showIsosurface
Class ShowIsosurface

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Panel
              java.applet.Applet
                  showIsosurface.ShowIsosurface

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible

public class ShowIsosurface
extends java.applet.Applet

Displays orbital isosurfaces given a point set.

Applet Parameters

NAME	Variable Type	Default	Description
CreateAxes	Boolean	False	Determines whether coordinate axes will be created.
EnableRotate	Boolean	True	Determines whether the scene may be rotated. Implemented only for ROTATE_SCENE
EnableTranslate	Boolean	True	Determines whether the scene may be translated.
EnableZoom	Boolean	True	Determines whether the scene zoom is available.
IsReady	String		JavaScript variable that will be set to true when applet has initialized. Must use MAYSCRIPT in APPLET tag to use this feature.
NbrAtoms	Integer	1	Number of atoms to be displayed.
RotateBehavior	Integer	0	Specifies the mouse rotation behavior. 0 (ROTATE_SCENE) entire scene rotates together 1 (ROTATE_ALL) all atoms rotate simultaneous about their locations (axes do not rotate) 2 (ROTATE_INDIVIDUAL) all atoms rotate individually and independent of other atoms

Version:

1.0

Author:

David N. Blauch

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class java.awt.Component

java.awt.Component.BaselineResizeBehavior

Field Summary

int	ROTATE_ALL
int	ROTATE_INDIVIDUAL
int	ROTATE_SCENE

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

ShowIsosurface()

Method Summary

void	createOrbital(int nAtom, int nIso) Creates a new Orbital object containing no isosurfaces
void	createOrbital(int nAtom, int nIso, java.lang.String fname) Creates a new Orbital object containing one isosurface, which is loaded from the specified VRML file
void	createOrbital(int nAtom, int nIso, java.lang.String fname, int nSurf) Creates a new Orbital object containing multiple isosurfaces, which are loaded from the specified VRML files
void	destroy()
java.lang.String	getAppletInfo()
java.util.BitSet	getChildMask(int nAtom) Returns the Switch child mask for the orbitals on the specified atom
boolean	getChildMask(int nAtom, int nOrb) Returns the Switch child mask setting for a specific orbital.
java.lang.String	getParameter(java.lang.String key, java.lang.String def)
java.lang.String[][]	getParameterInfo()
javax.vecmath.AxisAngle4d	getRotation() Provides the current setting for the system TransformGroup.
double	getRotationAngle() Returns the x component of the axis of rotation for the current transform
double	getRotationX() Returns the x component of the axis of rotation for the current transform
double	getRotationY() Returns the y component of the axis of rotation for the current transform
double	getRotationZ() Returns the z component of the axis of rotation for the current transform
void	init()
void	loadIsosurface(int nAtom, int nOrb, java.lang.String fname) Loads an isosurface from a VRML file into an orbital
void	loadIsosurfaces(int nAtom, int nOrb, java.lang.String fname, int nSurf) Loads a set of isosurfaces from VRML files into an orbital
void	setAtomPosition(int n, double x, double y, double z) Sets the position of the specified atom.
void	setAtomScale(int n, double s) Scales the geometry objects for the specified atom
void	setAtomView(int na, double x, double y, double z, double xa, double ya, double za, double a) Sets the rotation for a specific atom to view down the x axis.
void	setAxesLength(float r) Sets the range of all axes from -r to r.
void	setAxesLength(float xL, float xU, float yL, float yU, float zL, float zU) Sets the lengths of the axes.
void	setAxesVisible(boolean s) Indicates whether axes are visible
void	setChildMask(int nAtom, java.util.BitSet bs) For the specified atom, sets the Switch child mask.
void	setChildMask(int nAtom, int nOrb, boolean s) For the specified atom, sets the Switch child mask for the specified orbital.
void	setFontSize(int s) Sets the font size for the axes labels
void	setIsosurfaceVisible(int nAtom, int nOrb, int nIso, boolean s) Indicates whether an isosurface is visible
void	setNucleusColor(int n, float x, float y, float z) Sets the emissive color of the nucleus of the specified atom and sets the nucleus to be visible
void	setNucleusVisible(int n, boolean s) Determines whether the nucleus is visible as a small where sphere
void	setOrbitalActive(int nAtom, int nOrb) The orbital's BranchGroup is compiled and added to the atom's Switch node.
void	setOrbitalTransparency(int nAtom, int nOrb, float t) Sets the transparency of an orbital
void	setPosition(double x, double y, double z) Sets the position of the root transform.
void	setView(double x, double y, double z, double a) Sets the orientation to a specific value.
void	setViewDistance(float r) Sets the viewing distance.
void	setWhichOrbital(int nAtom, int nOrb) For the selected atom, specifies the orbital to be displayed.
void	setXView() Sets the orientation to view down the x axis.
void	setYView() Sets the orientation to view down the y axis.
void	setZView() Sets the orientation to view down the z axis.
void	start()
void	stop()

Methods inherited from class java.applet.Applet

getAccessibleContext, getAppletContext, getAudioClip, getAudioClip, getCodeBase, getDocumentBase, getImage, getImage, getLocale, getParameter, isActive, newAudioClip, play, play, resize, resize, setStub, showStatus

Methods inherited from class java.awt.Panel

addNotify

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getInsets, getLayout, getListeners, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paint, paintComponents, preferredSize, print, printComponents, remove, remove, removeAll, removeContainerListener, removeNotify, setComponentZOrder, setFocusCycleRoot, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, setLayout, transferFocusBackward, transferFocusDownCycle, update, validate

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, dispatchEvent, enable, enable, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphics, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getToolkit, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, printAll, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, requestFocusInWindow, reshape, setBackground, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setMinimumSize, setName, setPreferredSize, setSize, setSize, setVisible, show, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

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

Field Detail

ROTATE_SCENE

public final int ROTATE_SCENE

See Also:

Constant Field Values

ROTATE_ALL

public final int ROTATE_ALL

See Also:

Constant Field Values

ROTATE_INDIVIDUAL

public final int ROTATE_INDIVIDUAL

See Also:

Constant Field Values

Constructor Detail

ShowIsosurface

public ShowIsosurface()

Method Detail

getAppletInfo

public java.lang.String getAppletInfo()

Overrides:

getAppletInfo in class java.applet.Applet

getParameterInfo

public java.lang.String[][] getParameterInfo()

Overrides:

getParameterInfo in class java.applet.Applet

getParameter

public java.lang.String getParameter(java.lang.String key,
                                     java.lang.String def)

init

public void init()

Overrides:

init in class java.applet.Applet

start

public void start()

Overrides:

start in class java.applet.Applet

stop

public void stop()

Overrides:

stop in class java.applet.Applet

destroy

public void destroy()

Overrides:

destroy in class java.applet.Applet

createOrbital

public void createOrbital(int nAtom,
                          int nIso)

Creates a new Orbital object containing no isosurfaces

Parameters:

nAtom - index of the atom to contain the new orbital

nIso - number of isosurfaces for the new orbital

createOrbital

public void createOrbital(int nAtom,
                          int nIso,
                          java.lang.String fname)

Creates a new Orbital object containing one isosurface, which is loaded from the specified VRML file

Parameters:

nAtom - index of the atom to contain the new orbital

nIso - number of isosurfaces for the new orbital

fname - file name of the VRML file describing an isosurface

createOrbital

public void createOrbital(int nAtom,
                          int nIso,
                          java.lang.String fname,
                          int nSurf)

Creates a new Orbital object containing multiple isosurfaces, which are loaded from the specified VRML files

Parameters:

nAtom - index of the atom to contain the new orbital

nIso - number of isosurfaces for the orbital

fname - base file name of the VRML files describing isosurfaces

nSurf - number of isosurfaces to be loaded

getRotation

public javax.vecmath.AxisAngle4d getRotation()

Provides the current setting for the system TransformGroup.

Returns:

AxisAngle4d object for the current transform

getChildMask

public java.util.BitSet getChildMask(int nAtom)

Returns the Switch child mask for the orbitals on the specified atom

Parameters:

nAtom - atom of interest

See Also:

setWhichOrbital

getChildMask

public boolean getChildMask(int nAtom,
                            int nOrb)

Returns the Switch child mask setting for a specific orbital.

Parameters:

nAtom - atom of interest

nOrb - orbital of interest

See Also:

setWhichOrbital

setChildMask

public void setChildMask(int nAtom,
                         java.util.BitSet bs)

For the specified atom, sets the Switch child mask. Requires setWhichOrbital has been called with the CHILD_MASK option.

Parameters:

nAtom - atom of interest

bs - child mask

See Also:

setWhichOrbital

setChildMask

public void setChildMask(int nAtom,
                         int nOrb,
                         boolean s)

For the specified atom, sets the Switch child mask for the specified orbital. Requires setWhichOrbital has been called with the CHILD_MASK option.

Parameters:

nAtom - atom of interest

nOrb - orbital of interest

s - state for orbital

See Also:

setWhichOrbital

getRotationX

public double getRotationX()

Returns the x component of the axis of rotation for the current transform

Returns:

x-component of axis of rotation

getRotationY

public double getRotationY()

Returns the y component of the axis of rotation for the current transform

Returns:

y-component of axis of rotation

getRotationZ

public double getRotationZ()

Returns the z component of the axis of rotation for the current transform

Returns:

z-component of axis of rotation

getRotationAngle

public double getRotationAngle()

Returns the x component of the axis of rotation for the current transform

Returns:

angle of rotation

loadIsosurface

public void loadIsosurface(int nAtom,
                           int nOrb,
                           java.lang.String fname)

Loads an isosurface from a VRML file into an orbital

Parameters:

nAtom - index of atom

nOrb - index of orbital

fname - file name of the VRML file

loadIsosurfaces

public void loadIsosurfaces(int nAtom,
                            int nOrb,
                            java.lang.String fname,
                            int nSurf)

Loads a set of isosurfaces from VRML files into an orbital

Parameters:

nAtom - index of atom

nOrb - index of orbital

fname - base file name of the VRML files

nSurf - number of surfaces to be added

setAtomPosition

public void setAtomPosition(int n,
                            double x,
                            double y,
                            double z)

Sets the position of the specified atom.

Parameters:

n - index of the atoms

x - position of the atom along the x axis

y - position of the atom along the y axis

z - position of the atom along the z axis

setAtomScale

public void setAtomScale(int n,
                         double s)

Scales the geometry objects for the specified atom

Parameters:

n - atom index

s - scale

setAtomView

public void setAtomView(int na,
                        double x,
                        double y,
                        double z,
                        double xa,
                        double ya,
                        double za,
                        double a)

Sets the rotation for a specific atom to view down the x axis.

Parameters:

na - atom index

x - x position

y - y position

z - z position

xa - x-component of the axis of rotation

ya - y-component of the axis of rotation

za - z-component of the axis of rotation

a - angle of rotation

setAxesLength

public void setAxesLength(float r)

Sets the range of all axes from -r to r.

Parameters:

r - limits of each axis

setAxesLength

public void setAxesLength(float xL,
                          float xU,
                          float yL,
                          float yU,
                          float zL,
                          float zU)

Sets the lengths of the axes.

Parameters:

xL - lower limit of x axis

xU - upper limit of x axis

yL - lower limit of y axis

yU - upper limit of y axis

zL - lower limit of z axis

zU - upper limit of z axis

setAxesVisible

public void setAxesVisible(boolean s)

Indicates whether axes are visible

Parameters:

s - visibility state

setFontSize

public void setFontSize(int s)

Sets the font size for the axes labels

Parameters:

s - font size for the axes labels

setIsosurfaceVisible

public void setIsosurfaceVisible(int nAtom,
                                 int nOrb,
                                 int nIso,
                                 boolean s)

Indicates whether an isosurface is visible

Parameters:

nGroup - group in which isosurface exists

nSurface - isosurface to be affected

s - new state for visibility

setNucleusColor

public void setNucleusColor(int n,
                            float x,
                            float y,
                            float z)

Sets the emissive color of the nucleus of the specified atom and sets the nucleus to be visible

Parameters:

n - index of atom

x - x component

y - y component

z - z component

setNucleusVisible

public void setNucleusVisible(int n,
                              boolean s)

Determines whether the nucleus is visible as a small where sphere

Parameters:

n - index of atom

s - visibility state

setOrbitalActive

public void setOrbitalActive(int nAtom,
                             int nOrb)

The orbital's BranchGroup is compiled and added to the atom's Switch node.

Parameters:

nAtom - index of atom containing the orbital

nOrb - index of the orbital to be made active

setOrbitalTransparency

public void setOrbitalTransparency(int nAtom,
                                   int nOrb,
                                   float t)

Sets the transparency of an orbital

Parameters:

nAtom - index of atom containing the orbital

nOrb - index of the orbital

t - transparency

setPosition

public void setPosition(double x,
                        double y,
                        double z)

Sets the position of the root transform.

Parameters:

x - position of the atom along the x axis

y - position of the atom along the y axis

z - position of the atom along the z axis

setView

public void setView(double x,
                    double y,
                    double z,
                    double a)

Sets the orientation to a specific value.

Parameters:

x - x-component of the axis of rotation

y - y-component of the axis of rotation

z - z-component of the axis of rotation

a - angle of rotation (right hand rule)

setViewDistance

public void setViewDistance(float r)

Sets the viewing distance.

Parameters:

r - new viewing distance (along z axis)

See Also:

setBoundsRadius

setXView

public void setXView()

Sets the orientation to view down the x axis.

setYView

public void setYView()

Sets the orientation to view down the y axis.

setZView

public void setZView()

Sets the orientation to view down the z axis. (This is the original orientation.)

setWhichOrbital

public void setWhichOrbital(int nAtom,
                            int nOrb)

For the selected atom, specifies the orbital to be displayed.

Parameters:

nAtom - atom that contains the orbital

nOrb - orbital to be displayed Special values for nOrb:
-1 (CHILD_NONE) no orbitals shown
-2 (CHILD_ALL) all orbitals shown
-3 (CHILD_MASK) use setChildMask to control which orbitals are shown