umich.ms.datatypes.scan

Interface IScan

All Superinterfaces:

Serializable

All Known Implementing Classes:

AbstractScan, ScanDefault

public interface IScan
extends Serializable

If you are ever writing a wrapper for 3rd party Scan implementations you must implement this interface Author: Dmitry Avtonomov (dmitriya) Email: dmitriy.avtonomov@gmail.com

Method Summary

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)

Method Detail

getNum

int getNum()

Returns the internal scan number, which sometimes coincides with original scan numbers from raw mass-spec files. If you want to get the number from the original raw file though, you should consult the run index.

Returns:

internal scan number, starting from 1.

getScanCollection

IScanCollection getScanCollection()

setScanCollection

void setScanCollection(IScanCollection scans)

getRt

Double getRt()

setRt

void setRt(Double rt)

getMsLevel

Integer getMsLevel()

setMsLevel

void setMsLevel(Integer msLevel)

isCentroided

Boolean isCentroided()

getPolarity

Polarity getPolarity()

setPolarity

void setPolarity(Polarity polarity)

getScanType

ScanType getScanType()

setScanType

void setScanType(ScanType scanType)

getPrecursor

PrecursorInfo getPrecursor()

setPrecursor

void setPrecursor(PrecursorInfo precursor)

getChildScans

List<Integer> getChildScans()

setChildScans

void setChildScans(List<Integer> childScans)

getInstrument

Instrument getInstrument()

setInstrument

void setInstrument(Instrument instrument)

getInjectionInfo

InjectionInfo getInjectionInfo()

setInjectionInfo

void setInjectionInfo(InjectionInfo injectionInfo)

getBasePeakIntensity

Double getBasePeakIntensity()

setBasePeakIntensity

void setBasePeakIntensity(Double basePeakIntensity)

getBasePeakMz

Double getBasePeakMz()

setBasePeakMz

void setBasePeakMz(Double basePeakMz)

getTic

Double getTic()

setTic

void setTic(Double tic)

getScanMzWindowLower

Double getScanMzWindowLower()

setScanMzWindowLower

void setScanMzWindowLower(Double scanMzWindowLower)

getScanMzWindowUpper

Double getScanMzWindowUpper()

setScanMzWindowUpper

void setScanMzWindowUpper(Double scanMzWindowUpper)

getSpectrum

ISpectrum getSpectrum()

Get the spectrum, not trying to loead it from disk, if it wasn't parsed.

Returns:

if a ScanCollection wasn't set, and the spectrum wasn't explicitly set for this scan, then the spectrum returned might be null. If a scan collection was set, and the scan collection was set to IScanCollection.isAutoloadSpectra()

fetchSpectrum

ISpectrum fetchSpectrum()
                 throws FileParsingException

Get the spectrum, possibly preloading it from disk. Must only work if this Scan has been added to a ScanCollection via IScanCollection.addScan(IScan) and the scan collection was set to auto-load spectra (IScanCollection.isAutoloadSpectra(boolean))

Returns:

if a spectrum is available, will return it. null, if this scan is not a part of a scan collection, or if the scan collection was set to not auto-load spectra. Otherwise will try to parse from disk.

Throws:

FileParsingException

getStorageStrategy

StorageStrategy getStorageStrategy()

setStorageStrategy

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.

setCentroided

void setCentroided(Boolean centroided)

setSpectrum

void setSpectrum(ISpectrum spectrum,
                 boolean forceOverrideMinMaxSumVals)

Set the spectrumRef for this scan. In case the scan collection is cache-enabled, might put the spectrumRef into a SoftReference.

Parameters:

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.