public interface IScan extends Serializable
| Modifier and Type | Method and Description |
|---|---|
ISpectrum |
fetchSpectrum()
Get the spectrum, possibly preloading it from disk.
|
Double |
getBasePeakIntensity() |
Double |
getBasePeakMz() |
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() |
ISpectrum |
getSpectrum()
Get the spectrum, not trying to loead it from disk, if it wasn't parsed.
|
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,
boolean forceOverrideMinMaxSumVals)
Set the spectrumRef for this scan.
|
void |
setStorageStrategy(StorageStrategy strategy)
Implementors of IScan interface must respect the value of reftype in constructors
and
setSpectrum(umich.ms.datatypes.spectrum.ISpectrum, boolean) implementations
in order for memory management to work. |
void |
setTic(Double tic) |
int getNum()
IScanCollection getScanCollection()
Double getRt()
Integer getMsLevel()
Boolean isCentroided()
Polarity getPolarity()
ScanType getScanType()
PrecursorInfo getPrecursor()
Instrument getInstrument()
InjectionInfo getInjectionInfo()
Double getBasePeakIntensity()
Double getBasePeakMz()
Double getTic()
Double getScanMzWindowLower()
Double getScanMzWindowUpper()
ISpectrum getSpectrum()
IScanCollection.isAutoloadSpectra()ISpectrum fetchSpectrum() throws FileParsingException
IScanCollection.addScan(IScan) and the scan collection was set to
auto-load spectra (IScanCollection.isAutoloadSpectra(boolean))FileParsingExceptionStorageStrategy getStorageStrategy()
void setRt(Double rt)
void setScanCollection(IScanCollection scans)
void setMsLevel(Integer msLevel)
void setCentroided(Boolean centroided)
void setScanType(ScanType scanType)
void setPolarity(Polarity polarity)
void setPrecursor(PrecursorInfo precursor)
void setInstrument(Instrument instrument)
void setInjectionInfo(InjectionInfo injectionInfo)
void setBasePeakIntensity(Double basePeakIntensity)
void setBasePeakMz(Double basePeakMz)
void setTic(Double tic)
void setScanMzWindowLower(Double scanMzWindowLower)
void setScanMzWindowUpper(Double scanMzWindowUpper)
void setSpectrum(ISpectrum spectrum, boolean forceOverrideMinMaxSumVals)
spectrum - 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.void setStorageStrategy(StorageStrategy strategy)
setSpectrum(umich.ms.datatypes.spectrum.ISpectrum, boolean) implementations
in order for memory management to work.strategy - Copyright © 2017. All rights reserved.