G3DSys

java.lang.Object
- g3dsys.control.G3DSys

```
public class G3DSys
extends java.lang.Object
```
Abstraction and delegation container class to facilitate communication between the CoordMapper, FigureManager, and G3DPanel without deeply coupling them in their own definitions. Users need only instantiate G3DSys with the target AWT component and then start adding Figures for them to appear. No Figure constructors should be called directly, as the addFig method will do that itself based on the figure type argument (e.g.; BALL, LINE, BOX).

Field Summary

Fields
Modifier and Type	Field	Description
`static int`	`AXES`
`static int`	`BALL`	implemented shapes
`static int`	`BOX`
`static int`	`CYLINDER`
`static int`	`LINE`
`static int`	`RECTANGLE`
`static int`	`TIMEDBALL`

Constructor Summary

Constructors
Constructor Description

G3DSys(java.awt.Container window)

Constructors
Constructor	Description
`G3DSys(java.awt.Container window)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`addFig(Figure f)`	Adds the Figure to the associated FigureManager
`float`	`calcRotationRadius(Point3f center)`	Finds the atom distance furthest from the given point; for rotation
`void`	`calcZbufferLimits()`
`void`	`draw()`
`void`	`fastRefresh()`	A less thorough redraw for a quick refresh
`float`	`getAngstromDepth()`	Gets the Angstrom depth of the model
`float`	`getAngstromHeight()`	Gets the Angstrom height of the model
`float`	`getAngstromWidth()`	Gets the Angstrom width of the model
`Point3f`	`getAverageAtomPoint()`
`double[]`	`getBoundaryVectors()`	Gets the boundary vectors used for calculating image shells
`IndexIterator`	`getBoundaryVectorsIterator()`	Gets the index iterator used for calculating image shells
`Point3f`	`getBoundingBoxCenter()`
`Point3f`	`getCenterOfRotation()`
`static short`	`getColix(int argb)`	Converts the given argb int to a G3D Colix
`static short`	`getColix(java.awt.Color color)`	Converts the given AWT color to a G3D Colix
`double`	`getDepthPercent()`
`Figure[]`	`getFigs()`	For use only by ImageShell class for iteration
`g3dsys.control.FigureManager`	`getFM()`	Only to be used internally to escape endless delegation
`Graphics3D`	`getG3D()`	Get G3D
`float`	`getMaxX()`
`float`	`getMaxY()`
`float`	`getMaxZ()`
`float`	`getMinX()`
`float`	`getMinY()`
`float`	`getMinZ()`
`boolean`	`getPerspectiveDepth()`
`int`	`getPixelDepth()`	Gets the pixel depth of the display (zbuffer)
`int`	`getPixelHeight()`	Gets the pixel height of the display
`int`	`getPixelWidth()`	Gets the pixel width of the display
`double`	`getSlabPercent()`
`TransformManager`	`getTM()`
`boolean`	`isXFlipped()`
`boolean`	`isYFlipped()`
`short`	`perspective(int z, float d)`	Handles perspective based on depth and diameter.
`void`	`refresh()`	For a thorough redraw of the display
`Figure`	`removeFig(Figure f)`	Removes the Figure to from associated FigureManager
`void`	`rotateByX(float degrees)`	Rotate the display around the x axis
`void`	`rotateByXY(float degx, float degy)`	Rotate the display around the x and y axes
`void`	`rotateByY(float degrees)`	Rotate the display around the y axis
`void`	`rotateByZ(float degrees)`	Rotate the display around the z axis
`void`	`rotateToHome()`	Remove all rotation (and translation) and return to the home position
`void`	`scaleFitToScreen()`
`void`	`screenSpace(Point3f p, Point3i s)`	Converts molspace point p (in Angstroms) to a point on the display in pixels.
`void`	`setBGColor(java.awt.Color color)`	Change the background color of the G3D display
`void`	`setBoundaryVectors(double[] values)`	Sets the boundary vectors to be used for calculating image shells
`void`	`setBoundaryVectorsIterator(IndexIterator i)`	Sets the index iterator to use for calculating image shells
`void`	`setBoundingBox(float minx, float miny, float minz, float maxx, float maxy, float maxz)`	Set the min and maximum coordinates for the model.
`void`	`setCenterOfRotation(Point3f p)`	Set the molecule space location around which rotation occurs
`void`	`setDefaultRotation()`	Rescales slab and depth after image shell mode is toggled or the number of layers changed.
`void`	`setDepthPercent(float val)`
`void`	`setPerspectiveDepth(boolean b)`
`void`	`setSlabPercent(float val)`
`void`	`setXFlipped(boolean x)`
`void`	`setYFlipped(boolean y)`
`void`	`startRotation(int deltaY, int deltaX)`
`void`	`stopRotation()`
`void`	`xlateDown()`	Translate model 10% of pixel width down (+y)
`void`	`xlateLeft()`	Translate model 10% of pixel width to the left (-x)
`void`	`xlateRight()`	Translate model 10% of pixel width to the right (+x)
`void`	`xlateUp()`	Translate model 10% of pixel width up (-y)
`void`	`xlateXY(int x, int y)`	Trnaslate model x,y pixels
`void`	`zoomDown(int i)`	Decrease the zoom level by i percent
`void`	`zoomUp(int i)`	Increase the zoom level by i percent

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - BALL
```
public static final int BALL
```
    implemented shapes
    
    See Also:
    
    Constant Field Values
  - CYLINDER
```
public static final int CYLINDER
```
    See Also:
    
    Constant Field Values
  - RECTANGLE
```
public static final int RECTANGLE
```
    See Also:
    
    Constant Field Values
  - LINE
```
public static final int LINE
```
    See Also:
    
    Constant Field Values
  - BOX
```
public static final int BOX
```
    See Also:
    
    Constant Field Values
  - AXES
```
public static final int AXES
```
    See Also:
    
    Constant Field Values
  - TIMEDBALL
```
public static final int TIMEDBALL
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - G3DSys
```
public G3DSys(java.awt.Container window)
```
- Method Detail
  - refresh
```
public void refresh()
```
    For a thorough redraw of the display
  - fastRefresh
```
public void fastRefresh()
```
    A less thorough redraw for a quick refresh
  - setBGColor
```
public void setBGColor(java.awt.Color color)
```
    Change the background color of the G3D display
    
    Parameters:
    
    color - the G3d background color to use
  - getG3D
```
public Graphics3D getG3D()
```
    Get G3D
    
    Returns:
    
    associated Graphics3D object
  - getPixelWidth
```
public int getPixelWidth()
```
    Gets the pixel width of the display
    
    Returns:
    
    width of the g3d display area in pixels
  - getPixelHeight
```
public int getPixelHeight()
```
    Gets the pixel height of the display
    
    Returns:
    
    height of the g3d display area in pixels
  - getPixelDepth
```
public int getPixelDepth()
```
    Gets the pixel depth of the display (zbuffer)
    
    Returns:
    
    depth of the g3d display area in pixels
  - getAngstromWidth
```
public float getAngstromWidth()
```
    Gets the Angstrom width of the model
    
    Returns:
    
    width of the model in Angstroms
  - getAngstromHeight
```
public float getAngstromHeight()
```
    Gets the Angstrom height of the model
    
    Returns:
    
    height of the model in Angstroms
  - getAngstromDepth
```
public float getAngstromDepth()
```
    Gets the Angstrom depth of the model
    
    Returns:
    
    depth of the model in Angstroms
  - addFig
```
public void addFig(Figure f)
```
    Adds the Figure to the associated FigureManager
    
    Parameters:
    
    f - the Figure to add
  - removeFig
```
public Figure removeFig(Figure f)
```
    Removes the Figure to from associated FigureManager
    
    Parameters:
    
    f - the Figure to remove
  - isYFlipped
```
public boolean isYFlipped()
```
  - isXFlipped
```
public boolean isXFlipped()
```
  - setYFlipped
```
public void setYFlipped(boolean y)
```
  - setXFlipped
```
public void setXFlipped(boolean x)
```
  - rotateByXY
```
public void rotateByXY(float degx,
                       float degy)
```
    Rotate the display around the x and y axes
    
    Parameters:
    
    degx - the number of degrees to rotate x
    
    degy - the number of degrees to rotate y
  - rotateByX
```
public void rotateByX(float degrees)
```
    Rotate the display around the x axis
    
    Parameters:
    
    degrees - the number of degrees to rotate
  - rotateByY
```
public void rotateByY(float degrees)
```
    Rotate the display around the y axis
    
    Parameters:
    
    degrees - the number of degrees to rotate
  - rotateByZ
```
public void rotateByZ(float degrees)
```
    Rotate the display around the z axis
    
    Parameters:
    
    degrees - the number of degrees to rotate
  - rotateToHome
```
public void rotateToHome()
```
    Remove all rotation (and translation) and return to the home position
  - xlateLeft
```
public void xlateLeft()
```
    Translate model 10% of pixel width to the left (-x)
  - xlateRight
```
public void xlateRight()
```
    Translate model 10% of pixel width to the right (+x)
  - xlateUp
```
public void xlateUp()
```
    Translate model 10% of pixel width up (-y)
  - xlateDown
```
public void xlateDown()
```
    Translate model 10% of pixel width down (+y)
  - xlateXY
```
public void xlateXY(int x,
                    int y)
```
    Trnaslate model x,y pixels
  - setCenterOfRotation
```
public void setCenterOfRotation(Point3f p)
```
    Set the molecule space location around which rotation occurs
  - getCenterOfRotation
```
public Point3f getCenterOfRotation()
```
  - startRotation
```
public void startRotation(int deltaY,
                          int deltaX)
```
  - stopRotation
```
public void stopRotation()
```
  - setBoundingBox
```
public void setBoundingBox(float minx,
                           float miny,
                           float minz,
                           float maxx,
                           float maxy,
                           float maxz)
```
    Set the min and maximum coordinates for the model. The zoom level is set such that everything within the box is viewable.
    
    Parameters:
    
    minx - minimum x
    
    miny - minimum y
    
    minz - minimum z
    
    maxx - maximum x
    
    maxy - maximum y
    
    maxz - maximum z
  - getBoundingBoxCenter
```
public Point3f getBoundingBoxCenter()
```
  - screenSpace
```
public void screenSpace(Point3f p,
                        Point3i s)
```
    Converts molspace point p (in Angstroms) to a point on the display in pixels.
    
    Parameters:
    
    p - the point to convert
  - perspective
```
public short perspective(int z,
                         float d)
```
    Handles perspective based on depth and diameter.
    
    Parameters:
    
    z - depth of an object
    
    d - diameter of an object
    
    Returns:
    
    the new perspective-scaled diameter for the object
  - zoomUp
```
public void zoomUp(int i)
```
    Increase the zoom level by i percent
    
    Parameters:
    
    i - the percentage amount to increase
  - zoomDown
```
public void zoomDown(int i)
```
    Decrease the zoom level by i percent
    
    Parameters:
    
    i - the percentage amount to decrease
  - setPerspectiveDepth
```
public void setPerspectiveDepth(boolean b)
```
  - getPerspectiveDepth
```
public boolean getPerspectiveDepth()
```
  - getSlabPercent
```
public double getSlabPercent()
```
  - getDepthPercent
```
public double getDepthPercent()
```
  - setSlabPercent
```
public void setSlabPercent(float val)
```
  - setDepthPercent
```
public void setDepthPercent(float val)
```
  - scaleFitToScreen
```
public void scaleFitToScreen()
```
  - getMinX
```
public float getMinX()
```
  - getMinY
```
public float getMinY()
```
  - getMinZ
```
public float getMinZ()
```
  - getMaxX
```
public float getMaxX()
```
  - getMaxY
```
public float getMaxY()
```
  - getMaxZ
```
public float getMaxZ()
```
  - draw
```
public void draw()
```
  - setBoundaryVectors
```
public void setBoundaryVectors(double[] values)
```
    Sets the boundary vectors to be used for calculating image shells
    
    Parameters:
    
    values - the vectors to use
  - setBoundaryVectorsIterator
```
public void setBoundaryVectorsIterator(IndexIterator i)
```
    Sets the index iterator to use for calculating image shells
    
    Parameters:
    
    i - the iterator to use
  - getBoundaryVectorsIterator
```
public IndexIterator getBoundaryVectorsIterator()
```
    Gets the index iterator used for calculating image shells
    
    Returns:
    
    returns the index iterator
  - getBoundaryVectors
```
public double[] getBoundaryVectors()
```
    Gets the boundary vectors used for calculating image shells
    
    Returns:
    
    returns the boundary vectors
  - getColix
```
public static short getColix(java.awt.Color color)
```
    Converts the given AWT color to a G3D Colix
    
    Parameters:
    
    color - the color to be converted
  - getColix
```
public static short getColix(int argb)
```
    Converts the given argb int to a G3D Colix
    
    Parameters:
    
    argb - the argb integer to be converted.
    
    Returns:
    
    a Colix as a short
  - calcRotationRadius
```
public float calcRotationRadius(Point3f center)
```
    Finds the atom distance furthest from the given point; for rotation
    
    Parameters:
    
    center - the reference point
    
    Returns:
    
    the furthest distance found, in Angstroms
  - getAverageAtomPoint
```
public Point3f getAverageAtomPoint()
```
  - calcZbufferLimits
```
public void calcZbufferLimits()
```
  - getFigs
```
public Figure[] getFigs()
```
    For use only by ImageShell class for iteration
    
    Returns:
    
    returns the array of current Figures
  - setDefaultRotation
```
public void setDefaultRotation()
```
    Rescales slab and depth after image shell mode is toggled or the number of layers changed.
  - getFM
```
public g3dsys.control.FigureManager getFM()
```
    Only to be used internally to escape endless delegation
    
    Returns:
    
    returns the FigureManager
  - getTM
```
public TransformManager getTM()
```

Class G3DSys

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

BALL

CYLINDER

RECTANGLE

LINE

BOX

AXES

TIMEDBALL

Constructor Detail

G3DSys

Method Detail

refresh

fastRefresh

setBGColor

getG3D

getPixelWidth

getPixelHeight

getPixelDepth

getAngstromWidth

getAngstromHeight

getAngstromDepth

addFig

removeFig

isYFlipped

isXFlipped

setYFlipped

setXFlipped

rotateByXY

rotateByX

rotateByY

rotateByZ

rotateToHome

xlateLeft

xlateRight

xlateUp

xlateDown

xlateXY

setCenterOfRotation

getCenterOfRotation

startRotation

stopRotation

setBoundingBox

getBoundingBoxCenter

screenSpace

perspective

zoomUp

zoomDown

setPerspectiveDepth

getPerspectiveDepth

getSlabPercent

getDepthPercent

setSlabPercent

setDepthPercent

scaleFitToScreen

getMinX

getMinY

getMinZ

getMaxX

getMaxY

getMaxZ

draw

setBoundaryVectors

setBoundaryVectorsIterator

getBoundaryVectorsIterator

getBoundaryVectors

getColix

getColix

calcRotationRadius

getAverageAtomPoint

calcZbufferLimits

getFigs

setDefaultRotation

getFM

getTM