIsotope)
minIsotope
- the minimal isotopemaxIsotope
- the maximal isotopepublic int getIsotopeNumber(int minIsotope, int maxIsotope)
minIsotope
- the minimal isotopemaxIsotope
- the maximal isotopepublic double getError(boolean isPpm, int minIsotope, int maxIsotope)
isPpm
- a boolean indicating whether the error should be retrieved
in ppm (true) or in Dalton (false)minIsotope
- the minimal isotopemaxIsotope
- the maximal isotopepublic double getError(boolean isPpm)
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 chargepublic static String getMatchKey(Ion ion, int charge)
ion
- the ion matchedcharge
- the chargepublic static String getMatchKey(Ion ion, int charge, IonMatchKeysCache ionMatchKeysCache)
ion
- the ion matchedcharge
- the chargeionMatchKeysCache
- a cache for the ion match keyspublic static String getMatchKey(int ionTypeIndex, int ionSubType, int fragmentIonNumber, String neutralLossesAsString, int charge)
ionTypeIndex
- the index of the ion typeionSubType
- the index of the ion subtypefragmentIonNumber
- the number of the ion, 0 if noneneutralLossesAsString
- the neutral losses as a stringcharge
- the chargepublic 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 chargepublic String getPeakAnnotation(boolean html)
html
- if true, returns the annotation as HTML with subscripts tagspublic CvTerm getMZPrideCvTerm()
public CvTerm getIntensityPrideCvTerm()
public CvTerm getIonMassErrorPrideCvTerm(int minIsotope, int maxIsotope)
minIsotope
- the minimal isotopemaxIsotope
- the maximal isotopepublic CvTerm getChargePrideCvTerm()
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