jspecview.common

Class Coordinate

java.lang.Object

jspecview.common.Coordinate

Direct Known Subclasses:

Annotation

public class Coordinate
extends java.lang.Object

The Coordinate class stores the x and y values of a coordinate.

Author:

Debbie-Ann Facey, Khari A. Bryan, Prof Robert J. Lancashire

Constructor Summary

Constructors

Constructor and Description
Coordinate() Constructor
Coordinate(double x, double y) Constructor

Method Summary

Methods

Modifier and Type	Method and Description
static void	applyScale(Coordinate[] xyCoords, double xScale, double yScale) Apply the scale factor to the coordinates
static void	applyShiftReference(Coordinate[] xyCoords, int dataPointNum, double firstX, double lastX, double offset, double observedFreq, int shiftRefType) Applies the shift reference to all coordinates
Coordinate	copy() Returns a new coordinate that has the same x and y values of this coordinate
static double	deltaX(double last, double first, int numPoints) Returns the Delta X value
boolean	equals(Coordinate coord) Indicates whether some other Coordinate is equal to this one
static double	findXForPeakNearest(Coordinate[] xyCoords, double x, boolean isMin)
static double	getMaxX(Coordinate[] coords, int start, int end) Returns the minimum x value of an array of Coordinates
static double	getMaxX(java.util.List<JDXSpectrum> spectra, jspecview.common.ViewData vd) Returns the maximum x value value from an array of arrays of Coordinates.
static double	getMaxY(Coordinate[] coords, int start, int end) Returns the maximum y value of an array of Coordinates
static double	getMaxYUser(java.util.List<JDXSpectrum> spectra, jspecview.common.ViewData vd) Returns the maximum y value value from an array of arrays of Coordinates.
static double	getMinX(Coordinate[] coords, int start, int end) Returns the minimum x value of an array of Coordinates
static double	getMinX(java.util.List<JDXSpectrum> spectra, jspecview.common.ViewData vd) Returns the minimum x value value from an array of arrays of Coordinates.
static double	getMinY(Coordinate[] coords, int start, int end) Returns the minimum y value of an array of Coordinates
static double	getMinYUser(java.util.List<JDXSpectrum> spectra, jspecview.common.ViewData vd) Returns the minimum y value value from an array of arrays of Coordinates.
static int	getNearestIndexForX(Coordinate[] xyCoords, double xPt)
static double	getNearestXWithYAbove(Coordinate[] xyCoords, double x, double y, boolean inverted, boolean andGreaterThanX) discovers nearest peak left or right of x that is above threshold y
java.lang.String	getXString() Returns the x value of the coordinate formatted to a maximum of eight decimal places
double	getXVal() Returns the x value of the coordinate
java.lang.String	getYString() Returns the y value of the coordinate formatted to a maximum of eight decimal places
double	getYVal() Returns the y value of the coordinate
static double	getYValueAt(Coordinate[] xyCoords, double xPt)
static double	intoRange(double x, double x0, double x1)
static int	intoRange(int i, int i0, int i1)
static boolean	isYInRange(Coordinate[] xyCoords, double min, double max) Determines if the y values of a spectrum are in a certain range
static Coordinate[]	normalise(Coordinate[] xyCoords, double min, double max) Normalises the y values of a spectrum to a certain range
static double	parabolicInterpolation(Coordinate[] xyCoords, int pt) see https://ccrma.stanford.edu/~jos/sasp/Quadratic_Interpolation_Spectral_Peaks.html
static Coordinate[]	parseDSV(java.lang.String dataPoints, double xFactor, double yFactor) Parses data stored in x, y format
static void	removeScale(Coordinate[] xyCoords, double xScale, double yScale) Removes the scale factor from the coordinates
static Coordinate[]	reverse(Coordinate[] x)
void	setXVal(double val) Sets the x value of the coordinate
void	setYVal(double val) Sets the y value of the coordinate
java.lang.String	toString() Overides Objects toString() method

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Coordinate

public Coordinate()

Constructor

Coordinate

public Coordinate(double x,
          double y)

Constructor

Parameters:

x - the x value

y - the y value

Method Detail

getXVal

public double getXVal()

Returns the x value of the coordinate

Returns:

the x value of the coordinate

getYVal

public double getYVal()

Returns the y value of the coordinate

Returns:

the y value of the coordinate

getXString

public java.lang.String getXString()

Returns the x value of the coordinate formatted to a maximum of eight decimal places

Returns:

Returns the x value of the coordinate formatted to a maximum of eight decimal places

getYString

public java.lang.String getYString()

Returns the y value of the coordinate formatted to a maximum of eight decimal places

Returns:

Returns the y value of the coordinate formatted to a maximum of eight decimal places

setXVal

public void setXVal(double val)

Sets the x value of the coordinate

Parameters:

val - the x value

setYVal

public void setYVal(double val)

Sets the y value of the coordinate

Parameters:

val - the y value

copy

public Coordinate copy()

Returns a new coordinate that has the same x and y values of this coordinate

Returns:

Returns a new coordinate that has the same x and y values of this coordinate

equals

public boolean equals(Coordinate coord)

Indicates whether some other Coordinate is equal to this one

Parameters:

coord - the reference coordinate

Returns:

true if the coordinates are equal, false otherwise

toString

public java.lang.String toString()

Overides Objects toString() method

Overrides:

toString in class java.lang.Object

Returns:

the String representation of this coordinate

isYInRange

public static boolean isYInRange(Coordinate[] xyCoords,
                 double min,
                 double max)

Determines if the y values of a spectrum are in a certain range

Parameters:

xyCoords -

min -

max -

Returns:

true is in range, otherwise false

normalise

public static Coordinate[] normalise(Coordinate[] xyCoords,
                     double min,
                     double max)

Normalises the y values of a spectrum to a certain range

Parameters:

xyCoords -

min -

max -

Returns:

array of normalised coordinates

reverse

public static Coordinate[] reverse(Coordinate[] x)

parseDSV

public static Coordinate[] parseDSV(java.lang.String dataPoints,
                    double xFactor,
                    double yFactor)

Parses data stored in x, y format

Parameters:

dataPoints - the data as string

xFactor - the factor to apply to x values

yFactor - the factor to apply to y values

Returns:

an array of Coordinates

deltaX

public static double deltaX(double last,
            double first,
            int numPoints)

Returns the Delta X value

Parameters:

last - the last x value

first - the first x value

numPoints - the number of data points

Returns:

the Delta X value

removeScale

public static void removeScale(Coordinate[] xyCoords,
               double xScale,
               double yScale)

Removes the scale factor from the coordinates

Parameters:

xyCoords - the array of coordinates

xScale - the scale for the x values

yScale - the scale for the y values

applyScale

public static void applyScale(Coordinate[] xyCoords,
              double xScale,
              double yScale)

Apply the scale factor to the coordinates

Parameters:

xyCoords - the array of coordinates

xScale - the scale for the x values

yScale - the scale for the y values

applyShiftReference

public static void applyShiftReference(Coordinate[] xyCoords,
                       int dataPointNum,
                       double firstX,
                       double lastX,
                       double offset,
                       double observedFreq,
                       int shiftRefType)
                                throws java.lang.IndexOutOfBoundsException

Applies the shift reference to all coordinates

Parameters:

xyCoords - an array of coordinates

dataPointNum - the number of the data point in the the spectrum, indexed from 1

firstX - the first X value

lastX - the last X value

offset - the offset value

observedFreq - the observed frequency

shiftRefType - the type of shift

Throws:

java.lang.IndexOutOfBoundsException

getMinX

public static double getMinX(Coordinate[] coords,
             int start,
             int end)

Returns the minimum x value of an array of Coordinates

Parameters:

coords - the coordinates

start - the starting index

end - the ending index

Returns:

the maximum x value of an array of Coordinates

getMinX

public static double getMinX(java.util.List<JDXSpectrum> spectra,
             jspecview.common.ViewData vd)

Returns the minimum x value value from an array of arrays of Coordinates.

Parameters:

spectra -

vd -

Returns:

the minimum x value value from an array of arrays of Coordinates

getMaxX

public static double getMaxX(Coordinate[] coords,
             int start,
             int end)

Returns the minimum x value of an array of Coordinates

Parameters:

coords - the coordinates

start - the starting index

end - the ending index

Returns:

the minimum x value of an array of Coordinates

getMaxX

public static double getMaxX(java.util.List<JDXSpectrum> spectra,
             jspecview.common.ViewData vd)

Returns the maximum x value value from an array of arrays of Coordinates.

Parameters:

spectra -

vd -

Returns:

the maximum x value value from an array of arrays of Coordinates

getMinY

public static double getMinY(Coordinate[] coords,
             int start,
             int end)

Returns the minimum y value of an array of Coordinates

Parameters:

coords - the coordinates

start - the starting index

end - the ending index

Returns:

the minimum y value of an array of Coordinates

getMinYUser

public static double getMinYUser(java.util.List<JDXSpectrum> spectra,
                 jspecview.common.ViewData vd)

Returns the minimum y value value from an array of arrays of Coordinates.

Parameters:

spectra -

vd -

Returns:

the minimum y value value from an array of arrays of Coordinates

getMaxY

public static double getMaxY(Coordinate[] coords,
             int start,
             int end)

Returns the maximum y value of an array of Coordinates

Parameters:

coords - the coordinates

start - the starting index

end - the ending index

Returns:

the maximum y value of an array of Coordinates

getMaxYUser

public static double getMaxYUser(java.util.List<JDXSpectrum> spectra,
                 jspecview.common.ViewData vd)

Returns the maximum y value value from an array of arrays of Coordinates.

Parameters:

spectra -

vd -

Returns:

the maximum y value value from an array of arrays of Coordinates

getYValueAt

public static double getYValueAt(Coordinate[] xyCoords,
                 double xPt)

intoRange

public static int intoRange(int i,
            int i0,
            int i1)

intoRange

public static double intoRange(double x,
               double x0,
               double x1)

getNearestIndexForX

public static int getNearestIndexForX(Coordinate[] xyCoords,
                      double xPt)

findXForPeakNearest

public static double findXForPeakNearest(Coordinate[] xyCoords,
                         double x,
                         boolean isMin)

parabolicInterpolation

public static double parabolicInterpolation(Coordinate[] xyCoords,
                            int pt)

see https://ccrma.stanford.edu/~jos/sasp/Quadratic_Interpolation_Spectral_Peaks.html

Parameters:

xyCoords -

pt -

Returns:

center

getNearestXWithYAbove

public static double getNearestXWithYAbove(Coordinate[] xyCoords,
                           double x,
                           double y,
                           boolean inverted,
                           boolean andGreaterThanX)

discovers nearest peak left or right of x that is above threshold y

Parameters:

xyCoords -

x -

y -

inverted -

andGreaterThanX -

Returns:

interpolated x value or NaN