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:
Serializable, 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.
 CvTerm getChargePrideCvTerm()
          Returns the pride CV term for the ion match charge.
 double getError()
          Deprecated. replaced by getAbsoluteError() and getRelativeError()
 double getError(boolean isPpm)
          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.
 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.
 
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 m/z matching error in ppm.

Returns:
the relative matching error

getError

public double getError(boolean isPpm)
Returns the error.

Parameters:
isPpm - a boolean indicating whether the error should be retrieved in ppm (true) or in Dalton (false)
Returns:
the match m/z error

getPeakAnnotation

public String getPeakAnnotation()
Returns the annotation to use for the ion match as a String.

Returns:
the annotation to use for the given ion match

getPeakAnnotation

public static String getPeakAnnotation(Ion ion,
                                       Charge charge)
Returns the annotation to use for a given ion and charge as a String.

Parameters:
ion - the given ion
charge - the given charge
Returns:
the annotation to use for the given ion match

getPeakAnnotation

public static String getPeakAnnotation(boolean html,
                                       Ion ion,
                                       Charge charge)
Returns the annotation to use for a given ion and charge as a String.

Parameters:
html - if true, returns the annotation as HTML with subscripts tags
ion - the given ion
charge - the given charge
Returns:
the annotation to use for the given ion match

getPeakAnnotation

public String getPeakAnnotation(boolean html)
Returns the annotation to use for the given ion match as a String.

Parameters:
html - if true, returns the annotation as HTML with subscripts tags
Returns:
the annotation to use for the given ion match

getMZPrideCvTerm

public CvTerm getMZPrideCvTerm()
Returns the pride CV term for the ion match m/z.

Returns:
the pride CV term for the ion match m/z

getIntensityPrideCvTerm

public CvTerm getIntensityPrideCvTerm()
Returns the pride CV term for the ion match intensity.

Returns:
the pride CV term for the ion match intensity

getIonMassErrorPrideCvTerm

public CvTerm getIonMassErrorPrideCvTerm()
Returns the pride CV term for the ion match error.

Returns:
the pride CV term for the ion match error

getChargePrideCvTerm

public CvTerm getChargePrideCvTerm()
Returns the pride CV term for the ion match charge.

Returns:
the pride CV term for the ion match charge


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