io.github.msdk.featuredetection.adap3d.algorithms

Class FeatureTools

java.lang.Object

io.github.msdk.featuredetection.adap3d.algorithms.FeatureTools

public class FeatureTools
extends Object

FeatureTools class.

Author:

owen myers Modified by Dharak Shah to include in MSDK

Constructor Summary

Constructors

Constructor and Description
FeatureTools()

Method Summary

Modifier and Type	Method and Description
static double	findMeanOfSignal(double[] intensities, int peakLeft, int peakRight) findMeanOfSignal.
static double	findMinIntensityOfSignal(double[] intensities, int peakLeft, int peakRight) findMinIntensityOfSignal.
static int	fixLeftBoundry(double[] intensities, int peakLeft) fixLeftBoundry.
static int	fixRightBoundry(double[] intensities, int peakRight) fixRightBoundry.
static boolean	isShared(double[] rt, double[] intensities, int peakLeft, int peakRight, double edgeToHeightRatio, double deltaToHeightRatio) isShared.
static boolean	isShared(List<Double> intensities, double edgeToHeightThreshold, double deltaToHeightThreshold) Return true if 1) there are more then one local maximum 2) at least one of left-to-apex, right-to-apex, or delta-to-apex ratios is higher then the corresponding threshold
static double	sharpnessAngleAvgAngles(double[] rt, double[] intensities, int peakLeft, int peakRight) sharpnessAngleAvgAngles.
static double	sharpnessAngleAvgSlopes(double[] rt, double[] intensities, int peakLeft, int peakRight) sharpnessAngleAvgSlopes.This returns the angle calculated between the two "means" of the slopes on each side of the peak
static double	sharpnessYang(double[] rt, double[] intensities, int peakLeft, int peakRight) sharpnessYang.
static double	sharpnessYang(NavigableMap<Double,Double> chromatogram) sharpnessYang.
static double	trapazoidAreaUnderCurve(double[] intensities, double[] retentionTimes, int peakLeft, int peakRight) trapazoidAreaUnderCurve.

Methods inherited from class java.lang.Object

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

Constructor Detail

FeatureTools

public FeatureTools()

Method Detail

fixRightBoundry

public static int fixRightBoundry(double[] intensities,
                                  int peakRight)

fixRightBoundry.

Parameters:

intensities - an array of double.

peakRight - a int.

Returns:

a int.

fixLeftBoundry

public static int fixLeftBoundry(double[] intensities,
                                 int peakLeft)

fixLeftBoundry.

Parameters:

intensities - an array of double.

peakLeft - a int.

Returns:

a int.

isShared

public static boolean isShared(double[] rt,
                               double[] intensities,
                               int peakLeft,
                               int peakRight,
                               double edgeToHeightRatio,
                               double deltaToHeightRatio)

isShared.

Parameters:

rt - an array of double.

intensities - an array of double.

peakLeft - a int.

peakRight - a int.

edgeToHeightRatio - a double.

deltaToHeightRatio - a double.

Returns:

a boolean.

isShared

public static boolean isShared(List<Double> intensities,
                               double edgeToHeightThreshold,
                               double deltaToHeightThreshold)

Return true if 1) there are more then one local maximum 2) at least one of left-to-apex, right-to-apex, or delta-to-apex ratios is higher then the corresponding threshold

Parameters:

intensities - list of peak intensities

edgeToHeightThreshold - threshold for left-to-apex and right-to-apex ratios

deltaToHeightThreshold - threshold for delta-to-apex ratio

Returns:

true one of the conditions 1) or 2) is satisfied, false otherwise

sharpnessAngleAvgSlopes

public static double sharpnessAngleAvgSlopes(double[] rt,
                                             double[] intensities,
                                             int peakLeft,
                                             int peakRight)

sharpnessAngleAvgSlopes.This returns the angle calculated between the two "means" of the slopes on each side of the peak

Parameters:

rt - an array of double.

intensities - an array of double.

peakLeft - a int.

peakRight - a int.

Returns:

a double.

sharpnessYang

public static double sharpnessYang(NavigableMap<Double,Double> chromatogram)

sharpnessYang.

Parameters:

chromatogram - a NavigableMap object.

Returns:

a double.

sharpnessYang

public static double sharpnessYang(double[] rt,
                                   double[] intensities,
                                   int peakLeft,
                                   int peakRight)

sharpnessYang.

Parameters:

rt - an array of double.

intensities - an array of double.

peakLeft - a int.

peakRight - a int.

Returns:

a double.

sharpnessAngleAvgAngles

public static double sharpnessAngleAvgAngles(double[] rt,
                                             double[] intensities,
                                             int peakLeft,
                                             int peakRight)

sharpnessAngleAvgAngles. This returns the angle calculated between the two "means" of the slopes on each side of the peak.

Parameters:

rt - an array of double.

intensities - an array of double.

peakLeft - a int.

peakRight - a int.

Returns:

a double.

findMeanOfSignal

public static double findMeanOfSignal(double[] intensities,
                                      int peakLeft,
                                      int peakRight)

findMeanOfSignal.

Parameters:

intensities - an array of double.

peakLeft - a int.

peakRight - a int.

Returns:

a double.

findMinIntensityOfSignal

public static double findMinIntensityOfSignal(double[] intensities,
                                              int peakLeft,
                                              int peakRight)

findMinIntensityOfSignal.

Parameters:

intensities - an array of double.

peakLeft - a int.

peakRight - a int.

Returns:

a double.

trapazoidAreaUnderCurve

public static double trapazoidAreaUnderCurve(double[] intensities,
                                             double[] retentionTimes,
                                             int peakLeft,
                                             int peakRight)

trapazoidAreaUnderCurve.

Parameters:

intensities - an array of double.

retentionTimes - an array of double.

peakLeft - a int.

peakRight - a int.

Returns:

a double.