peakml
Class Centroid

java.lang.Object
  peakml.Annotatable
      peakml.IPeak
          peakml.Peak
              peakml.Centroid

public class Centroid
extends Peak

Implementation of a centroid or data-point in a mass spectrometry spectrum or profile. This class keeps track of a single mass, intensity and optional scanid value, which makes up a single data-point in a measurement. It's been chosen to mis-use the centroid value for a data-point as they are essential the same thing. The actual data associated to a Centroid instance is stored in a PeakData instance.

The centroid is the smallest (indivisible) component of mass spectrometry data.

Nested Class Summary

static class

Centroid.Factory Factory for creating a Centroid instance.

Nested classes/interfaces inherited from class peakml.IPeak

IPeak.AnnotationAscending, IPeak.AnnotationDescending, IPeak.MatchCompare<Type>, IPeak.RelationCompare<Type>

Field Summary

static PeakData.PeakFactory<Centroid>

factory Static instance for the factory, so not everybody will need to produce one

Fields inherited from class peakml.IPeak

relationid, sort_intensity_ascending, sort_intensity_descending, sort_mass_ascending, sort_mass_descending, sort_patternid_ascending, sort_patternid_descending, sort_profileid_ascending, sort_profileid_descending, sort_retentiontime_ascending, sort_retentiontime_descending, sort_scanid_ascending, sort_scanid_descending

Constructor Summary

Centroid(PeakData<Centroid> peakdata, int index)
Constructs a new Centroid instance linked to the given PeakData instance.

Method Summary

double	getIntensity() Retrieves the measured intensity for this peak.
double	getMass() Retrieves the mass of this peak.
int	getMeasurementID() Returns an optional measurement-id for this peak.
int	getPatternID() Returns an optional id for the peak.
double	getRetentionTime() Retrieves the retention time for this peak.
int	getScanID() Retrieves the scan-id for this peak.
Signal	getSignal() Calculates the signal for this IPeak object.
void	setIntensity(double intensity) Sets the intensity of this peak, for more information on mass see IPeak.getIntensity().
void	setMass(double mass) Sets the mass of this peak, for more information on mass see IPeak.getMass().
void	setMeasurementID(int id) Sets the profile-id of this peak, for more information on mass see IPeak.getMeasurementID().
void	setPatternID(int id) Sets the pattern-id of this peak, for more information on mass see IPeak.getPatternID().
void	setRetentionTime(double retentiontime) Sets the retention time for this peak, for more information on retention time see IPeak.setRetentionTime(double).
void	setScanID(int scan) Sets the scan-id for this peak, for more information on scan-id see IPeak.getScanID().

Methods inherited from class peakml.IPeak

findRelatedPeaks, getBestPeakOnMass, getBestPeakOnRT, match, match, peaksOfMeasurements, sha1, unpack

Methods inherited from class peakml.Annotatable

addAnnotation, addAnnotation, addAnnotation, addAnnotation, addAnnotation, addAnnotations, getAnnotation, getAnnotations, removeAllAnnotations, removeAnnotation

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

factory

public static PeakData.PeakFactory<Centroid> factory

Static instance for the factory, so not everybody will need to produce one

Constructor Detail

Centroid

public Centroid(PeakData<Centroid> peakdata,
                int index)

Constructs a new Centroid instance linked to the given PeakData instance. The given index is used to find the correct data in the collection of peaks contained in the PeakData instance.

Parameters:

peakdata - A PeakData instance containing all the data.

index - The index indicating the location of the data in the PeakData instance.

Method Detail

getMass

public double getMass()

Description copied from class: IPeak

Retrieves the mass of this peak. For a single peak implementation this would be the real mass, but for a chromatographic peak for example this would consist of the mean of a cluster of peaks.

Specified by:

getMass in class IPeak

Returns:

The mass of the peak.

setMass

public void setMass(double mass)

Description copied from class: IPeak

Sets the mass of this peak, for more information on mass see IPeak.getMass(). It is possible that the class implementing this interface does not support this method.

Specified by:

setMass in class IPeak

Parameters:

mass - The new mass for this peak.

getIntensity

public double getIntensity()

Description copied from class: IPeak

Retrieves the measured intensity for this peak. For a single peak implementation this would be the real measured intensity, but for a chromatographic peak for example this would consist of the mean measured intensity for a cluster of peaks.

Specified by:

getIntensity in class IPeak

Returns:

The measured intensity of the peak.

setIntensity

public void setIntensity(double intensity)

Description copied from class: IPeak

Sets the intensity of this peak, for more information on mass see IPeak.getIntensity(). It is possible that the class implementing this interface does not support this method.

Specified by:

setIntensity in class IPeak

Parameters:

intensity - The new intensity for this peak.

getScanID

public int getScanID()

Description copied from class: IPeak

Retrieves the scan-id for this peak. For a single peak implementation this would be the scan at which it was measured, but for a chromatographic peak for example this would be the scan with the most intense peak.

Specified by:

getScanID in class IPeak

Returns:

The scan at which the peak was measured.

setScanID

public void setScanID(int scan)

Description copied from class: IPeak

Sets the scan-id for this peak, for more information on scan-id see IPeak.getScanID(). It is possible that the class implementing this interface does not support this method.

Specified by:

setScanID in class IPeak

Parameters:

scan - The new scan for this peak.

getRetentionTime

public double getRetentionTime()

Description copied from class: IPeak

Retrieves the retention time for this peak. The retention time is closely linked to the scan-id, which is the index or order at which a particular measurement was made. The time is expressed in seconds (all parsers make sure the time-value stored in a file is converted to this convention) and can easily be converted into minutes and seconds with:

 double rt = peak.getRetentionTime();
 int minutes = (int) (rt / 60);
 int seconds = (int) (rt % 60);
 

Specified by:

getRetentionTime in class IPeak

Returns:

The retention time at which the peak was measured.

setRetentionTime

public void setRetentionTime(double retentiontime)

Description copied from class: IPeak

Sets the retention time for this peak, for more information on retention time see IPeak.setRetentionTime(double). It is possible that the class implementing this interface does not support this method.

Specified by:

setRetentionTime in class IPeak

Parameters:

retentiontime - The new retention time for this peak.

getMeasurementID

public int getMeasurementID()

Description copied from class: IPeak

Returns an optional measurement-id for this peak. This is a convenience mechanism for locating the measurement-information for this peak in the Header.

Specified by:

getMeasurementID in class IPeak

Returns:

The profile-id of this peak.

setMeasurementID

public void setMeasurementID(int id)

Description copied from class: IPeak

Sets the profile-id of this peak, for more information on mass see IPeak.getMeasurementID(). It is possible that the class implementing this interface does not support this method.

Specified by:

setMeasurementID in class IPeak

Parameters:

id - The new profile-id for this peak.

getPatternID

public int getPatternID()

Description copied from class: IPeak

Returns an optional id for the peak. This id can for example be used for peak sequence identification. Beware that this mechanism is highly volatile and can only be used in a single-threaded environment within a strictly controlled environment like a single function or a completely controlled application.

Specified by:

getPatternID in class IPeak

Returns:

The id of this peak.

setPatternID

public void setPatternID(int id)

Description copied from class: IPeak

Sets the pattern-id of this peak, for more information on mass see IPeak.getPatternID(). It is possible that the class implementing this interface does not support this method.

Specified by:

setPatternID in class IPeak

Parameters:

id - The new id for this peaks

getSignal

public Signal getSignal()

Description copied from class: IPeak

Calculates the signal for this IPeak object. For a single data-point this will be a signal of one element. For a collection of IPeaks it will be a compounded version.

Specified by:

getSignal in class IPeak

Returns:

The calculated signal.