io.github.msdk.util

Class MsSpectrumUtil

java.lang.Object

io.github.msdk.util.MsSpectrumUtil

public class MsSpectrumUtil
extends Object

MsSpectrumUtil class.

Constructor Summary

Constructors

Constructor and Description
MsSpectrumUtil()

Method Summary

Modifier and Type	Method and Description
static List<MsSpectrum>	filterMsSpectra(List<MsSpectrum> spectra, int listLimit) Method preprocesses list of spectra, limits its amount Filtering of Spectrum objects is done by retrieving top N Spectrum objects with largest intensity values
static MsSpectrum	filterMsSpectrum(MsSpectrum ms, Integer pairsLimit) Filters with only N most intense elements.
static Integer	getBasePeakIndex(double[] mzValues, float[] intensityValues, Integer size, com.google.common.collect.Range<Double> mzRange) Returns the index of the highest intensity value.
static Integer	getBasePeakIndex(float[] intensityValues, Integer size) Returns the index of the highest intensity value.
static Float	getMaxIntensity(double[] mzValues, float[] intensityValues, Integer size, com.google.common.collect.Range<Double> mzRange) Returns the highest intensity value.
static Float	getMaxIntensity(float[] intensityValues, Integer size) Returns the highest intensity value.
static com.google.common.collect.Range<Double>	getMzRange(double[] mzValues, Integer size) Returns the m/z range of given data points.
static Float	getTIC(double[] mzValues, float[] intensityValues, Integer size, com.google.common.collect.Range<Double> mzRange) Calculates the total ion current (=sum of all intensity values)
static Float	getTIC(float[] intensityValues, Integer size) Calculates the total ion current (=sum of all intensity values)
static String	msSpectrumToString(double[] mzValues, float[] intensityValues, Integer size) msSpectrumToString.
static String	msSpectrumToString(MsSpectrum spectrum) msSpectrumToString.
static void	normalizeIntensity(float[] intensityValues, Integer size, Float scale) normalizeIntensity.

Methods inherited from class java.lang.Object

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

Constructor Detail

MsSpectrumUtil

public MsSpectrumUtil()

Method Detail

getMzRange

@Nullable
public static com.google.common.collect.Range<Double> getMzRange(@Nonnull
                                                                           double[] mzValues,
                                                                           @Nonnull
                                                                           Integer size)

Returns the m/z range of given data points. Can return null if the data point list is empty.

Parameters:

mzValues - an array of double.

size - a Integer object.

Returns:

a Range object.

getTIC

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

Calculates the total ion current (=sum of all intensity values)

Parameters:

intensityValues - an array of float.

size - a Integer object.

Returns:

a Float object.

getTIC

@Nonnull
public static Float getTIC(@Nonnull
                                    double[] mzValues,
                                    @Nonnull
                                    float[] intensityValues,
                                    @Nonnull
                                    Integer size,
                                    @Nonnull
                                    com.google.common.collect.Range<Double> mzRange)

Calculates the total ion current (=sum of all intensity values)

Parameters:

intensityValues - an array of float.

size - a Integer object.

mzValues - an array of double.

mzRange - a Range object.

Returns:

a Float object.

getMaxIntensity

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

Returns the highest intensity value. Returns 0 if the list has no data points.

Parameters:

intensityValues - an array of float.

size - a Integer object.

Returns:

a Float object.

getMaxIntensity

@Nonnull
public static Float getMaxIntensity(@Nonnull
                                             double[] mzValues,
                                             @Nonnull
                                             float[] intensityValues,
                                             @Nonnull
                                             Integer size,
                                             @Nonnull
                                             com.google.common.collect.Range<Double> mzRange)

Returns the highest intensity value. Returns 0 if the list has no data points.

Parameters:

intensityValues - an array of float.

size - a Integer object.

mzValues - an array of double.

mzRange - a Range object.

Returns:

a Float object.

getBasePeakIndex

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

Returns the index of the highest intensity value. Returns null if the list has no data points.

Parameters:

intensityValues - an array of float.

size - a Integer object.

Returns:

a Integer object.

getBasePeakIndex

@Nullable
public static Integer getBasePeakIndex(@Nonnull
                                                 double[] mzValues,
                                                 @Nonnull
                                                 float[] intensityValues,
                                                 @Nonnull
                                                 Integer size,
                                                 @Nonnull
                                                 com.google.common.collect.Range<Double> mzRange)

Returns the index of the highest intensity value. Returns null if the list has no data points or if no data point was found within the mz range.

Parameters:

mzRange - a Range object.

mzValues - an array of double.

intensityValues - an array of float.

size - a Integer object.

Returns:

a Integer object.

normalizeIntensity

public static void normalizeIntensity(@Nonnull
                                      float[] intensityValues,
                                      @Nonnull
                                      Integer size,
                                      @Nonnull
                                      Float scale)

normalizeIntensity.

Parameters:

intensityValues - an array of float.

size - a Integer object.

scale - a Float object.

msSpectrumToString

@Nonnull
public static String msSpectrumToString(MsSpectrum spectrum)

msSpectrumToString.

Parameters:

spectrum - a MsSpectrum object.

Returns:

a String object.

msSpectrumToString

@Nonnull
public static String msSpectrumToString(@Nonnull
                                                 double[] mzValues,
                                                 @Nonnull
                                                 float[] intensityValues,
                                                 @Nonnull
                                                 Integer size)

msSpectrumToString.

Parameters:

mzValues - an array of double.

intensityValues - an array of float.

size - a Integer object.

Returns:

a String object.

filterMsSpectrum

@Nonnull
public static MsSpectrum filterMsSpectrum(@Nonnull
                                                   MsSpectrum ms,
                                                   @Nonnull
                                                   Integer pairsLimit)

Filters with only N most intense elements.

Parameters:

spectrum - - ms spectrum

pairsLimit - - maximum amount of items in a new Spectrum

Returns:

filterMsSpectra

public static List<MsSpectrum> filterMsSpectra(List<MsSpectrum> spectra,
                                               int listLimit)

Method preprocesses list of spectra, limits its amount Filtering of Spectrum objects is done by retrieving top N Spectrum objects with largest intensity values

Parameters:

spectra - - list of spectrum to be preprocessed

listLimit - - maximum amount of items to be in a new list

Returns:

filtered lists