io.github.msdk.io.netcdf

Class NetCDFMsScan

java.lang.Object

io.github.msdk.datamodel.AbstractMsSpectrum

io.github.msdk.datamodel.SimpleMsScan

io.github.msdk.io.netcdf.NetCDFMsScan

All Implemented Interfaces:

MsScan, MsSpectrum

public class NetCDFMsScan
extends SimpleMsScan

NetCDFMsScan class.

Constructor Summary

Constructors

Constructor and Description
NetCDFMsScan(Integer scanNumber, int[] scanStartPositions, float[] scanRetentionTimes, ucar.nc2.Variable massValueVariable, ucar.nc2.Variable intensityValueVariable, double massValueScaleFactor, double intensityValueScaleFactor) Constructor for NetCDFMsScan

Method Summary

Modifier and Type	Method and Description
float[]	getIntensityValues(float[] intensityValues) Returns the intensity values of this spectrum.
double[]	getMzValues(double[] mzValues) Returns the m/z values of this spectrum.
Integer	getNumberOfDataPoints() getNumberOfDataPoints.
Float	getRetentionTime() Returns the retention time in seconds
Integer	getScanIndex() The Scan Index is the inde of the scan in the array
MsSpectrumType	getSpectrumType() Returns the type of this mass spectrum.
void	parseScan() The mass and intensity arrays are loaded once this method is called

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

getIsolations, getMsFunction, getMsLevel, getMsScanType, getMzTolerance, getPolarity, getRawDataFile, getScanDefinition, getScanningRange, getScanNumber, getSourceInducedFragmentation, setMsFunction, setMsLevel, setMsScanType, setMzTolerance, setPolarity, setRawDataFile, setRetentionTime, setScanDefinition, setScanningRange, setScanNumber, setSourceInducedFragmentation

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

getMzRange, 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, getMzRange, getMzValues, getTIC

Constructor Detail

NetCDFMsScan

public NetCDFMsScan(Integer scanNumber,
                    int[] scanStartPositions,
                    float[] scanRetentionTimes,
                    ucar.nc2.Variable massValueVariable,
                    ucar.nc2.Variable intensityValueVariable,
                    double massValueScaleFactor,
                    double intensityValueScaleFactor)

Constructor for NetCDFMsScan

Parameters:

scanNumber - the Scan Number

id - the Scan ID

scanStartPositions - an int[] containing start positions of all scans, and an extra element containing the stop position of the last scan

scanRetentionTimes - a float[] containing retention times of all scans

massValueVariable - Variable containing the m/z data of the scans

intensityValueVariable - Variable containing the intensity data of the scans

massValueScaleFactor - double value by which the mass values have been scaled by to

intensityValueScaleFactor - double value by which the intensity values have been scaled by to

Method Detail

getIntensityValues

public float[] getIntensityValues(float[] intensityValues)

Returns the intensity values of this spectrum. Note: this method may need to read data from disk, therefore it may be quite slow.

Specified by:

getIntensityValues in interface MsSpectrum

Overrides:

getIntensityValues in class AbstractMsSpectrum

Returns:

an array of float.

getMzValues

public double[] getMzValues(double[] mzValues)

Returns the m/z values of this spectrum. Note: this method may need to read data from disk, therefore it may be quite slow.

Specified by:

getMzValues in interface MsSpectrum

Overrides:

getMzValues in class AbstractMsSpectrum

Returns:

an array of double.

getNumberOfDataPoints

public Integer getNumberOfDataPoints()

getNumberOfDataPoints.

Specified by:

getNumberOfDataPoints in interface MsSpectrum

Overrides:

getNumberOfDataPoints in class AbstractMsSpectrum

Returns:

a Integer object.

getRetentionTime

public Float getRetentionTime()

Returns the retention time in seconds

Specified by:

getRetentionTime in interface MsScan

Overrides:

getRetentionTime in class SimpleMsScan

Returns:

RT

getSpectrumType

public MsSpectrumType getSpectrumType()

Returns the type of this mass spectrum. For spectra that are loaded from raw data files, the type is detected automatically. For calculated spectra, the type depends on the method of calculation.

Specified by:

getSpectrumType in interface MsSpectrum

Overrides:

getSpectrumType in class AbstractMsSpectrum

Returns:

spectrum type (profile, centroided, thresholded)

getScanIndex

public Integer getScanIndex()

The Scan Index is the inde of the scan in the array

Returns:

the scan index of the scan

parseScan

public void parseScan()
               throws IOException,
                      ucar.ma2.InvalidRangeException

The mass and intensity arrays are loaded once this method is called

Throws:

IOException

ucar.ma2.InvalidRangeException