org.systemsbiology.jrap.stax
Class ScanHeader

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

All Implemented Interfaces:

java.io.Serializable

public class ScanHeader
extends java.lang.Object
implements java.io.Serializable

ScanHeader is a class that contains all information associated with a Scan, except for the actual peakList. The separation between the peaklist and the other information was made because parsing the peaklist costs a lot of time, and in this way, programs can parse headers separately, and not parse the peaklist when it's not needed.

See Also:

Serialized Form

Field Summary

protected float	basePeakIntensity TODO: Describe
protected float	basePeakMz TODO: Describe
protected java.lang.String	byteOrder Peaks attribute for mzXML_3.0
protected int	centroided TODO: Describe
protected int	chargeDeconvoluted TODO: Describe
protected float	collisionEnergy TODO: Describe
protected int	compressedLen
protected java.lang.String	compressionType
protected java.lang.String	contentType
protected int	deisotoped TODO: Describe
protected float	endMz TODO: Describe
protected java.lang.String	filterLine for S(M)RM
protected float	highMz TODO: Describe
protected int	intenCompressedLen
protected java.lang.String	intenCompressionType
protected int	intenPrecision
protected float	ionisationEnergy TODO: Describe
protected float	lowMz TODO: Describe
protected int	massCompressedLen
protected java.lang.String	massCompressionType
protected int	massPrecision for mzML
protected int	msLevel MS Scan Level
protected int	num Scan Number
protected int	peaksCount Number of peaks in scan
protected java.lang.String	polarity TODO: Describe
protected int	precision TODO: Describe
protected int	precursorCharge TODO: Describe
protected float	precursorIntensity
protected float	precursorMz TODO: Describe
protected int	precursorScanNum TODO: Describe
protected java.lang.String	retentionTime TODO: Describe
protected double	rt for mzML
protected java.lang.String	scanType TODO: Describe
protected float	startMz TODO: Describe
protected float	totIonCurrent TODO: Describe

Constructor Summary

ScanHeader()

Method Summary

float	getBasePeakIntensity()
float	getBasePeakMz()
java.lang.String	getByteOrder()
int	getCentroided()
int	getChargeDeconvoluted()
float	getCollisionEnergy()
int	getCompressedLen()
java.lang.String	getCompressionType()
java.lang.String	getContentType()
int	getDeisotoped()
double	getDoubleRetentionTime()
float	getEndMz()
java.lang.String	getFilterLine()
float	getHighMz()
int	getIntenCompressedLen()
java.lang.String	getIntenCompressionType()
int	getIntenPrecision()
float	getIonisationEnergy()
float	getLowMz()
int	getMassCompressedLen()
java.lang.String	getMassCompressionType()
int	getMassPrecision()
int	getMsLevel()
int	getNum()
int	getPeaksCount()
java.lang.String	getPolarity()
int	getPrecision()
int	getPrecursorCharge()
float	getPrecursorIntensity()
float	getPrecursorMz()
int	getPrecursorScanNum()
java.lang.String	getRetentionTime()
double	getRT()
java.lang.String	getScanType()
float	getStartMz()
float	getTotIonCurrent()
void	setBasePeakIntensity(float basePeakIntensity)
void	setBasePeakMz(float basePeakMz)
void	setByteOrder(java.lang.String byteOrder)
void	setCentroided(int centroided)
void	setChargeDeconvoluted(int chargeDeconvoluted)
void	setCollisionEnergy(float collisionEnergy)
void	setCompressedLen(int compressedLen)
void	setCompressionType(java.lang.String compressionType)
void	setContentType(java.lang.String contentType)
void	setDeisotoped(int deisotoped)
void	setEndMz(float endMz)
void	setFilterLine(java.lang.String filterLine)
void	setHighMz(float highMz)
void	setIntenCompressedLen(int intenCompressedLen)
void	setIntenCompressionType(java.lang.String intenCompressionType)
void	setIntenPrecision(int intenPrecision)
void	setIonisationEnergy(float ionisationEnergy)
void	setLowMz(float lowMz)
void	setMassCompressedLen(int massCompressedLen)
void	setMassCompressionType(java.lang.String massCompressionType)
void	setMassPrecision(int massPrecision)
void	setMsLevel(int msLevel)
void	setNum(int num)
void	setPeaksCount(int peaksCount)
void	setPolarity(java.lang.String polarity)
void	setPrecision(int precision)
void	setPrecursorCharge(int precursorCharge)
void	setPrecursorIntensity(float precursorIntensity)
void	setPrecursorMz(float precursorMz)
void	setPrecursorScanNum(int precursorScanNum)
void	setRetentionTime(java.lang.String retentionTime)
void	setRT(double rt)
void	setScanType(java.lang.String scanType)
void	setStartMz(float startMz)
void	setTotIonCurrent(float totIonCurrent)
java.lang.String	toString() String respresentation of a ScanHeader object.

Methods inherited from class java.lang.Object

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

Field Detail

num

protected int num

Scan Number

msLevel

protected int msLevel

MS Scan Level

peaksCount

protected int peaksCount

Number of peaks in scan

polarity

protected java.lang.String polarity

TODO: Describe

scanType

protected java.lang.String scanType

TODO: Describe

centroided

protected int centroided

TODO: Describe

deisotoped

protected int deisotoped

TODO: Describe

chargeDeconvoluted

protected int chargeDeconvoluted

TODO: Describe

retentionTime

protected java.lang.String retentionTime

TODO: Describe

rt

protected double rt

for mzML

startMz

protected float startMz

TODO: Describe

endMz

protected float endMz

TODO: Describe

lowMz

protected float lowMz

TODO: Describe

highMz

protected float highMz

TODO: Describe

basePeakMz

protected float basePeakMz

TODO: Describe

basePeakIntensity

protected float basePeakIntensity

TODO: Describe

totIonCurrent

protected float totIonCurrent

TODO: Describe

precursorMz

protected float precursorMz

TODO: Describe

precursorScanNum

protected int precursorScanNum

TODO: Describe

precursorCharge

protected int precursorCharge

TODO: Describe

precursorIntensity

protected float precursorIntensity

collisionEnergy

protected float collisionEnergy

TODO: Describe

ionisationEnergy

protected float ionisationEnergy

TODO: Describe

precision

protected int precision

TODO: Describe

filterLine

protected java.lang.String filterLine

for S(M)RM

byteOrder

protected java.lang.String byteOrder

Peaks attribute for mzXML_3.0

contentType

protected java.lang.String contentType

compressionType

protected java.lang.String compressionType

compressedLen

protected int compressedLen

massPrecision

protected int massPrecision

for mzML

massCompressionType

protected java.lang.String massCompressionType

massCompressedLen

protected int massCompressedLen

intenPrecision

protected int intenPrecision

intenCompressionType

protected java.lang.String intenCompressionType

intenCompressedLen

protected int intenCompressedLen

Constructor Detail

ScanHeader

public ScanHeader()

Method Detail

getBasePeakIntensity

public float getBasePeakIntensity()

Returns:

Returns the basePeakIntensity.

setBasePeakIntensity

public void setBasePeakIntensity(float basePeakIntensity)

Parameters:

basePeakIntensity - The basePeakIntensity to set.

getBasePeakMz

public float getBasePeakMz()

Returns:

Returns the basePeakMz.

setBasePeakMz

public void setBasePeakMz(float basePeakMz)

Parameters:

basePeakMz - The basePeakMz to set.

getByteOrder

public java.lang.String getByteOrder()

Returns:

returns the byteOrder

setByteOrder

public void setByteOrder(java.lang.String byteOrder)

Parameters:

set - the byteOrder

getCentroided

public int getCentroided()

Returns:

Returns the centroided.

setCentroided

public void setCentroided(int centroided)

Parameters:

centroided - The centroided to set.

getChargeDeconvoluted

public int getChargeDeconvoluted()

Returns:

Returns the chargeDeconvoluted.

setChargeDeconvoluted

public void setChargeDeconvoluted(int chargeDeconvoluted)

Parameters:

chargeDeconvoluted - The chargeDeconvoluted to set.

getCollisionEnergy

public float getCollisionEnergy()

Returns:

Returns the collisionEnergy.

setCollisionEnergy

public void setCollisionEnergy(float collisionEnergy)

Parameters:

collisionEnergy - The collisionEnergy to set.

getCompressionType

public java.lang.String getCompressionType()

Returns:

returns compressionType

setCompressionType

public void setCompressionType(java.lang.String compressionType)

Parameters:

set - compressionType

getCompressedLen

public int getCompressedLen()

Returns:

returns compressedLen

setCompressedLen

public void setCompressedLen(int compressedLen)

Parameters:

set - compressedLen

getContentType

public java.lang.String getContentType()

Returns:

returns the contentType

setContentType

public void setContentType(java.lang.String contentType)

Parameters:

set - the contentType

getDeisotoped

public int getDeisotoped()

Returns:

Returns the deisotoped.

setDeisotoped

public void setDeisotoped(int deisotoped)

Parameters:

deisotoped - The deisotoped to set.

getEndMz

public float getEndMz()

Returns:

Returns the endMz.

setEndMz

public void setEndMz(float endMz)

Parameters:

endMz - The endMz to set.

getFilterLine

public java.lang.String getFilterLine()

Returns:

Returns the filterLine.

setFilterLine

public void setFilterLine(java.lang.String filterLine)

Parameters:

filterLine -

getHighMz

public float getHighMz()

Returns:

Returns the highMz.

setHighMz

public void setHighMz(float highMz)

Parameters:

highMz - The highMz to set.

getIonisationEnergy

public float getIonisationEnergy()

Returns:

Returns the ionisationEnergy.

setIonisationEnergy

public void setIonisationEnergy(float ionisationEnergy)

Parameters:

ionisationEnergy - The ionisationEnergy to set.

getLowMz

public float getLowMz()

Returns:

Returns the lowMz.

setLowMz

public void setLowMz(float lowMz)

Parameters:

lowMz - The lowMz to set.

getMsLevel

public int getMsLevel()

Returns:

Returns the msLevel.

setMsLevel

public void setMsLevel(int msLevel)

Parameters:

msLevel - The msLevel to set.

getNum

public int getNum()

Returns:

Returns the num.

setNum

public void setNum(int num)

Parameters:

num - The num to set.

getPeaksCount

public int getPeaksCount()

Returns:

Returns the peaksCount.

setPeaksCount

public void setPeaksCount(int peaksCount)

Parameters:

peaksCount - The peaksCount to set.

getPolarity

public java.lang.String getPolarity()

Returns:

Returns the polarity.

setPolarity

public void setPolarity(java.lang.String polarity)

Parameters:

polarity - The polarity to set.

getPrecision

public int getPrecision()

Returns:

Returns the precision.

setPrecision

public void setPrecision(int precision)

Parameters:

precision - The precision to set.

getPrecursorCharge

public int getPrecursorCharge()

Returns:

Returns the precursorCharge.

setPrecursorCharge

public void setPrecursorCharge(int precursorCharge)

Parameters:

precursorCharge - The precursorCharge to set.

getPrecursorMz

public float getPrecursorMz()

Returns:

Returns the precursorMz.

setPrecursorMz

public void setPrecursorMz(float precursorMz)

Parameters:

precursorMz - The precursorMz to set.

getPrecursorScanNum

public int getPrecursorScanNum()

Returns:

Returns the precursorScanNum.

setPrecursorScanNum

public void setPrecursorScanNum(int precursorScanNum)

Parameters:

precursorScanNum - The precursorScanNum to set.

getPrecursorIntensity

public float getPrecursorIntensity()

Returns:

Returns the precursorIntensity

setPrecursorIntensity

public void setPrecursorIntensity(float precursorIntensity)

Parameters:

precursorIntensity - The precursorIntensity to set

getRetentionTime

public java.lang.String getRetentionTime()

Returns:

Returns the retentionTime.

setRetentionTime

public void setRetentionTime(java.lang.String retentionTime)

Parameters:

retentionTime - The retentionTime to set.

getRT

public double getRT()

Parameters:

rt - The retentionTime for mzML.

setRT

public void setRT(double rt)

getScanType

public java.lang.String getScanType()

Returns:

Returns the scanType.

setScanType

public void setScanType(java.lang.String scanType)

Parameters:

scanType - The scanType to set.

getStartMz

public float getStartMz()

Returns:

Returns the startMz.

setStartMz

public void setStartMz(float startMz)

Parameters:

startMz - The startMz to set.

getTotIonCurrent

public float getTotIonCurrent()

Returns:

Returns the totIonCurrent.

setTotIonCurrent

public void setTotIonCurrent(float totIonCurrent)

Parameters:

totIonCurrent - The totIonCurrent to set.

getDoubleRetentionTime

public double getDoubleRetentionTime()

getMassPrecision

public int getMassPrecision()

Returns:

massPrecision

setMassPrecision

public void setMassPrecision(int massPrecision)

Parameters:

massPrecision - to set

getMassCompressionType

public java.lang.String getMassCompressionType()

Returns:

massCompressionType

setMassCompressionType

public void setMassCompressionType(java.lang.String massCompressionType)

Parameters:

massCompressionType -

getMassCompressedLen

public int getMassCompressedLen()

Returns:

massCompressionLen

setMassCompressedLen

public void setMassCompressedLen(int massCompressedLen)

Parameters:

massCompressedLen -

getIntenPrecision

public int getIntenPrecision()

Returns:

intenPrecision

setIntenPrecision

public void setIntenPrecision(int intenPrecision)

Parameters:

intenPrecision -

getIntenCompressionType

public java.lang.String getIntenCompressionType()

Returns:

intenCompressionType

setIntenCompressionType

public void setIntenCompressionType(java.lang.String intenCompressionType)

Parameters:

intenCompressionType -

getIntenCompressedLen

public int getIntenCompressedLen()

Returns:

intenCompressedLen

setIntenCompressedLen

public void setIntenCompressedLen(int intenCompressedLen)

Parameters:

intenCompressedLen -

toString

public java.lang.String toString()

String respresentation of a ScanHeader object. Note: This is most likely not an optimal way to build the string. Hopefully this method will only be used for testing.

Overrides:

toString in class java.lang.Object