org.systemsbiology.jrap
Class ScanHeader

java.lang.Object
  extended by org.systemsbiology.jrap.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.

Author:
M. Vogelzang
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  float highMz
          TODO: Describe
protected  float ionisationEnergy
          TODO: Describe
protected  float lowMz
          TODO: Describe
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 precursorMz
          TODO: Describe
protected  int precursorScanNum
          TODO: Describe
protected  java.lang.String retentionTime
          TODO: Describe
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()
           
 float getHighMz()
           
 float getIonisationEnergy()
           
 float getLowMz()
           
 int getMsLevel()
           
 int getNum()
           
 int getPeaksCount()
           
 java.lang.String getPolarity()
           
 int getPrecision()
           
 int getPrecursorCharge()
           
 float getPrecursorMz()
           
 int getPrecursorScanNum()
           
 java.lang.String getRetentionTime()
           
 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 setHighMz(float highMz)
           
 void setIonisationEnergy(float ionisationEnergy)
           
 void setLowMz(float lowMz)
           
 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 setPrecursorMz(float precursorMz)
           
 void setPrecursorScanNum(int precursorScanNum)
           
 void setRetentionTime(java.lang.String retentionTime)
           
 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


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


collisionEnergy

protected float collisionEnergy
TODO: Describe


ionisationEnergy

protected float ionisationEnergy
TODO: Describe


precision

protected int precision
TODO: Describe


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
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.

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.

getRetentionTime

public java.lang.String getRetentionTime()
Returns:
Returns the retentionTime.

setRetentionTime

public void setRetentionTime(java.lang.String retentionTime)
Parameters:
retentionTime - The retentionTime to set.

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()

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


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