io.github.msdk.util

Class ChromatogramUtil

java.lang.Object

io.github.msdk.util.ChromatogramUtil

public class ChromatogramUtil
extends Object

ChromatogramUtil class.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ChromatogramUtil.CalculationMethod Calculates the m/z value of the chromatogram based on the list of m/z values

Constructor Summary

Constructors

Constructor and Description
ChromatogramUtil()

Method Summary

Modifier and Type	Method and Description
static Double	calculateMz(double[] mzValues, float[] intensityValues, Integer size, ChromatogramUtil.CalculationMethod method) calculateMz.
static Float	getArea(float[] rtValues, float[] intensityValues, Integer size) Returns the area of this feature.
static Double	getAsymmetryFactor(float[] rtValues, float[] intensityValues, Integer size) Returns the asymmetry factor of this feature.
static com.google.common.collect.Range<Float>	getDataPointsChromatographyRange(float[] rtValues, Integer size) Returns the range of Float of all data points in this feature.
static com.google.common.collect.Range<Float>	getDataPointsIntensityRange(Float[] intensityValues, Integer size) Returns the range of intensity values of all data points in this chromatogram.
static Float	getDuration(float[] rtValues, Integer size) Returns the duration of this feature.
static Double	getFwhm(float[] rtValues, float[] intensityValues, Integer size) Returns the full width at half maximum (FWHM) of this feature.
static Float	getMaxHeight(float[] intensityValues, Integer size) Returns the maximum height of this chromatogram, or null if size == 0.
static Double	getMedianMz(double[] mzValues, Integer size) Returns median m/z value of the chromatogram
static Float	getRt(float[] rtValues, float[] intensityValues, Integer size) Returns the retention time of this feature.
static Float	getRtEnd(float[] rtValues, Integer size) Returns the end retention time of this feature.
static com.google.common.collect.Range<Float>	getRtRange(float[] rtValues, Integer size) Returns the RT range
static Float	getRtStart(float[] rtValues, Integer size) Returns the start retention time of this feature.
static Double	getTailingFactor(float[] rtValues, float[] intensityValues, Integer size) Returns the tailing factor of this feature.

Methods inherited from class java.lang.Object

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

Constructor Detail

ChromatogramUtil

public ChromatogramUtil()

Method Detail

getMedianMz

@Nullable
public static Double getMedianMz(@Nonnull
                                           double[] mzValues,
                                           @Nonnull
                                           Integer size)

Returns median m/z value of the chromatogram

Parameters:

mzValues - an array of double.

size - a Integer object.

Returns:

a Double object.

getRtRange

@Nullable
public static com.google.common.collect.Range<Float> getRtRange(@Nonnull
                                                                          float[] rtValues,
                                                                          @Nonnull
                                                                          Integer size)

Returns the RT range

Parameters:

rtValues - an array of float.

size - a Integer object.

Returns:

a Range object.

getDataPointsChromatographyRange

@Nonnull
public static com.google.common.collect.Range<Float> getDataPointsChromatographyRange(@Nonnull
                                                                                               float[] rtValues,
                                                                                               @Nonnull
                                                                                               Integer size)

Returns the range of Float of all data points in this feature.

Parameters:

rtValues - an array of

size - a

Returns:

a

getDataPointsIntensityRange

@Nullable
public static com.google.common.collect.Range<Float> getDataPointsIntensityRange(@Nonnull
                                                                                           Float[] intensityValues,
                                                                                           @Nonnull
                                                                                           Integer size)

Returns the range of intensity values of all data points in this chromatogram.

Parameters:

intensityValues - an array of

size - a

Returns:

a

calculateMz

@Nullable
public static Double calculateMz(@Nonnull
                                           double[] mzValues,
                                           @Nonnull
                                           float[] intensityValues,
                                           @Nonnull
                                           Integer size,
                                           @Nonnull
                                           ChromatogramUtil.CalculationMethod method)

calculateMz.

Parameters:

intensityValues - an array of float.

mzValues - an array of double.

method - a

size - a

Returns:

a

getRt

@Nullable
public static Float getRt(@Nonnull
                                    float[] rtValues,
                                    @Nonnull
                                    float[] intensityValues,
                                    @Nonnull
                                    Integer size)

Returns the retention time of this feature.

Parameters:

rtValues - an array of

intensityValues - an array of float.

size - a

Returns:

a float.

getRtStart

@Nullable
public static Float getRtStart(@Nonnull
                                         float[] rtValues,
                                         @Nonnull
                                         Integer size)

Returns the start retention time of this feature.

Parameters:

rtValues - an array of

size - a

Returns:

a Float.

getRtEnd

public static Float getRtEnd(@Nonnull
                             float[] rtValues,
                             @Nonnull
                             Integer size)

Returns the end retention time of this feature.

Parameters:

rtValues - an array of

size - a

Returns:

a Float.

getDuration

@Nullable
public static Float getDuration(@Nonnull
                                          float[] rtValues,
                                          @Nonnull
                                          Integer size)

Returns the duration of this feature.

Parameters:

rtValues - an array of

size - a

Returns:

a float.

getMaxHeight

@Nullable
public static Float getMaxHeight(@Nonnull
                                           float[] intensityValues,
                                           @Nonnull
                                           Integer size)

Returns the maximum height of this chromatogram, or null if size == 0.

Parameters:

intensityValues - an array of float.

size - a

Returns:

a double.

getArea

@Nullable
public static Float getArea(@Nonnull
                                      float[] rtValues,
                                      @Nonnull
                                      float[] intensityValues,
                                      @Nonnull
                                      Integer size)

Returns the area of this feature.

Parameters:

rtValues - an array of

intensityValues - an array of float.

size - a

Returns:

a double.

getFwhm

@Nullable
public static Double getFwhm(@Nonnull
                                       float[] rtValues,
                                       @Nonnull
                                       float[] intensityValues,
                                       @Nonnull
                                       Integer size)

Returns the full width at half maximum (FWHM) of this feature.

Parameters:

rtValues - rt values

intensityValues - an array of float.

size - a

Returns:

a

getTailingFactor

@Nullable
public static Double getTailingFactor(@Nonnull
                                                float[] rtValues,
                                                @Nonnull
                                                float[] intensityValues,
                                                @Nonnull
                                                Integer size)

Returns the tailing factor of this feature.

Parameters:

rtValues - an array of

intensityValues - an array of float.

size - a

Returns:

a

getAsymmetryFactor

@Nullable
public static Double getAsymmetryFactor(@Nonnull
                                                  float[] rtValues,
                                                  @Nonnull
                                                  float[] intensityValues,
                                                  @Nonnull
                                                  Integer size)

Returns the asymmetry factor of this feature.

Parameters:

rtValues - an array

intensityValues - an array of float.

size - a

Returns:

a