org.systemsbiology.jrap.stax
Class DataProcessingInfo

java.lang.Object
  org.systemsbiology.jrap.stax.DataProcessingInfo

public class DataProcessingInfo
extends java.lang.Object

DataProcessingInfo contains information about what settings and software were used to process the data contained in an mzXML file.

Field Summary

protected int	baseLineReduced
protected int	centroided
protected int	chargeDeconvoluted
protected int	deisotoped
protected double	intensityCutoff
protected int	lowIntensityDataRemoved
static int	NO
protected int	peakPicked
protected int	smoothed
protected int	spotIntegration
static int	UNKNOWN
static int	YES

Constructor Summary

DataProcessingInfo()

Method Summary

int	getBaseLineReduced() Were chromatogram base line reduced?
int	getCentroided() Was the data centroided?
int	getChargeDeconvoluted() Was the data charge deconvoluted?
int	getDeisotoped() Was the data charge deisotoped?
double	getIntensityCutoff() Return the intensity cutoff that was used to eliminate low-signal peaks.
int	getLowIntensityDataRemoved() Were chromatogram remove low intensity data
int	getPeakPicked() Were peaks extracted?
int	getSmoothed() Were Chromatogram smoothed?
java.util.ArrayList<SoftwareInfo>	getSoftwareUsed() Return an array of information about all software that was used to process the data, in chronological order.
int	getSpotIntegration() Were spots integrated?
void	setBaseLineReduced(int baseLineReduced)
void	setCentroided(int centroided) Set centroided to one of UNKNOWN, YES or NO.
void	setChargeDeconvoluted(int chargeDeconvoluted) Set charge deconvoluted to one of UNKNOWN, YES or NO.
void	setDeisotoped(int deisotoped) Set deisotoped to one of UNKNOWN, YES or NO.
void	setIntensityCutoff(double intensityCutoff) Set the intensity cutoff that was used to eliminate low-signal peaks.
void	setLowIntensityDataRemoved(int lowIntensityDataRemoved)
void	setPeakPicked(int peakPicked) set value of peakPicked to one of UNKNOWN, YES or NO
void	setSmoothed(int smoothed)
void	setSoftwareUsed(java.util.ArrayList<SoftwareInfo> softwareUsed) Set the chronological array of used software for data processing.
void	setSpotIntegration(int spotIntegration) Set spot integration to one of UNKNOWN, YES or NO.
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

UNKNOWN

public static final int UNKNOWN

See Also:

Constant Field Values

YES

public static final int YES

See Also:

Constant Field Values

NO

public static final int NO

See Also:

Constant Field Values

intensityCutoff

protected double intensityCutoff

centroided

protected int centroided

deisotoped

protected int deisotoped

chargeDeconvoluted

protected int chargeDeconvoluted

spotIntegration

protected int spotIntegration

peakPicked

protected int peakPicked

smoothed

protected int smoothed

baseLineReduced

protected int baseLineReduced

lowIntensityDataRemoved

protected int lowIntensityDataRemoved

Constructor Detail

DataProcessingInfo

public DataProcessingInfo()

Method Detail

getCentroided

public int getCentroided()

Was the data centroided?

Returns:

UNKNOWN, YES or NO.

setCentroided

public void setCentroided(int centroided)

Set centroided to one of UNKNOWN, YES or NO.

Parameters:

centroided - The value to set.

getChargeDeconvoluted

public int getChargeDeconvoluted()

Was the data charge deconvoluted?

Returns:

UNKNOWN, YES or NO.

setChargeDeconvoluted

public void setChargeDeconvoluted(int chargeDeconvoluted)

Set charge deconvoluted to one of UNKNOWN, YES or NO.

Parameters:

chargeDeconvoluted - The value to set.

getDeisotoped

public int getDeisotoped()

Was the data charge deisotoped?

Returns:

UNKNOWN, YES or NO.

setDeisotoped

public void setDeisotoped(int deisotoped)

Set deisotoped to one of UNKNOWN, YES or NO.

Parameters:

deisotoped - The value to set.

getIntensityCutoff

public double getIntensityCutoff()

Return the intensity cutoff that was used to eliminate low-signal peaks. A negative value means the cutoff is not known.

Returns:

Returns the intensityCutoff, or a negative value when the cutoff is not known.

setIntensityCutoff

public void setIntensityCutoff(double intensityCutoff)

Set the intensity cutoff that was used to eliminate low-signal peaks. A negative value means the cutoff is not known.

Parameters:

intensityCutoff - The intensityCutoff to set.

getSoftwareUsed

public java.util.ArrayList<SoftwareInfo> getSoftwareUsed()

Return an array of information about all software that was used to process the data, in chronological order.

Returns:

An array of information about software

setSoftwareUsed

public void setSoftwareUsed(java.util.ArrayList<SoftwareInfo> softwareUsed)

Set the chronological array of used software for data processing.

Parameters:

softwareUsed - The array of info about software.

getSpotIntegration

public int getSpotIntegration()

Were spots integrated?

Returns:

UNKNOWN, YES or NO.

setSpotIntegration

public void setSpotIntegration(int spotIntegration)

Set spot integration to one of UNKNOWN, YES or NO.

Parameters:

spotIntegration - The value to set.

getPeakPicked

public int getPeakPicked()

Were peaks extracted?

Returns:

UNKNOWN, YES or NO

setPeakPicked

public void setPeakPicked(int peakPicked)

set value of peakPicked to one of UNKNOWN, YES or NO

Parameters:

peakPicked -

getSmoothed

public int getSmoothed()

Were Chromatogram smoothed?

Returns:

UNKNOWN, YES, NO

setSmoothed

public void setSmoothed(int smoothed)

getBaseLineReduced

public int getBaseLineReduced()

Were chromatogram base line reduced?

Returns:

UNKNOWN,YES or No

setBaseLineReduced

public void setBaseLineReduced(int baseLineReduced)

getLowIntensityDataRemoved

public int getLowIntensityDataRemoved()

Were chromatogram remove low intensity data

Returns:

UNKNOWN, YES or NO

setLowIntensityDataRemoved

public void setLowIntensityDataRemoved(int lowIntensityDataRemoved)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object