Class MolecGraphics

java.lang.Object
  |
  +--MolecGraphics

public class MolecGraphics

extends java.lang.Object

Responsible for drawing and updating the molecule graphics.

Field Summary

static int	BACK Enumeration indicating back light
javax.media.j3d.DirectionalLight	backLight DirectionalLight for back light
static int	BGR Enumeration for color gradient blue-green-red
static int	BONDS Enumeration indicating Bonds drawing representation
static int	BW Enumeration for color gradient black-white
static int	BWR Enumeration for color gradient blue-white-red
static int	CARTOON Enumeration indicating mixed drawing representations
ColorCategory	cc ColorCategory for determining and changing colors
static int	CHAIN Enumeration indicating coloring by atom chain
static int	CPK Enumeration indicating CPK drawing representation
javax.media.j3d.ExponentialFog	exponentialFog Fog for depth cueing
static int	FRONT Enumeration indicating front light
javax.media.j3d.DirectionalLight	frontLight DirectionalLight for front light
static int	INDEX Enumeration indicating coloring by atom index
static int	LICORICE Enumeration indicating Cartoon drawing representation
static int	LINES Enumeration indicating Lines drawing representation
static int	LOWER Enumeration indicating lower light
javax.media.j3d.DirectionalLight	lowerLight DirectionalLight for lower light
javax.media.j3d.BranchGroup	m_bgCalculating
javax.media.j3d.BranchGroup	m_bgLoading
util.SoftHashMap	m_map SoftHashMap for storing BranchGroups
java.lang.String	m_strFilename filename of the current molecule
static int	MIX Enumeration indicating Licorice drawing representation
static int	NAME Enumeration indicating coloring by atom name
static int	RESNAME Enumeration indicating coloring by atom residue
static int	RGB Enumeration for color gradient red-green-blue
static int	RWB Enumeration for color gradient red-white-blue
static int	SEGNAME Enumeration indicating coloring by atom segment
static int	STEREO_OFF Enumeration indicating Stereo mode off
static int	STEREO_ON Enumeration indicating Stereo mode on
static int	STRUCTURE Enumeration indicating coloring by structure
static int	TRACE Enumeration indicating Trace drawing representation
static int	TUBE Enumeration indicating Tube drawing representation
static int	UPPER Enumeration indicating upper light
javax.media.j3d.DirectionalLight	upperLight DirectionalLight for upper light
static int	VDW Enumeration indicating VDW drawing representation
static int	VRML Enumeration indicating a VRML scene
static int	WB Enumeration for color gradient white-black

Constructor Summary

MolecGraphics()
Constructor

Method Summary

void	addUtilities(javax.media.j3d.BranchGroup objRoot) Adds lights, rotations to the main branch group
void	changeColors(Molecule molec, int rep, int newScheme) Changes the color of an already drawn molecule
void	changeColorsInBranchGroup(javax.media.j3d.BranchGroup bg, Molecule molec, int rep, int newScheme) Changes the color for a BranchGroup containing a molecule (or part of a molecule)
void	changeDepth(int on) Toggles depth cueing
void	changeGradient(int grad) Sets gradient based on the selected option
void	changeLights(int light) Turns a light in the scene on or off
void	changeStereoMode(int mode) Sets the stereo mode
static javax.media.j3d.Appearance	createAPR(float r, float g, float b) Creates an Appearance with the given color uses default shininess, etc
javax.media.j3d.BranchGroup	createSceneGraph(Molecule molecule, int rep, int colorScheme, java.util.Vector v) Creates the entire sceneGraph used when changing molecules
IndexedBranchGroup	drawAllCylinders(Molecule molecule, int colorScheme, float scale) Draws the bonds of a molecule as cylinders
javax.media.j3d.BranchGroup	drawAtoms(Molecule molec, java.util.Vector v) Draws atoms on a per atom basis
IndexedBranchGroup	drawBondAtom(Molecule molec, int colorScheme, float scale, int index) Draws an atom in Bond representation
javax.media.j3d.BranchGroup	drawBonds(Molecule molecule, int colorScheme) Draws line representation
javax.media.j3d.TransformGroup	drawCylinder(float[] coords, int startPt, int endPt, javax.media.j3d.Appearance currentAppearance, float scale, boolean full) Creates a single cylinder
javax.media.j3d.Shape3D	drawLineAtoms(Molecule molecule, PubSynchBean.DrawAtoms da) Draws some atoms of a molecule in Lines representation
javax.media.j3d.BranchGroup	drawMolecule(Molecule molecule, int rep, int colorScheme) Returns a branchGroup from the given molecule, with the given representation used when changing the representation.
javax.media.j3d.TransformGroup	drawOneSphere(Molecule molecule, int colorScheme, float scale, int index) Draws one atom as a sphere for a given molecule
javax.media.j3d.TransformGroup	drawOneSphere(Molecule molecule, int colorScheme, float scale, int index, boolean radScale) Draws one atom as a sphere for a given molecule
IndexedBranchGroup	drawSpheres(Molecule molecule, int colorScheme, float scale) Draws atoms as spheres for a given molecule
IndexedBranchGroup	drawSpheres(Molecule molecule, int colorScheme, float scale, boolean radScale) Draws atoms as spheres for a given molecule
javax.media.j3d.BranchGroup	drawTrace(Molecule molec, int colorScheme) Draws a molecule in Trace representation
javax.media.j3d.BranchGroup	drawTraceAtom(Molecule molec, int colorScheme, int index) Draws a specified atom in Trace representation
javax.media.j3d.BranchGroup	drawTube(Molecule molec, int colorScheme, float scale) Draws the molecule in Tube representation
javax.media.j3d.BranchGroup	drawTubeAtom(Molecule molec, int colorScheme, float scale, int index) Draw a single atom in Tube rep
float[]	getColorArray(Molecule molec, int scheme) Gets the array of colors for a LineArray
float[]	getColorArray(Molecule molec, int scheme, java.util.Vector v) Creates the array of colors for a LineArray
void	init(java.awt.Panel p) Initializes the scene and add it to the panel for display
void	loadVRMLFile(java.lang.String file)
static javax.media.j3d.BranchGroup	messageScreen(java.lang.String strMessage) Creates a quick message screen to display (such as while a molecule is being loaded and created)
int	redraw(Molecule molec, int rep, int colorScheme, boolean redrawScene) Redraws molecule.
int	redraw(Molecule molec, int rep, int colorScheme, boolean redrawScene, java.util.Vector v) Redraws molecule.
static javax.media.j3d.BranchGroup	titleScreen() Displays the JMV title screen

Methods inherited from class java.lang.Object

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

Field Detail

cc

public ColorCategory cc

ColorCategory for determining and changing colors

frontLight

public javax.media.j3d.DirectionalLight frontLight

DirectionalLight for front light

backLight

public javax.media.j3d.DirectionalLight backLight

DirectionalLight for back light

upperLight

public javax.media.j3d.DirectionalLight upperLight

DirectionalLight for upper light

lowerLight

public javax.media.j3d.DirectionalLight lowerLight

DirectionalLight for lower light

exponentialFog

public javax.media.j3d.ExponentialFog exponentialFog

Fog for depth cueing

STEREO_OFF

public static final int STEREO_OFF

Enumeration indicating Stereo mode off

See Also:

Constant Field Values

STEREO_ON

public static final int STEREO_ON

Enumeration indicating Stereo mode on

See Also:

Constant Field Values

LINES

public static final int LINES

Enumeration indicating Lines drawing representation

See Also:

Constant Field Values

VDW

public static final int VDW

Enumeration indicating VDW drawing representation

See Also:

Constant Field Values

BONDS

public static final int BONDS

Enumeration indicating Bonds drawing representation

See Also:

Constant Field Values

CPK

public static final int CPK

Enumeration indicating CPK drawing representation

See Also:

Constant Field Values

TRACE

public static final int TRACE

Enumeration indicating Trace drawing representation

See Also:

Constant Field Values

TUBE

public static final int TUBE

Enumeration indicating Tube drawing representation

See Also:

Constant Field Values

LICORICE

public static final int LICORICE

Enumeration indicating Cartoon drawing representation

See Also:

Constant Field Values

CARTOON

public static final int CARTOON

Enumeration indicating mixed drawing representations

See Also:

Constant Field Values

MIX

public static final int MIX

Enumeration indicating Licorice drawing representation

See Also:

Constant Field Values

VRML

public static final int VRML

Enumeration indicating a VRML scene

See Also:

Constant Field Values

NAME

public static final int NAME

Enumeration indicating coloring by atom name

See Also:

Constant Field Values

INDEX

public static final int INDEX

Enumeration indicating coloring by atom index

See Also:

Constant Field Values

RESNAME

public static final int RESNAME

Enumeration indicating coloring by atom residue

See Also:

Constant Field Values

CHAIN

public static final int CHAIN

Enumeration indicating coloring by atom chain

See Also:

Constant Field Values

SEGNAME

public static final int SEGNAME

Enumeration indicating coloring by atom segment

See Also:

Constant Field Values

STRUCTURE

public static final int STRUCTURE

Enumeration indicating coloring by structure

See Also:

Constant Field Values

FRONT

public static final int FRONT

Enumeration indicating front light

See Also:

Constant Field Values

BACK

public static final int BACK

Enumeration indicating back light

See Also:

Constant Field Values

UPPER

public static final int UPPER

Enumeration indicating upper light

See Also:

Constant Field Values

LOWER

public static final int LOWER

Enumeration indicating lower light

See Also:

Constant Field Values

RGB

public static final int RGB

Enumeration for color gradient red-green-blue

See Also:

Constant Field Values

BGR

public static final int BGR

Enumeration for color gradient blue-green-red

See Also:

Constant Field Values

RWB

public static final int RWB

Enumeration for color gradient red-white-blue

See Also:

Constant Field Values

BWR

public static final int BWR

Enumeration for color gradient blue-white-red

See Also:

Constant Field Values

BW

public static final int BW

Enumeration for color gradient black-white

See Also:

Constant Field Values

WB

public static final int WB

Enumeration for color gradient white-black

See Also:

Constant Field Values

m_strFilename

public java.lang.String m_strFilename

filename of the current molecule

m_map

public util.SoftHashMap m_map

SoftHashMap for storing BranchGroups

m_bgLoading

public javax.media.j3d.BranchGroup m_bgLoading

m_bgCalculating

public javax.media.j3d.BranchGroup m_bgCalculating

Constructor Detail

MolecGraphics

public MolecGraphics()

Constructor

Method Detail

createAPR

public static javax.media.j3d.Appearance createAPR(float r,
                                                   float g,
                                                   float b)

Creates an Appearance with the given color uses default shininess, etc

Parameters:

r - red component

g - green component

b - blue component

Returns:

an Appearance with the rgb color and default shininess

changeGradient

public void changeGradient(int grad)

Sets gradient based on the selected option

Parameters:

grad - the gradient enumeration to use

drawBonds

public javax.media.j3d.BranchGroup drawBonds(Molecule molecule,
                                             int colorScheme)

Draws line representation

Parameters:

molecule - the molecule to draw

colorScheme - the color scheme to use

Returns:

a BranchGroup that represents molecule drawn in line representation

drawLineAtoms

public javax.media.j3d.Shape3D drawLineAtoms(Molecule molecule,
                                             PubSynchBean.DrawAtoms da)

Draws some atoms of a molecule in Lines representation

Parameters:

molecule - the molecule to draw

da - the DrawAtoms containing the color scheme and Vector of which atoms to draw

Returns:

a Shape3D containing the atoms listed in 'da' drawn in Lines representation

See Also:

PubSynchBean.DrawAtoms

drawMolecule

public javax.media.j3d.BranchGroup drawMolecule(Molecule molecule,
                                                int rep,
                                                int colorScheme)

Returns a branchGroup from the given molecule, with the given representation used when changing the representation.

Parameters:

molecule - the molecule to draw

rep - the representation (Lines, VDW, etc)

colorScheme - the color scheme to use

Returns:

a BranchGroup that contains the Java3D objects for displaying this molecule

createSceneGraph

public javax.media.j3d.BranchGroup createSceneGraph(Molecule molecule,
                                                    int rep,
                                                    int colorScheme,
                                                    java.util.Vector v)

Creates the entire sceneGraph used when changing molecules

Parameters:

molecule - the new Molecule object to draw

rep - the representation (lines, vdw, etc).

colorScheme - the colorization to use when coloring atoms

v - Vector of PubSynchBean.DrawAtoms's. Only used if rep == MIX.

Returns:

the BranchGroup for the new Molecule

addUtilities

public void addUtilities(javax.media.j3d.BranchGroup objRoot)

Adds lights, rotations to the main branch group

Parameters:

objRoot - the main branchGroup

init

public void init(java.awt.Panel p)

Initializes the scene and add it to the panel for display

Parameters:

p - Panel to add scene to

redraw

public int redraw(Molecule molec,
                  int rep,
                  int colorScheme,
                  boolean redrawScene)

Redraws molecule. Used when molecule changes.

Parameters:

molec - the new molecule to draw

rep - the representation

colorScheme - the color scheme to use

redrawScene - redraws the entire scene if true (entirely new molecule), else just redraws the molecule (new representation of already drawn molecule)

redraw

public int redraw(Molecule molec,
                  int rep,
                  int colorScheme,
                  boolean redrawScene,
                  java.util.Vector v)

Redraws molecule. Used when molecule changes.

Parameters:

molec - the new molecule to draw

rep - the representation

colorScheme - the color scheme to use

redrawScene - redraws the entire scene if true (entirely new molecule), else just redraws the molecule (new representation of already drawn molecule)

v - Vector of PubSynchBean.DrawAtoms's. Only used if rep==MIX. (otherwise null)

changeStereoMode

public void changeStereoMode(int mode)

Sets the stereo mode

Parameters:

mode - STEREO_ON to turn it on or STEREO_OFF to turn it off

changeColorsInBranchGroup

public void changeColorsInBranchGroup(javax.media.j3d.BranchGroup bg,
                                      Molecule molec,
                                      int rep,
                                      int newScheme)

Changes the color for a BranchGroup containing a molecule (or part of a molecule)

Parameters:

bg - the BranchGroup to change the color of

molec - the molecule to be colored

rep - the current representation of the molecule

newScheme - the new color scheme to use in coloring the molecule

changeColors

public void changeColors(Molecule molec,
                         int rep,
                         int newScheme)

Changes the color of an already drawn molecule

Parameters:

molec - the molecule to be colored

rep - the current representation of the molecule

newScheme - the new color scheme to use in coloring the molecule

getColorArray

public float[] getColorArray(Molecule molec,
                             int scheme,
                             java.util.Vector v)

Creates the array of colors for a LineArray

Parameters:

molec - the Molecule to get the colors for

scheme - the color scheme to get colors for

v - Vector of Integers of which atoms to get colors for

Returns:

a float array of rgb colors to color the LineArray

getColorArray

public float[] getColorArray(Molecule molec,
                             int scheme)

Gets the array of colors for a LineArray

Parameters:

molec - the Molecule to get the colors for

scheme - the color scheme to get colors for

Returns:

a float array of rgb colors to color the LineArray

drawCylinder

public javax.media.j3d.TransformGroup drawCylinder(float[] coords,
                                                   int startPt,
                                                   int endPt,
                                                   javax.media.j3d.Appearance currentAppearance,
                                                   float scale,
                                                   boolean full)

Creates a single cylinder

Parameters:

coords - the coordinates for the molecule

startPt - the index of the first atom

endPt - the index of the second atom

currentAppearance - the Appearance used to color the cylinder

scale - factor to scale the cylinder radius. The original radius is determined in MolecGraphicsProperties.

full - if true, draws a full cylinder from startPt to endPt if false, draws a cylinder starting at startPt, and ending 1/2 way between startPt and endPt.

Returns:

a TransformGroup whose child is the Cylinder

drawAllCylinders

public IndexedBranchGroup drawAllCylinders(Molecule molecule,
                                           int colorScheme,
                                           float scale)

Draws the bonds of a molecule as cylinders

Parameters:

molecule - the molecule to draw bonds for

colorScheme - the color scheme used to color the cylinders

scale - factor to scale the cylinder radius. The original radius is determined in MolecGraphicsProperties.

Returns:

a BranchGroup containing all the rotated Cylinders to that represent the bonds of the molecule

drawSpheres

public IndexedBranchGroup drawSpheres(Molecule molecule,
                                      int colorScheme,
                                      float scale)

Draws atoms as spheres for a given molecule

Parameters:

molecule - the Molecule to draw

colorScheme - the color scheme used to color the spheres

scale - the factor to scale the spheres. The original sizes are determined by atom name

Returns:

a BranchGroup containing all the translated Spheres representing the atoms of this molecule

drawSpheres

public IndexedBranchGroup drawSpheres(Molecule molecule,
                                      int colorScheme,
                                      float scale,
                                      boolean radScale)

Draws atoms as spheres for a given molecule

Parameters:

molecule - the Molecule to draw

colorScheme - the color scheme used to color the spheres

scale - the factor to scale the spheres. The original sizes are determined by atom name

radScale - true if scale based on the atom type, false if not

Returns:

a BranchGroup containing all the translated Spheres representing the atoms of this molecule

drawOneSphere

public javax.media.j3d.TransformGroup drawOneSphere(Molecule molecule,
                                                    int colorScheme,
                                                    float scale,
                                                    int index)

Draws one atom as a sphere for a given molecule

Parameters:

molecule - the Molecule the atom is in

colorScheme - the color scheme used to color the sphere

scale - the factor to scale the sphere. The original sizes are determined by atom name

index - the atom index of the atom to draw

Returns:

a BranchGroup containing a translated Sphere representing an atom of this molecule

drawOneSphere

public javax.media.j3d.TransformGroup drawOneSphere(Molecule molecule,
                                                    int colorScheme,
                                                    float scale,
                                                    int index,
                                                    boolean radScale)

Draws one atom as a sphere for a given molecule

Parameters:

molecule - the Molecule the atom is in

colorScheme - the color scheme used to color the sphere

scale - the factor to scale the sphere. The original sizes are determined by atom name

index - the atom index of the atom to draw

radScale - true if you scale based on the atom type, false if not

Returns:

a BranchGroup containing a translated Sphere representing an atom of this molecule

drawTrace

public javax.media.j3d.BranchGroup drawTrace(Molecule molec,
                                             int colorScheme)

Draws a molecule in Trace representation

Parameters:

molec - the molecule to draw

colorScheme - the color scheme to use

Returns:

a BranchGroup containing the Molecule drawn in Trace representation

drawTraceAtom

public javax.media.j3d.BranchGroup drawTraceAtom(Molecule molec,
                                                 int colorScheme,
                                                 int index)

Draws a specified atom in Trace representation

Parameters:

molec - the molecule the atom is in

colorScheme - the color scheme used to color the atom

index - the atom index of the atom

Returns:

a BranchGroup containing the atom drawn in Trace representation

drawBondAtom

public IndexedBranchGroup drawBondAtom(Molecule molec,
                                       int colorScheme,
                                       float scale,
                                       int index)

Draws an atom in Bond representation

Parameters:

molec - the molecule the atom is in

colorScheme - the color scheme to use

scale - the scale of the cylinder radius

index - the atom index of the atom to draw

Returns:

an IndexedBranchGroup containing the atom in Bond representation

drawTube

public javax.media.j3d.BranchGroup drawTube(Molecule molec,
                                            int colorScheme,
                                            float scale)

Draws the molecule in Tube representation

Parameters:

molec - the molecule to draw

colorScheme - the color scheme to use

scale - the scale for the cylinder radius

Returns:

a BranchGroup containing the molecule drawn in Tube representation

drawTubeAtom

public javax.media.j3d.BranchGroup drawTubeAtom(Molecule molec,
                                                int colorScheme,
                                                float scale,
                                                int index)

Draw a single atom in Tube rep

Parameters:

molec - the molecule

colorScheme - the color scheme used to color the atom

scale - the scale for cylinder radius

index - the index of the atom to draw

Returns:

a BranchGroup containing the atom drawn in Tube representation

drawAtoms

public javax.media.j3d.BranchGroup drawAtoms(Molecule molec,
                                             java.util.Vector v)

Draws atoms on a per atom basis

Parameters:

molec - the molecule to draw

v - the Vector of PubSynch.DrawAtoms's to draw

Returns:

a BranchGroup containing the Molecule drawn as the DrawAtoms's in Vector v specify.

See Also:

PubSynchBean.DrawAtoms

changeLights

public void changeLights(int light)

Turns a light in the scene on or off

Parameters:

light - the index of the light to toggle

changeDepth

public void changeDepth(int on)

Toggles depth cueing

Parameters:

on - 1 if it is to be turned on, else 0

titleScreen

public static javax.media.j3d.BranchGroup titleScreen()

Displays the JMV title screen

Returns:

a BranchGroup displaying the JMV title screen and credits

messageScreen

public static javax.media.j3d.BranchGroup messageScreen(java.lang.String strMessage)

Creates a quick message screen to display (such as while a molecule is being loaded and created)

Returns:

a BranchGroup displaying a message screen

loadVRMLFile

public void loadVRMLFile(java.lang.String file)