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java.lang.Objectorg.systemsbiology.jrap.Scan
public final class Scan
A simple class to hold the contents of a scan from a MSXML file. This is a start. For those who want to get more fancy you should only have to modify the SAX2ScanHandler to replace this.
Field Summary | |
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protected double[][] |
doubleMassIntensityList
|
protected float[][] |
floatMassIntensityList
A 2-dimensional array, element 0 contains a list of masses of peaks, element 1 contains a list of intensities of peaks. |
protected ScanHeader |
header
|
Constructor Summary | |
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Scan()
Default constructor, initializes an empty Scan. |
Method Summary | |
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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[][] |
getDoubleMassIntensityList()
|
double |
getDoubleRetentionTime()
|
float |
getEndMz()
|
float[][] |
getFloatMassIntensityList()
Return the peaks in this scan as two lists: one of mass values and one of intensity values. |
ScanHeader |
getHeader()
|
float |
getHighMz()
|
float |
getIonisationEnergy()
|
float |
getLowMz()
|
int |
getMsLevel()
|
int |
getNum()
|
float[][] |
getPeakList()
|
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 newValue)
Set the intensity of the base peak |
void |
setBasePeakMz(float newValue)
Set the base peak m/z value for this scan |
void |
setByteOrder(java.lang.String newValue)
|
void |
setCentroided(int newValue)
Set if this scan was centroided or not |
void |
setChargeDeconvoluted(int newValue)
Set if this scan was charge deconvoluted or not |
void |
setCollisionEnergy(float newValue)
Set the collision energy used in this scan. |
void |
setCompressedLen(int newValue)
|
void |
setCompressionType(java.lang.String newValue)
|
void |
setContentType(java.lang.String newValue)
|
void |
setDeisotoped(int newValue)
Set if this scan was deisotoped or not |
void |
setDoubleMassIntensityList(double[][] newValue)
|
void |
setEndMz(float newValue)
|
void |
setFloatMassIntensityList(float[][] newValue)
|
void |
setHeader(ScanHeader header)
|
void |
setHighMz(float newValue)
|
void |
setIonisationEnergy(float newValue)
Set the ionisation energy used in this scan. |
void |
setLowMz(float newValue)
|
void |
setMsLevel(int newValue)
Set the MS level of this scan |
void |
setNum(int newValue)
Set the number of this scan in the file. |
void |
setPeakList(float[][] newValue)
|
void |
setPeaksCount(int newValue)
Set the number of peaks in this scan. |
void |
setPolarity(java.lang.String newValue)
Set the polarity of this scan |
void |
setPrecision(int newValue)
|
void |
setPrecursorCharge(int newValue)
Set the charge of the precursor of this scan |
void |
setPrecursorMz(float newValue)
Set the precursor m/z value for this scan |
void |
setPrecursorScanNum(int newValue)
Set the scan number in which the precursor of this scan was acquired |
void |
setRetentionTime(java.lang.String newValue)
Set the retention time at which this scan was acquired |
void |
setScanType(java.lang.String newValue)
Set the type of this scan |
void |
setStartMz(float newValue)
|
void |
setTotIonCurrent(float newValue)
Set the total ion current of this scan |
java.lang.String |
toString()
String respresentation of a Scan object. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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protected ScanHeader header
protected float[][] floatMassIntensityList
protected double[][] doubleMassIntensityList
Constructor Detail |
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public Scan()
Method Detail |
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public void setNum(int newValue)
public void setMsLevel(int newValue)
newValue
- the new MS level of this scanpublic void setPeaksCount(int newValue)
newValue
- the new number of peaks in this scan.public void setPolarity(java.lang.String newValue)
newValue
- the new polarity of this scanpublic void setScanType(java.lang.String newValue)
newValue
- the new type of this scanpublic void setCentroided(int newValue)
newValue
- 0 if this scan was not centroided, 1 if it waspublic void setDeisotoped(int newValue)
newValue
- 0 if this scan was not deisotoped, 1 if it waspublic void setChargeDeconvoluted(int newValue)
newValue
- 0 if this scan was not charge deconvoluted, 1 if it waspublic void setRetentionTime(java.lang.String newValue)
newValue
- the new value for the retention time.public void setStartMz(float newValue)
public void setEndMz(float newValue)
public void setLowMz(float newValue)
public void setHighMz(float newValue)
public void setBasePeakMz(float newValue)
newValue
- the new value to setpublic void setBasePeakIntensity(float newValue)
newValue
- the new value to setpublic void setTotIonCurrent(float newValue)
newValue
- the new value to setpublic void setPrecursorMz(float newValue)
newValue
- the new value to set.public void setPrecursorScanNum(int newValue)
newValue
- the new value to setpublic void setPrecursorCharge(int newValue)
newValue
- the new value to set.public void setCollisionEnergy(float newValue)
newValue
- the new value to set.public void setIonisationEnergy(float newValue)
newValue
- the new value to setpublic void setPrecision(int newValue)
public void setPeakList(float[][] newValue)
public void setFloatMassIntensityList(float[][] newValue)
public void setDoubleMassIntensityList(double[][] newValue)
public void setByteOrder(java.lang.String newValue)
public void setContentType(java.lang.String newValue)
public void setCompressionType(java.lang.String newValue)
public void setCompressedLen(int newValue)
public int getNum()
public int getMsLevel()
public int getPeaksCount()
public java.lang.String getPolarity()
public java.lang.String getScanType()
public int getCentroided()
public int getDeisotoped()
public int getChargeDeconvoluted()
public java.lang.String getRetentionTime()
public float getStartMz()
public float getEndMz()
public float getLowMz()
public float getHighMz()
public float getBasePeakMz()
public float getBasePeakIntensity()
public float getTotIonCurrent()
public float getPrecursorMz()
public int getPrecursorScanNum()
public int getPrecursorCharge()
public float getCollisionEnergy()
public float getIonisationEnergy()
public int getPrecision()
public java.lang.String getByteOrder()
public java.lang.String getContentType()
public java.lang.String getCompressionType()
public int getCompressedLen()
public float[][] getPeakList()
public float[][] getFloatMassIntensityList()
public double[][] getDoubleMassIntensityList()
public java.lang.String toString()
toString
in class java.lang.Object
public double getDoubleRetentionTime()
public ScanHeader getHeader()
public void setHeader(ScanHeader header)
header
- The ScanHeader to set.
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