public abstract class AbstractScan extends Object implements IScan
| Modifier and Type | Field and Description |
|---|---|
protected Double |
basePeakIntensity
Intensity of the most intense peak
|
protected Double |
basePeakMz
m/z of the most intense peak
|
protected List<Integer> |
childScans
A list of MS/MS scans, that originated from this one
|
static DecimalFormat |
FMT_DOUBLE_2_DIGITS_AFTER_DOT |
protected InjectionInfo |
injectionInfo
If a file contains injection information, it should be put here, otherwise this field might be null.
|
protected Instrument |
instrument
Should be a reference to one of the instruments listed in the ScanCollection
|
protected Boolean |
isCentroided
Data might come already centroided out of the instrument or post-processing algorithms
|
protected Integer |
msLevel |
protected int |
num
Serial number of this scan in an LC/MS run
|
protected Polarity |
polarity |
protected PrecursorInfo |
precursor
If this is an MS1 scan, this field is left null, indicating there was no precursor
|
protected Double |
rt
Retention time in minutes
|
protected Double |
scanMzWindowLower
Note that this number might not correspond to the lowest actual m/z in the spectrumRef.
|
protected Double |
scanMzWindowUpper
Note that this number might not correspond to the highest actual m/z in the spectrumRef.
|
protected IScanCollection |
scans
If this scan was added to a scan collection, this field should reference it
|
protected ScanType |
scanType
Type of scan (Full, Zoom, SIM, etc.).
|
protected StorageStrategy |
storageStrategy |
protected Double |
tic
Total ion current
|
| Modifier | Constructor and Description |
|---|---|
protected |
AbstractScan(int num)
Creates a scan with STRONG storage strategy.
|
| Modifier and Type | Method and Description |
|---|---|
Double |
getBasePeakIntensity() |
Double |
getBasePeakMz() |
Boolean |
getCentroided() |
List<Integer> |
getChildScans() |
InjectionInfo |
getInjectionInfo() |
Instrument |
getInstrument() |
Integer |
getMsLevel() |
int |
getNum()
Returns the internal scan number, which sometimes coincides with original scan numbers from raw mass-spec files.
|
Polarity |
getPolarity() |
PrecursorInfo |
getPrecursor() |
Double |
getRt() |
IScanCollection |
getScanCollection() |
Double |
getScanMzWindowLower() |
Double |
getScanMzWindowUpper() |
ScanType |
getScanType() |
StorageStrategy |
getStorageStrategy() |
Double |
getTic() |
Boolean |
isCentroided() |
void |
setBasePeakIntensity(Double basePeakIntensity) |
void |
setBasePeakMz(Double basePeakMz) |
void |
setCentroided(Boolean centroided) |
void |
setChildScans(List<Integer> childScans) |
void |
setInjectionInfo(InjectionInfo injectionInfo) |
void |
setInstrument(Instrument instrument) |
void |
setMsLevel(Integer msLevel) |
void |
setPolarity(Polarity polarity) |
void |
setPrecursor(PrecursorInfo precursor) |
void |
setRt(Double rt) |
void |
setScanCollection(IScanCollection scans) |
void |
setScanMzWindowLower(Double scanMzWindowLower) |
void |
setScanMzWindowUpper(Double scanMzWindowUpper) |
void |
setScanType(ScanType scanType) |
void |
setSpectrum(ISpectrum spectrum)
Method was added for backwards compatibility, consider using the full signature version
setSpectrum(umich.ms.datatypes.spectrum.ISpectrum, boolean). |
void |
setSpectrum(ISpectrum spectrum,
boolean forceOverrideMinMaxSumVals)
Set the spectrumRef for this scan.
|
protected abstract void |
setSpectrumImpl(ISpectrum spectrum)
The implementation of
IScan.setSpectrum(umich.ms.datatypes.spectrum.ISpectrum, boolean)
in this base class will set all the Scan-level variables for you according to the
spectrumRef provided, but you need to define how to store the spectrumRef itself. |
void |
setStorageStrategy(StorageStrategy storageStrategy)
Implementors of IScan interface must respect the value of reftype in constructors
and
IScan.setSpectrum(umich.ms.datatypes.spectrum.ISpectrum, boolean) implementations
in order for memory management to work. |
void |
setTic(Double tic) |
String |
toString() |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, waitfetchSpectrum, getSpectrumprotected int num
protected IScanCollection scans
protected PrecursorInfo precursor
protected InjectionInfo injectionInfo
protected Double rt
protected Integer msLevel
protected Polarity polarity
protected Instrument instrument
protected Boolean isCentroided
protected ScanType scanType
ScanType value.
Use ScanType.fromString(String) to parse a string representation, which
will give you ScanType.UNKNOWN, if the representation could not be parsed. If the value is not present in the
file, leave this field null.protected Double basePeakMz
protected Double basePeakIntensity
protected Double tic
protected Double scanMzWindowLower
protected Double scanMzWindowUpper
protected StorageStrategy storageStrategy
public static final DecimalFormat FMT_DOUBLE_2_DIGITS_AFTER_DOT
protected AbstractScan(int num)
num - public InjectionInfo getInjectionInfo()
getInjectionInfo in interface IScanpublic void setInjectionInfo(InjectionInfo injectionInfo)
setInjectionInfo in interface IScanpublic int getNum()
IScanpublic PrecursorInfo getPrecursor()
getPrecursor in interface IScanpublic void setPrecursor(PrecursorInfo precursor)
setPrecursor in interface IScanpublic ScanType getScanType()
getScanType in interface IScanpublic void setScanType(ScanType scanType)
setScanType in interface IScanpublic List<Integer> getChildScans()
getChildScans in interface IScanpublic void setChildScans(List<Integer> childScans)
setChildScans in interface IScanpublic Integer getMsLevel()
getMsLevel in interface IScanpublic void setMsLevel(Integer msLevel)
setMsLevel in interface IScanpublic Polarity getPolarity()
getPolarity in interface IScanpublic void setPolarity(Polarity polarity)
setPolarity in interface IScanpublic Instrument getInstrument()
getInstrument in interface IScanpublic void setInstrument(Instrument instrument)
setInstrument in interface IScanpublic Boolean getCentroided()
public void setCentroided(Boolean centroided)
setCentroided in interface IScanpublic Double getBasePeakMz()
getBasePeakMz in interface IScanpublic void setBasePeakMz(Double basePeakMz)
setBasePeakMz in interface IScanpublic Double getBasePeakIntensity()
getBasePeakIntensity in interface IScanpublic void setBasePeakIntensity(Double basePeakIntensity)
setBasePeakIntensity in interface IScanpublic Double getScanMzWindowLower()
getScanMzWindowLower in interface IScanpublic void setScanMzWindowLower(Double scanMzWindowLower)
setScanMzWindowLower in interface IScanpublic Double getScanMzWindowUpper()
getScanMzWindowUpper in interface IScanpublic void setScanMzWindowUpper(Double scanMzWindowUpper)
setScanMzWindowUpper in interface IScanpublic Boolean isCentroided()
isCentroided in interface IScanpublic StorageStrategy getStorageStrategy()
getStorageStrategy in interface IScanpublic IScanCollection getScanCollection()
getScanCollection in interface IScanpublic void setScanCollection(IScanCollection scans)
setScanCollection in interface IScanpublic void setStorageStrategy(StorageStrategy storageStrategy)
IScanIScan.setSpectrum(umich.ms.datatypes.spectrum.ISpectrum, boolean) implementations
in order for memory management to work.setStorageStrategy in interface IScanpublic final void setSpectrum(ISpectrum spectrum, boolean forceOverrideMinMaxSumVals)
IScansetSpectrum in interface IScanspectrum - the new spectrumRef to set. Can be null, to release the memory,
in which case forceOverrideMinMaxSumVals must be false.forceOverrideMinMaxSumVals - when true, will override any min/max/sum intensity fields previously set on this
scan by using values from the spectrumRef. Must be set to false
if spectrumRef is null.public void setSpectrum(ISpectrum spectrum)
setSpectrum(umich.ms.datatypes.spectrum.ISpectrum, boolean).spectrum - protected abstract void setSpectrumImpl(ISpectrum spectrum)
IScan.setSpectrum(umich.ms.datatypes.spectrum.ISpectrum, boolean)
in this base class will set all the Scan-level variables for you according to the
spectrumRef provided, but you need to define how to store the spectrumRef itself.spectrum - Copyright © 2017. All rights reserved.