Package jspecview.common

Class Coordinate

java.lang.Object
jspecview.common.Coordinate
Direct Known Subclasses:
Annotation
public class Coordinate extends 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
    Description
    Coordinate()
    Constructor

  • Method Summary

    Modifier and Type
    Method
    Description
    static void
    applyScale(Coordinate[] xyCoords, double xScale, double yScale)
    Apply the scale factor to the 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(Lst<Spectrum> spectra, ViewData vd)
    Returns the maximum x value value from an array of arrays of Coordinates.
    static double
    getMaxX(Coordinate[] coords, int start, int end)
    Returns the minimum x value of an array of Coordinates
    static double
    getMaxY(Coordinate[] coords, int start, int end)
    Returns the maximum y value of an array of Coordinates
    static double
    getMaxYUser(Lst<Spectrum> spectra, ViewData vd)
    Returns the maximum y value value from an array of arrays of Coordinates.
    static double
    getMinX(Lst<Spectrum> spectra, ViewData vd)
    Returns the minimum x 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
    getMinY(Coordinate[] coords, int start, int end)
    Returns the minimum y value of an array of Coordinates
    static double
    getMinYUser(Lst<Spectrum> spectra, 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
    double
    getXVal()
    Returns the x value of the coordinate
    double
    getYVal()
    Returns the y value of the coordinate
    static double
    getYValueAt(Coordinate[] xyCoords, double xPt)
     
    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(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)
     
    Coordinate
    set(double x, double y)
    Constructor
    void
    setXVal(double val)
    Sets the x value of the coordinate
    void
    setYVal(double val)
    Sets the y value of the coordinate
    static void
    shiftX(Coordinate[] xyCoords, double dx)
     
    String
    toString()
    Overides Objects toString() method

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • Coordinate

      public Coordinate()
      Constructor

  • Method Details

    • set

      public Coordinate set(double x, double y)
      Constructor
      Parameters:
      x - the x value
      y - the y value
      Returns:
      this

    • 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

    • 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 String toString()
      Overides Objects toString() method
      Overrides:
      toString in class 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(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

    • 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(Lst<Spectrum> spectra, 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(Lst<Spectrum> spectra, 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(Lst<Spectrum> spectra, 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(Lst<Spectrum> spectra, 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)

    • 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

    • shiftX

      public static void shiftX(Coordinate[] xyCoords, double dx)

    • 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