apollo.gui
Class Transformer

java.lang.Object
  apollo.gui.Transformer

public class Transformer
extends java.lang.Object

A class to perform coordinate transformations between pixel and user coordinates.

Nested Class Summary

class

Transformer.PixelRange

Field Summary

static int	DOWN
static int	LEFT
static int	RIGHT
static int	UP Directions for Y axis (setYOrientation)

Constructor Summary

Transformer(java.awt.Rectangle bounds)

Transformer(java.awt.Rectangle pixelBounds, java.awt.Rectangle userBounds)

Method Summary

Transformer.PixelRange	basepairRangeToPixelRange(RangeI range) This takes care of doing the inclusion at the end of base pair ranges and compensates for xOrientation.
java.lang.Object	clone()
java.awt.Point	fromPixel(java.awt.Point pixel)
java.awt.Point	fromUser(java.awt.Point user)
java.awt.Rectangle	getPixelBounds()
int	getXCentre()
double	getXCoordsPerPixel()
int	getXMaximum()
int	getXMinimum()
int	getXOrientation() This can be Transformer.LEFT and Transformer.RIGHT.
double	getXPixelsPerCoord()
int[]	getXRange()
int[]	getXVisibleRange()
int	getYCentre()
double	getYCoordsPerPixel()
int	getYMaximum()
int	getYMinimum()
int	getYOrientation()
double	getYPixelsPerCoord()
int[]	getYRange()
int[]	getYVisibleRange()
static void	main(java.lang.String[] argv)
int	maxXPixelAtUserCoord(int user) This gives the pixel value at the end of the base pair, which is halfway between the basepair(user) and the next basepair(user+1).
int	maxXUserCoordAtPixel(int pixel)
int	minXPixelAtUserCoord(int user) This gives the pixel value at the beginning of the base pair, which is halfway between the basepair(user) and the previous basepair(user-1).
int	minXUserCoordAtPixel(int pixel)
void	reset()
void	setPixelBounds(java.awt.Rectangle rect)
void	setXCentre(int centre)
void	setXMaximum(int max)
void	setXMinimum(int min)
void	setXOrientation(int orientation)
void	setXRange(int[] limits)
void	setXVisibleMinimum(int min)
void	setXZoomFactor(double factor)
void	setYCentre(int centre)
void	setYMaximum(int max)
void	setYMinimum(int min)
void	setYOrientation(int orientation)
void	setYRange(int[] limits)
void	setYVisibleMinimum(int min)
void	setYZoomFactor(double factor)
java.awt.Point	toPixel(int x, int y)
java.awt.Point	toPixel(java.awt.Point user)
int	toPixelX(int userX) used to be a long version of these functions as well - took them out because we dont need them anymore i believe.
int	toPixelY(int userY)
java.awt.Point	toUser(int x, int y)
java.awt.Point	toUser(java.awt.Point pixel)
void	writeFactors()

Methods inherited from class java.lang.Object

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

Field Detail

UP

public static final int UP

Directions for Y axis (setYOrientation)

See Also:

Constant Field Values

DOWN

public static final int DOWN

See Also:

Constant Field Values

LEFT

public static final int LEFT

See Also:

Constant Field Values

RIGHT

public static final int RIGHT

See Also:

Constant Field Values

Constructor Detail

Transformer

public Transformer(java.awt.Rectangle bounds)

Transformer

public Transformer(java.awt.Rectangle pixelBounds,
                   java.awt.Rectangle userBounds)

Method Detail

reset

public void reset()

setPixelBounds

public void setPixelBounds(java.awt.Rectangle rect)

getPixelBounds

public java.awt.Rectangle getPixelBounds()

setYOrientation

public void setYOrientation(int orientation)

setXOrientation

public void setXOrientation(int orientation)

setXZoomFactor

public void setXZoomFactor(double factor)

setYZoomFactor

public void setYZoomFactor(double factor)

setXRange

public void setXRange(int[] limits)

setYRange

public void setYRange(int[] limits)

setXMinimum

public void setXMinimum(int min)

setYMinimum

public void setYMinimum(int min)

setXMaximum

public void setXMaximum(int max)

setYMaximum

public void setYMaximum(int max)

setXCentre

public void setXCentre(int centre)

setYCentre

public void setYCentre(int centre)

getXRange

public int[] getXRange()

getYRange

public int[] getYRange()

getXMaximum

public int getXMaximum()

getYMaximum

public int getYMaximum()

getXMinimum

public int getXMinimum()

getYMinimum

public int getYMinimum()

getXCentre

public int getXCentre()

getYCentre

public int getYCentre()

getXVisibleRange

public int[] getXVisibleRange()

getYVisibleRange

public int[] getYVisibleRange()

setYVisibleMinimum

public void setYVisibleMinimum(int min)

setXVisibleMinimum

public void setXVisibleMinimum(int min)

writeFactors

public void writeFactors()

toPixelX

public int toPixelX(int userX)

used to be a long version of these functions as well - took them out because we dont need them anymore i believe. toPixelX actually returns the pixel value of the end of the base pair (which is halfway between the basepair(userX) and the next bp(userX+1). To the left for xorientation LEFT, to the right for xorientation RIGHT

basepairRangeToPixelRange

public Transformer.PixelRange basepairRangeToPixelRange(RangeI range)

This takes care of doing the inclusion at the end of base pair ranges and compensates for xOrientation. the low basepair needs to subtract one from it to include it. the low basepair is low in LEFT (normal) and high in RIGHT x orientation (revcomp), so hi and lo get flipped for revcomp.

toPixelY

public int toPixelY(int userY)

toPixel

public java.awt.Point toPixel(java.awt.Point user)

toPixel

public java.awt.Point toPixel(int x,
                              int y)

fromPixel

public java.awt.Point fromPixel(java.awt.Point pixel)

toUser

public java.awt.Point toUser(int x,
                             int y)

toUser

public java.awt.Point toUser(java.awt.Point pixel)

fromUser

public java.awt.Point fromUser(java.awt.Point user)

minXUserCoordAtPixel

public int minXUserCoordAtPixel(int pixel)

maxXUserCoordAtPixel

public int maxXUserCoordAtPixel(int pixel)

minXPixelAtUserCoord

public int minXPixelAtUserCoord(int user)

This gives the pixel value at the beginning of the base pair, which is halfway between the basepair(user) and the previous basepair(user-1). This is actually toPixelX(user-1) because toPixelX actually returns the pixel value of the end of the base pair (which is halfway between the basepair(user) and the next bp (user+1)

maxXPixelAtUserCoord

public int maxXPixelAtUserCoord(int user)

This gives the pixel value at the end of the base pair, which is halfway between the basepair(user) and the next basepair(user+1). This is actually toPixelX(user) because toPixelX actually returns the pixel value of the end of the base pair

getYCoordsPerPixel

public double getYCoordsPerPixel()

getXCoordsPerPixel

public double getXCoordsPerPixel()

getYPixelsPerCoord

public double getYPixelsPerCoord()

getXPixelsPerCoord

public double getXPixelsPerCoord()

getYOrientation

public int getYOrientation()

getXOrientation

public int getXOrientation()

This can be Transformer.LEFT and Transformer.RIGHT. I believe that LEFT is normal (left to right) and RIGHT is revcomped (axis goes right to left)

main

public static void main(java.lang.String[] argv)

clone

public java.lang.Object clone()
                       throws java.lang.CloneNotSupportedException

Overrides:

clone in class java.lang.Object

Throws:

java.lang.CloneNotSupportedException