A C E F G H I L N O P S T U V
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A

argWlenAsExpected(Integer) - Static method in class com.fa993.utils.PeakProminences

Validates and ensures the input window length (`wlen`) is of type `int` and greater than 1.

C

call(double[]) - Method in class com.fa993.FindPeaks

Finds peaks in a 1D signal.

call(double[], int[], double, double[], int[], int[]) - Static method in class com.fa993.utils.PeakWidth

Calculates the widths of peaks in the input data array using prominence information and a specified relative height.

call(double[], int[], int) - Static method in class com.fa993.utils.PeakProminences

Calculates the prominence of each peak in a signal.

call(double[], int[], Either.OfTwo<Double, double[]>, Either.OfTwo<Double, double[]>) - Static method in class com.fa993.utils.SelectByPeakThreshold

Evaluates which peaks in the input array fulfill the threshold condition.

call(double[], Either.OfTwo<Double, double[]>, Either.OfTwo<Double, double[]>) - Static method in class com.fa993.utils.SelectByProperty

Evaluates which peaks conform to a specified interval based on their properties.

call(double[], NumOrTwoSeqOrNdArr, NumOrTwoSeqOrNdArr, Double, NumOrTwoSeqOrNdArr, NumOrTwoSeqOrNdArr, Integer, Double, NumOrTwoSeqOrNdArr) - Method in class com.fa993.FindPeaks

Finds peaks in a 1D signal with various optional conditions and properties.

call(int[], double[], double) - Static method in class com.fa993.utils.SelectByPeakDistance

Evaluates which peaks fulfill the minimum distance condition based on their priorities.

call(int[], Either.OfTwo<Double, double[]>, Either.OfTwo<Double, double[]>) - Static method in class com.fa993.utils.SelectByProperty

Evaluates which peaks conform to a specified interval based on their properties.

call(NumOrTwoSeqOrNdArr, double[], int[]) - Static method in class com.fa993.utils.UnpackConditionArgs

Unpacks the interval arguments into a pair of lower and upper boundaries, applying the interval conditions to a subset of data defined by the peaks.

com.fa993 - package com.fa993

com.fa993.types - package com.fa993.types

com.fa993.types.supertype - package com.fa993.types.supertype

com.fa993.utils - package com.fa993.utils

com.fa993.variations - package com.fa993.variations

E

Either - Class in com.fa993.types.supertype

A utility class representing an exclusive choice between two or three possible types.

Either.OfThree<A,B,C> - Class in com.fa993.types.supertype

Represents an exclusive choice between three possible types.

Either.OfTwo<A,B> - Class in com.fa993.types.supertype

Represents an exclusive choice between two possible types.

Either.Selector - Enum in com.fa993.types.supertype

Enum representing the possible choices: First, Second, or Third.

equals(Object) - Method in class com.fa993.types.FindPeaksOutput

Compares this object to another object for equality.

equals(Object) - Method in class com.fa993.types.LocalMaximaOutput

Compares this object to another object for equality.

equals(Object) - Method in class com.fa993.types.PeakProminenceOutput

Compares this object to another object for equality.

equals(Object) - Method in class com.fa993.types.PeakWidthsOutput

Compares this object to another object for equality.

F

Filter - Class in com.fa993.utils

Utility class for filtering arrays and properties based on a boolean mask.

Filter() - Constructor for class com.fa993.utils.Filter

filterArray(double[], boolean[]) - Static method in class com.fa993.utils.Filter

Filters a double array based on a boolean mask.

filterArray(int[], boolean[]) - Static method in class com.fa993.utils.Filter

Filters an integer array based on a boolean mask.

filterProperties(Map<String, Object>, boolean[]) - Static method in class com.fa993.utils.Filter

Filters properties in a map based on a boolean mask.

FindPeaks - Class in com.fa993

A utility class for finding peaks in a 1D signal.

FindPeaks() - Constructor for class com.fa993.FindPeaks

Default constructor.

FindPeaks(LocalMaxima) - Constructor for class com.fa993.FindPeaks

Constructor that allows specifying a custom LocalMaxima implementation.

FindPeaksOutput - Class in com.fa993.types

Represents the output of a peak-finding operation.

FindPeaksOutput(int[], Map<String, Object>) - Constructor for class com.fa993.types.FindPeaksOutput

Constructs a new FindPeaksOutput object with the specified midpoints and properties.

first(A) - Static method in class com.fa993.types.supertype.Either.OfThree

Creates an OfThree instance with the first value selected.

first(A) - Static method in class com.fa993.types.supertype.Either.OfTwo

Creates an OfTwo instance with the first value selected.

first(Double) - Static method in class com.fa993.types.supertype.NumOrTwoSeqOrNdArr

Creates a NumOrTwoSeqOrNdArr instance with the Double value selected.

First - com.fa993.types.supertype.Either.Selector

Represents the first choice.

G

getFirst() - Method in class com.fa993.types.supertype.Either.OfThree

Gets the first value if selected.

getFirst() - Method in class com.fa993.types.supertype.Either.OfTwo

Gets the first value if selected.

getFirst() - Method in class com.fa993.types.supertype.Pair

Gets the first element of the pair.

getKeep() - Method in class com.fa993.types.SelectThresholdOutput

Gets the boolean array indicating which elements are retained.

getLeftBases() - Method in class com.fa993.types.PeakProminenceOutput

Returns the indices of the left bases of the detected peaks.

getLeftEdges() - Method in class com.fa993.types.LocalMaximaOutput

Returns the left edges of the detected local maxima.

getLeftIps() - Method in class com.fa993.types.PeakWidthsOutput

Gets the array of left intersection points (IPs) of the widths on the curve.

getLeftThresholds() - Method in class com.fa993.types.SelectThresholdOutput

Gets the array of left thresholds associated with the elements.

getMidpoints() - Method in class com.fa993.types.FindPeaksOutput

Returns the indices of the midpoints of detected peaks.

getMidpoints() - Method in class com.fa993.types.LocalMaximaOutput

Returns the midpoints of the detected local maxima.

getProminences() - Method in class com.fa993.types.PeakProminenceOutput

Returns the prominence values of the detected peaks.

getProperties() - Method in class com.fa993.types.FindPeaksOutput

Returns the additional properties associated with the peaks.

getRightBases() - Method in class com.fa993.types.PeakProminenceOutput

Returns the indices of the right bases of the detected peaks.

getRightEdges() - Method in class com.fa993.types.LocalMaximaOutput

Returns the right edges of the detected local maxima.

getRightIps() - Method in class com.fa993.types.PeakWidthsOutput

Gets the array of right intersection points (IPs) of the widths on the curve.

getRightThresholds() - Method in class com.fa993.types.SelectThresholdOutput

Gets the array of right thresholds associated with the elements.

getSecond() - Method in class com.fa993.types.supertype.Either.OfThree

Gets the second value if selected.

getSecond() - Method in class com.fa993.types.supertype.Either.OfTwo

Gets the second value if selected.

getSecond() - Method in class com.fa993.types.supertype.Pair

Gets the second element of the pair.

getSelector() - Method in class com.fa993.types.supertype.Either.OfThree

Gets the current selector.

getSelector() - Method in class com.fa993.types.supertype.Either.OfTwo

Gets the current selector.

getThird() - Method in class com.fa993.types.supertype.Either.OfThree

Gets the third value if selected.

getWidthHeights() - Method in class com.fa993.types.PeakWidthsOutput

Gets the array of heights at which the widths of the peaks are measured.

getWidths() - Method in class com.fa993.types.PeakWidthsOutput

Gets the array of widths of the detected peaks.

H

hashCode() - Method in class com.fa993.types.FindPeaksOutput

Computes the hash code for this FindPeaksOutput object.

hashCode() - Method in class com.fa993.types.LocalMaximaOutput

Computes the hash code for this LocalMaximaOutput object.

hashCode() - Method in class com.fa993.types.PeakProminenceOutput

Computes the hash code for this PeakProminenceOutput object.

hashCode() - Method in class com.fa993.types.PeakWidthsOutput

Computes the hash code for this PeakWidthsOutput object.

I

isFirst() - Method in enum com.fa993.types.supertype.Either.Selector

Checks if the current selection is First.

isSecond() - Method in enum com.fa993.types.supertype.Either.Selector

Checks if the current selection is Second.

isThird() - Method in enum com.fa993.types.supertype.Either.Selector

Checks if the current selection is Third.

L

LocalMaxima - Interface in com.fa993.variations

Unifying Interface for different LocalMaxima Implementations.

localMaxima1D(double[]) - Method in interface com.fa993.variations.LocalMaxima

Detects local maxima in a 1D signal.

localMaxima1D(double[]) - Method in class com.fa993.variations.LocalMaximaCC

Detects local maxima in a 1D signal.

localMaxima1D(double[]) - Method in class com.fa993.variations.LocalMaximaJIU

Finds local maxima in a 1-dimensional array of points.

LocalMaximaCC - Class in com.fa993.variations

Implementation of the LocalMaxima interface using a direct translation of the numpy-based algorithm for finding local maxima in a 1D signal.

LocalMaximaCC() - Constructor for class com.fa993.variations.LocalMaximaCC

LocalMaximaJIU - Class in com.fa993.variations

Implementation of the LocalMaxima interface using a method adapted from the scipy library's numpy-based peak-finding utility.

LocalMaximaJIU() - Constructor for class com.fa993.variations.LocalMaximaJIU

LocalMaximaOutput - Class in com.fa993.types

Represents the output of a local maxima detection operation.

LocalMaximaOutput(int[], int[], int[]) - Constructor for class com.fa993.types.LocalMaximaOutput

Constructs a new LocalMaximaOutput object with the specified midpoints, left edges, and right edges.

N

NumOrTwoSeqOrNdArr - Class in com.fa993.types.supertype

Represents a specialized version of Either.OfThree that can hold one of three types: A Double value An array of two double values A 2D array of double values This class enforces specific constraints on the second type, requiring it to be a sequence of exactly two doubles.

NumOrTwoSeqOrNdArr(Double, double[], double[][], Either.Selector) - Constructor for class com.fa993.types.supertype.NumOrTwoSeqOrNdArr

Constructs a NumOrTwoSeqOrNdArr instance with the specified value and selector.

O

OfThree(A, B, C, Either.Selector) - Constructor for class com.fa993.types.supertype.Either.OfThree

Constructs an OfThree object with the specified values and selector.

OfTwo(A, B, Either.Selector) - Constructor for class com.fa993.types.supertype.Either.OfTwo

Constructs an OfTwo object with the specified values and selector.

P

Pair<P,Q> - Class in com.fa993.types.supertype

A generic class representing a pair of two related objects.

Pair(P, Q) - Constructor for class com.fa993.types.supertype.Pair

Constructs a new Pair with the specified elements.

PairOfDoubleOrDArr - Class in com.fa993.types.supertype

Represents a pair where each element is an instance of Either.OfTwo that can hold: A Double value An array of double values

PairOfDoubleOrDArr(Either.OfTwo<Double, double[]>, Either.OfTwo<Double, double[]>) - Constructor for class com.fa993.types.supertype.PairOfDoubleOrDArr

Constructs a PairOfDoubleOrDArr with the specified first and second elements.

PeakProminenceOutput - Class in com.fa993.types

Represents the output of a peak prominence calculation.

PeakProminenceOutput(double[], int[], int[]) - Constructor for class com.fa993.types.PeakProminenceOutput

Constructs a new PeakProminenceOutput object with the specified prominences, left bases, and right bases.

PeakProminences - Class in com.fa993.utils

Utility class for calculating the prominence of peaks in a signal.

PeakProminences() - Constructor for class com.fa993.utils.PeakProminences

PeakWidth - Class in com.fa993.utils

Utility class for calculating the widths of peaks in a given dataset.

PeakWidth() - Constructor for class com.fa993.utils.PeakWidth

PeakWidthsOutput - Class in com.fa993.types

Represents the output of peak width calculations.

PeakWidthsOutput(double[], double[], double[], double[]) - Constructor for class com.fa993.types.PeakWidthsOutput

Constructs a new PeakWidthsOutput object with the specified widths, width heights, left intersection points, and right intersection points.

S

second(double[]) - Static method in class com.fa993.types.supertype.NumOrTwoSeqOrNdArr

Creates a NumOrTwoSeqOrNdArr instance with the array of two double values selected.

second(B) - Static method in class com.fa993.types.supertype.Either.OfThree

Creates an OfThree instance with the second value selected.

second(B) - Static method in class com.fa993.types.supertype.Either.OfTwo

Creates an OfTwo instance with the second value selected.

Second - com.fa993.types.supertype.Either.Selector

Represents the second choice.

SelectByPeakDistance - Class in com.fa993.utils

Utility class for selecting peaks based on a specified minimum distance condition.

SelectByPeakDistance() - Constructor for class com.fa993.utils.SelectByPeakDistance

SelectByPeakThreshold - Class in com.fa993.utils

Utility class for evaluating peaks in a dataset based on threshold conditions.

SelectByPeakThreshold() - Constructor for class com.fa993.utils.SelectByPeakThreshold

SelectByProperty - Class in com.fa993.utils

Utility class for evaluating properties of peaks against defined intervals.

SelectByProperty() - Constructor for class com.fa993.utils.SelectByProperty

SelectThresholdOutput - Class in com.fa993.types

Represents the output of a threshold selection process.

SelectThresholdOutput(boolean[], double[], double[]) - Constructor for class com.fa993.types.SelectThresholdOutput

Constructs a new SelectThresholdOutput object with the specified keep array, left thresholds, and right thresholds.

T

third(double[][]) - Static method in class com.fa993.types.supertype.NumOrTwoSeqOrNdArr

Creates a NumOrTwoSeqOrNdArr instance with the 2D array of double values selected.

third(C) - Static method in class com.fa993.types.supertype.Either.OfThree

Creates an OfThree instance with the third value selected.

Third - com.fa993.types.supertype.Either.Selector

Represents the third choice.

toString() - Method in class com.fa993.types.FindPeaksOutput

Returns a string representation of this FindPeaksOutput object.

U

UnpackConditionArgs - Class in com.fa993.utils

Utility class for unpacking and transforming interval arguments into appropriate formats based on specified conditions.

UnpackConditionArgs() - Constructor for class com.fa993.utils.UnpackConditionArgs

V

valueOf(String) - Static method in enum com.fa993.types.supertype.Either.Selector

Returns the enum constant of this type with the specified name.

values() - Static method in enum com.fa993.types.supertype.Either.Selector

Returns an array containing the constants of this enum type, in the order they are declared.

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