io.github.msdk.datamodel

Class SimpleMsScan

java.lang.Object

io.github.msdk.datamodel.AbstractMsSpectrum

io.github.msdk.datamodel.SimpleMsScan

All Implemented Interfaces:

MsScan, MsSpectrum

Direct Known Subclasses:

NetCDFMsScan

public class SimpleMsScan
extends AbstractMsSpectrum
implements MsScan

Simple implementation of the Scan interface.

Constructor Summary

Constructors

Constructor and Description
SimpleMsScan(Integer scanNumber) Constructor for SimpleMsScan.
SimpleMsScan(Integer scanNumber, String msFunction) Constructor for SimpleMsScan.

Method Summary

Modifier and Type	Method and Description
List<IsolationInfo>	getIsolations() Returns a list of isolations performed for this scan.
String	getMsFunction() Returns the MS function of this scan, e.g.
Integer	getMsLevel() Returns MS level (1 = default, 2 = MS/MS, 3 = MS3 etc.).
MsScanType	getMsScanType() Returns the type of the MS scan.
MzTolerance	getMzTolerance() Returns an object that implements the MzTolerance interface.
PolarityType	getPolarity() Returns the polarity of this scan.
RawDataFile	getRawDataFile() Returns the raw data file that contains this scan.
Float	getRetentionTime() Returns the retention time in seconds
String	getScanDefinition() Returns the instrument-specific textual definition of the scan parameters.
com.google.common.collect.Range<Double>	getScanningRange() Returns the scanning range of the instrument.
Integer	getScanNumber() Returns the number of this scan, represented by an integer, typically positive.
ActivationInfo	getSourceInducedFragmentation() Returns the fragmentation parameters of ion source-induced fragmentation, or null if no such information is known.
void	setMsFunction(String newFunction)
void	setMsLevel(Integer msLevel)
void	setMsScanType(MsScanType newMsScanType)
void	setMzTolerance(MzTolerance mzTolerance) Setter for the field mzTolerance.
void	setPolarity(PolarityType newPolarity)
void	setRawDataFile(RawDataFile newRawDataFile)
void	setRetentionTime(Float rt)
void	setScanDefinition(String scanDefinition)
void	setScanningRange(com.google.common.collect.Range<Double> newScanRange)
void	setScanNumber(Integer scanNumber)
void	setSourceInducedFragmentation(ActivationInfo newFragmentationInfo)

Methods inherited from class io.github.msdk.datamodel.AbstractMsSpectrum

getIntensityValues, getMzRange, getMzValues, getNumberOfDataPoints, getSpectrumType, getTIC, setDataPoints, setSpectrumType

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface io.github.msdk.datamodel.MsSpectrum

getIntensityValues, getIntensityValues, getMzRange, getMzValues, getMzValues, getNumberOfDataPoints, getSpectrumType, getTIC

Constructor Detail

SimpleMsScan

public SimpleMsScan(@Nonnull
                    Integer scanNumber)

Constructor for SimpleMsScan.

Parameters:

scanNumber - a Integer object.

SimpleMsScan

public SimpleMsScan(@Nonnull
                    Integer scanNumber,
                    String msFunction)

Constructor for SimpleMsScan.

Parameters:

scanNumber - a Integer object.

msFunction - a io.github.msdk.datamodel.rawdata.MsFunction object.

Method Detail

getRawDataFile

@Nullable
public RawDataFile getRawDataFile()

Returns the raw data file that contains this scan. This might return null when the scan is created, but once the scan is added to the raw data file by calling RawDataFile.addScan(), the RawDataFile automatically calls the MsScan.setRawDataFile() method to update this reference.

Specified by:

getRawDataFile in interface MsScan

Returns:

RawDataFile containing this MsScan, or null.

See Also:

RawDataFile

setRawDataFile

public void setRawDataFile(@Nonnull
                           RawDataFile newRawDataFile)

Parameters:

newRawDataFile - a RawDataFile object.

getScanNumber

@Nonnull
public Integer getScanNumber()

Returns the number of this scan, represented by an integer, typically positive. Typically, the scan number will be unique within the file. However, the data model does not guarantee that, and in some cases multiple scans with the same number may be present in the file.

Specified by:

getScanNumber in interface MsScan

Returns:

Scan number

setScanNumber

public void setScanNumber(@Nonnull
                          Integer scanNumber)

Parameters:

scanNumber - a Integer object.

getScanDefinition

@Nullable
public String getScanDefinition()

Returns the instrument-specific textual definition of the scan parameters. For example, in Thermo raw data this may look like: FTMS + p ESI Full ms2 209.09@hcd35.00 [50.00-230.00] The scan definition can be null if not specified in the raw data.

Specified by:

getScanDefinition in interface MsScan

Returns:

Scan definition

setScanDefinition

public void setScanDefinition(@Nullable
                              String scanDefinition)

Parameters:

scanDefinition - a String object.

getMsFunction

@Nullable
public String getMsFunction()

Returns the MS function of this scan, e.g. "Full ms", or "SRM".

Specified by:

getMsFunction in interface MsScan

Returns:

MS function.

setMsFunction

public void setMsFunction(@Nullable
                          String newFunction)

Parameters:

newFunction - a io.github.msdk.datamodel.rawdata.MsFunction object.

getMsLevel

@Nullable
public Integer getMsLevel()

Returns MS level (1 = default, 2 = MS/MS, 3 = MS3 etc.).

Specified by:

getMsLevel in interface MsScan

Returns:

MS level

setMsLevel

public void setMsLevel(@Nonnull
                       Integer msLevel)

Parameters:

msLevel - a Integer object.

getScanningRange

@Nullable
public com.google.common.collect.Range<Double> getScanningRange()

Returns the scanning range of the instrument. Note that this value is different from that returned by getMzRange() from the MassSpectrum interface. getMzRange() returns the range of the actual data points (lowest and highest m/z) getScanningRange() returns the instrument scanning range that was configured in the experiment setup.

Specified by:

getScanningRange in interface MsScan

Returns:

The scanning m/z range of the instrument

setScanningRange

public void setScanningRange(@Nullable
                             com.google.common.collect.Range<Double> newScanRange)

Parameters:

newScanRange - a Range object.

getPolarity

@Nonnull
public PolarityType getPolarity()

Returns the polarity of this scan. If unknown, PolarityType.UNKNOWN is returned.

Specified by:

getPolarity in interface MsScan

Returns:

Polarity of this scan.

setPolarity

public void setPolarity(@Nonnull
                        PolarityType newPolarity)

Parameters:

newPolarity - a PolarityType object.

getMsScanType

@Nonnull
public MsScanType getMsScanType()

Returns the type of the MS scan. If unknown, MsScanType.UNKNOWN is returned.

Specified by:

getMsScanType in interface MsScan

Returns:

MS scan type

setMsScanType

public void setMsScanType(@Nonnull
                          MsScanType newMsScanType)

Parameters:

newMsScanType - a MsScanType object.

getMzTolerance

public MzTolerance getMzTolerance()

Returns an object that implements the MzTolerance interface. If not MzTolernace is available, then null is returned.

Specified by:

getMzTolerance in interface MsSpectrum

Overrides:

getMzTolerance in class AbstractMsSpectrum

Returns:

m/z tolerance for the scan

setMzTolerance

public void setMzTolerance(MzTolerance mzTolerance)

Setter for the field mzTolerance.

Setter for the field mzTolerance.

Overrides:

setMzTolerance in class AbstractMsSpectrum

Parameters:

mzTolerance - a MzTolerance object.

getRetentionTime

@Nullable
public Float getRetentionTime()

Returns the retention time in seconds

Specified by:

getRetentionTime in interface MsScan

Returns:

RT

setRetentionTime

public void setRetentionTime(@Nullable
                             Float rt)

Parameters:

rt - a Float object.

getSourceInducedFragmentation

@Nullable
public ActivationInfo getSourceInducedFragmentation()

Returns the fragmentation parameters of ion source-induced fragmentation, or null if no such information is known.

Specified by:

getSourceInducedFragmentation in interface MsScan

Returns:

Fragmentation info of ion source-induced fragmentation, or null.

setSourceInducedFragmentation

public void setSourceInducedFragmentation(@Nullable
                                          ActivationInfo newFragmentationInfo)

Parameters:

newFragmentationInfo - a ActivationInfo object.

getIsolations

@Nonnull
public List<IsolationInfo> getIsolations()

Returns a list of isolations performed for this scan. These isolations may also include fragmentations (tandem MS).

Specified by:

getIsolations in interface MsScan

Returns:

A mutable list of isolations. New isolation items can be added to this list.