Package org.jmol.g3d

Class Graphics3D

java.lang.Object

org.jmol.util.GData

org.jmol.g3d.Graphics3D

public final class Graphics3D
extends GData

Provides high-level graphics primitives for 3D visualization for the software renderers. These methods should not have to be used with WebGL or OpenGL or other hardware accelerators. This module is linked to via reflection from org.jmol.viewer.Viewer Bob Hanson 9/2/2012

A pure software implementation of a 3D graphics engine. No hardware required. Depending upon what you are rendering ... some people say it is pretty fast.

Field Summary

Fields

Modifier and Type	Field	Description
protected int[]	pbuf
protected int[]	pbufT
static java.util.Comparator<org.jmol.g3d.TextString>	sort
protected int	translucencyMask
protected boolean	translucentCoverOnly
protected int[]	zbuf
protected int[]	zbufT
protected int	zMargin

Fields inherited from class org.jmol.util.GData

antialiasEnabled, antialiasThisFrame, apiPlatform, argbCurrent, backgroundImage, bgcolor, bufferSize, changeableColixMap, colixCurrent, depth, displayMaxX, displayMaxY, displayMinX, displayMinY, ENDCAPS_FLAT, ENDCAPS_NONE, ENDCAPS_OPEN, ENDCAPS_OPENEND, ENDCAPS_SPHERICAL, EXPORT_CARTESIAN, EXPORT_NOT, EXPORT_RAYTRACER, graphicsForMetrics, height, inGreyscaleMode, isPass2, newAntialiasing, newWindowHeight, newWindowWidth, slab, width, windowHeight, windowWidth, xGT, xLast, xLT, yGT, yLast, yLT, zDepth, zGT, zLT, zShadeB, zShadeG, zShadePower, zShadeR, zSlab

Constructor Summary

Constructors

Constructor	Description
Graphics3D()

Method Summary

Modifier and Type	Method	Description
void	applyAnaglygh(EnumStereoMode stereoMode, int[] stereoColors)
void	applyBlueAnaglyph()
void	applyCustomAnaglyph(int[] stereoColors)
void	applyCyanAnaglyph()
void	applyGreenAnaglyph()
void	beginRendering(Matrix3f rotationMatrix)
boolean	canDoTriangles()
boolean	checkTranslucent(boolean isAlphaTranslucent)
void	clear()
void	clearFontCache()
boolean	currentlyRendering()
void	destroy()
void	drawBond(Point3f atomA, Point3f atomB, short colixA, short colixB, byte endcaps, short mad, int bondOrder)
void	drawDashedLine(int run, int rise, Point3i pointA, Point3i pointB)
void	drawDottedLine(Point3i pointA, Point3i pointB)
boolean	drawEllipse(Point3f ptAtom, Point3f ptX, Point3f ptY, boolean fillArc, boolean wireframeOnly)
void	drawFilledCircle(short colixRing, short colixFill, int diameter, int x, int y, int z)
void	drawHermite4(int tension, Point3i s0, Point3i s1, Point3i s2, Point3i s3)
void	drawHermite7(boolean fill, boolean border, int tension, Point3i s0, Point3i s1, Point3i s2, Point3i s3, Point3i s4, Point3i s5, Point3i s6, Point3i s7, int aspectRatio, short colixBack)
void	drawImage(java.lang.Object objImage, int x, int y, int z, int zSlab, short bgcolix, int width, int height)
void	drawLine(short colixA, short colixB, int x1, int y1, int z1, int x2, int y2, int z2)
void	drawLineAB(Point3i pointA, Point3i pointB)
void	drawLineXYZ(int x1, int y1, int z1, int x2, int y2, int z2)
void	drawPixel(int x, int y, int z)
void	drawPoints(int count, int[] coordinates, int scale)
void	drawQuadrilateral(short colix, Point3i screenA, Point3i screenB, Point3i screenC, Point3i screenD)
void	drawRect(int x, int y, int z, int zSlab, int rWidth, int rHeight)	draws a rectangle
void	drawString(java.lang.String str, JmolFont font3d, int xBaseline, int yBaseline, int z, int zSlab, short bgColix)	draws the specified string in the current font.
void	drawStringNoSlab(java.lang.String str, JmolFont font3d, int xBaseline, int yBaseline, int z, short bgColix)	draws the specified string in the current font.
void	drawSurface(MeshSurface meshSurface, short colix)
void	drawTriangle3C(Point3i screenA, short colixA, Point3i screenB, short colixB, Point3i screenC, short colixC, int check)
void	drawTriangle3I(Point3i screenA, Point3i screenB, Point3i screenC, int check)
void	endRendering()
void	fillConeSceen3f(byte endcap, int screenDiameter, Point3f screenBase, Point3f screenTip)
void	fillConeScreen(byte endcap, int screenDiameter, Point3i screenBase, Point3i screenTip, boolean isBarb)
void	fillCylinder(byte endcaps, int diameter, Point3i screenA, Point3i screenB)
void	fillCylinderBits(byte endcaps, int diameter, Point3f screenA, Point3f screenB)
void	fillCylinderScreen(byte endcaps, int diameter, int xA, int yA, int zA, int xB, int yB, int zB)
void	fillCylinderScreen3I(byte endcaps, int diameter, Point3i screenA, Point3i screenB, Point3f pt0f, Point3f pt1f, float radius)
void	fillCylinderXYZ(short colixA, short colixB, byte endcaps, int diameter, int xA, int yA, int zA, int xB, int yB, int zB)
void	fillEllipsoid(Point3f center, Point3f[] points, int x, int y, int z, int diameter, Matrix3f mToEllipsoidal, double[] coef, Matrix4f mDeriv, int selectedOctant, Point3i[] octantPoints)
void	fillHermite(int tension, int diameterBeg, int diameterMid, int diameterEnd, Point3i s0, Point3i s1, Point3i s2, Point3i s3)
void	fillQuadrilateral(Point3f screenA, Point3f screenB, Point3f screenC, Point3f screenD)
void	fillQuadrilateral3i(Point3i screenA, short colixA, short normixA, Point3i screenB, short colixB, short normixB, Point3i screenC, short colixC, short normixC, Point3i screenD, short colixD, short normixD)
void	fillRect(int x, int y, int z, int zSlab, int widthFill, int heightFill)	fills background rectangle for label
void	fillSphere(int diameter, Point3f center)	fills a solid sphere
void	fillSphereI(int diameter, Point3i center)	fills a solid sphere
void	fillSphereXYZ(int diameter, int x, int y, int z)	fills a solid sphere
void	fillTriangle(Point3i screenA, short colixA, short normixA, Point3i screenB, short colixB, short normixB, Point3i screenC, short colixC, short normixC, float factor)
void	fillTriangle3CN(Point3i screenA, short colixA, short normixA, Point3i screenB, short colixB, short normixB, Point3i screenC, short colixC, short normixC)
void	fillTriangle3f(Point3f screenA, Point3f screenB, Point3f screenC, boolean setNoisy)
void	fillTriangle3i(Point3i screenA, Point3i screenB, Point3i screenC, Point3f ptA, Point3f ptB, Point3f ptC)
void	fillTriangleTwoSided(short normix, int xScreenA, int yScreenA, int zScreenA, int xScreenB, int yScreenB, int zScreenB, int xScreenC, int yScreenC, int zScreenC)
java.lang.String	finalizeOutput()
java.lang.String	getExportName()
int	getExportType()
JmolFont	getFont3DCurrent()
GData	getGData()	underlying GData object handles all general graphics setup.
double	getPrivateKey()
java.lang.Object	getScreenImage()
int	getShadeIndex(short normix)
Vector3f[]	getTransformedVertexVectors()
boolean	hasContent()
boolean	haveTranslucentObjects()
void	initialize(ApiPlatform apiPlatform)
boolean	isCartesianExport()
boolean	isDirectedTowardsCamera(short normix)
void	plotImage(int x, int y, int z, java.lang.Object image, Graphics3D jmolRenderer, short bgcolix, int width, int height)
void	plotImagePixel(int argb, int x, int y, int z, int shade, int bgargb)
void	plotPixelClippedP3i(Point3i screen)
void	plotText(int x, int y, int z, int argb, int bgargb, java.lang.String text, JmolFont font3d, Graphics3D jmolRenderer)
void	releaseScreenImage()
void	renderAllStrings(java.lang.Object jmolRenderer)
void	renderBackground(Graphics3D jmolRenderer)
void	renderCrossHairs(int[] minMax, int screenWidth, int screenHeight, Point3f navOffset, float navDepth)
void	setBackgroundTransparent(boolean TF)
boolean	setColix(short colix)	sets current color from colix color index
void	setColor(int argb)
void	setFont(JmolFont font3d)
void	setFontFid(byte fid)
void	setNoisySurfaceShade(Point3i screenA, Point3i screenB, Point3i screenC)	used by CartoonRenderer (DNA surface) and GeoSurfaceRenderer (face) to assign a noisy shade to the surface it will render
boolean	setPass2(boolean antialiasTranslucent)
void	setRotationMatrix(Matrix3f rotationMatrix)
void	setTempZSlab(int zSlab)
void	setTranslucentCoverOnly(boolean TF)
void	setWindowParameters(int width, int height, boolean antialias)
void	setZShade(boolean zShade, int zSlab, int zDepth, int zShadePower)
void	snapshotAnaglyphChannelBytes()
void	volumeRender(boolean TF)
void	volumeRender4(int diameter, int x, int y, int z)

Methods inherited from class org.jmol.util.GData

changeColixArgb, clipCode, clipCode3, getAmbientPercent, getBgColixes, getChangeableColix, getColorArgbOrGray, getDepth, getDiffusePercent, getFont3D, getFont3DFS, getFont3DFSS, getFont3DScaled, getFontFid, getFontFidFS, getFontStyleID, getLightSource, getPhongExponent, getRenderHeight, getRenderWidth, getShades, getSlab, getSpecular, getSpecularExponent, getSpecularPercent, getSpecularPower, isAntialiased, isClipped, isClipped3, isClippedXY, isClippedZ, isDisplayAntialiased, isInDisplayRange, isPass2, plotImage, roundInt, setAmbientPercent, setBackgroundArgb, setBackgroundImage, setDepth, setDiffusePercent, setGreyscaleMode, setNewWindowParametersForExport, setPhongExponent, setSlab, setSpecular, setSpecularExponent, setSpecularPercent, setSpecularPower, setWidthHeight

Methods inherited from class java.lang.Object

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

Field Detail

translucentCoverOnly

protected boolean translucentCoverOnly

pbuf

protected int[] pbuf

pbufT

protected int[] pbufT

zbuf

protected int[] zbuf

zbufT

protected int[] zbufT

translucencyMask

protected int translucencyMask

zMargin

protected int zMargin

sort

public static java.util.Comparator<org.jmol.g3d.TextString> sort

Constructor Detail

Graphics3D

public Graphics3D()

Method Detail

clear

public void clear()

Overrides:

clear in class GData

destroy

public void destroy()

Overrides:

destroy in class GData

getGData

public GData getGData()

underlying GData object handles all general graphics setup.

Returns:

"this" in the case of Graphics3D and this.g3d in the case of Export3D

setTranslucentCoverOnly

public void setTranslucentCoverOnly(boolean TF)

initialize

public void initialize(ApiPlatform apiPlatform)

Overrides:

initialize in class GData

currentlyRendering

public boolean currentlyRendering()

setWindowParameters

public void setWindowParameters(int width,
                                int height,
                                boolean antialias)

Overrides:

setWindowParameters in class GData

checkTranslucent

public boolean checkTranslucent(boolean isAlphaTranslucent)

beginRendering

public void beginRendering(Matrix3f rotationMatrix)

Overrides:

beginRendering in class GData

setBackgroundTransparent

public void setBackgroundTransparent(boolean TF)

Overrides:

setBackgroundTransparent in class GData

setPass2

public boolean setPass2(boolean antialiasTranslucent)

Overrides:

setPass2 in class GData

Returns:

true if need a second (translucent) pass

endRendering

public void endRendering()

Overrides:

endRendering in class GData

applyAnaglygh

public void applyAnaglygh(EnumStereoMode stereoMode,
                          int[] stereoColors)

Overrides:

applyAnaglygh in class GData

snapshotAnaglyphChannelBytes

public void snapshotAnaglyphChannelBytes()

Overrides:

snapshotAnaglyphChannelBytes in class GData

applyCustomAnaglyph

public void applyCustomAnaglyph(int[] stereoColors)

applyGreenAnaglyph

public void applyGreenAnaglyph()

applyBlueAnaglyph

public void applyBlueAnaglyph()

applyCyanAnaglyph

public void applyCyanAnaglyph()

getScreenImage

public java.lang.Object getScreenImage()

Overrides:

getScreenImage in class GData

releaseScreenImage

public void releaseScreenImage()

Overrides:

releaseScreenImage in class GData

haveTranslucentObjects

public boolean haveTranslucentObjects()

setTempZSlab

public void setTempZSlab(int zSlab)

setZShade

public void setZShade(boolean zShade,
                      int zSlab,
                      int zDepth,
                      int zShadePower)

Overrides:

setZShade in class GData

Parameters:

zShade - whether to shade along z front to back

zSlab - for zShade

zDepth - for zShade

hasContent

public boolean hasContent()

setColor

public void setColor(int argb)

Overrides:

setColor in class GData

setColix

public boolean setColix(short colix)

sets current color from colix color index

Overrides:

setColix in class GData

Parameters:

colix - the color index

Returns:

true or false if this is the right pass

drawFilledCircle

public void drawFilledCircle(short colixRing,
                             short colixFill,
                             int diameter,
                             int x,
                             int y,
                             int z)

volumeRender4

public void volumeRender4(int diameter,
                          int x,
                          int y,
                          int z)

fillSphereXYZ

public void fillSphereXYZ(int diameter,
                          int x,
                          int y,
                          int z)

fills a solid sphere

Parameters:

diameter - pixel count

x - center x

y - center y

z - center z

volumeRender

public void volumeRender(boolean TF)

fillSphereI

public void fillSphereI(int diameter,
                        Point3i center)

fills a solid sphere

Parameters:

diameter - pixel count

center - javax.vecmath.Point3i defining the center

fillSphere

public void fillSphere(int diameter,
                       Point3f center)

fills a solid sphere

Parameters:

diameter - pixel count

center - a javax.vecmath.Point3f ... floats are casted to ints

fillEllipsoid

public void fillEllipsoid(Point3f center,
                          Point3f[] points,
                          int x,
                          int y,
                          int z,
                          int diameter,
                          Matrix3f mToEllipsoidal,
                          double[] coef,
                          Matrix4f mDeriv,
                          int selectedOctant,
                          Point3i[] octantPoints)

drawRect

public void drawRect(int x,
                     int y,
                     int z,
                     int zSlab,
                     int rWidth,
                     int rHeight)

draws a rectangle

Parameters:

x - upper left x

y - upper left y

z - upper left z

zSlab - z for slab check (for set labelsFront)

rWidth - pixel count

rHeight - pixel count

fillRect

public void fillRect(int x,
                     int y,
                     int z,
                     int zSlab,
                     int widthFill,
                     int heightFill)

fills background rectangle for label

Parameters:

x - upper left x

y - upper left y

z - upper left z

zSlab - z value for slabbing

widthFill - pixel count

heightFill - pixel count

drawString

public void drawString(java.lang.String str,
                       JmolFont font3d,
                       int xBaseline,
                       int yBaseline,
                       int z,
                       int zSlab,
                       short bgColix)

draws the specified string in the current font. no line wrapping -- axis, labels, measures

Parameters:

str - the String

font3d - the Font3D

xBaseline - baseline x

yBaseline - baseline y

z - baseline z

zSlab - z for slab calculation

bgColix -

drawStringNoSlab

public void drawStringNoSlab(java.lang.String str,
                             JmolFont font3d,
                             int xBaseline,
                             int yBaseline,
                             int z,
                             short bgColix)

draws the specified string in the current font. no line wrapping -- echo, frank, hover, molecularOrbital, uccage

Parameters:

str - the String

font3d - the Font3D

xBaseline - baseline x

yBaseline - baseline y

z - baseline z

bgColix -

renderAllStrings

public void renderAllStrings(java.lang.Object jmolRenderer)

Overrides:

renderAllStrings in class GData

plotText

public void plotText(int x,
                     int y,
                     int z,
                     int argb,
                     int bgargb,
                     java.lang.String text,
                     JmolFont font3d,
                     Graphics3D jmolRenderer)

Overrides:

plotText in class GData

bgargb - TODO

drawImage

public void drawImage(java.lang.Object objImage,
                      int x,
                      int y,
                      int z,
                      int zSlab,
                      short bgcolix,
                      int width,
                      int height)

plotImage

public void plotImage(int x,
                      int y,
                      int z,
                      java.lang.Object image,
                      Graphics3D jmolRenderer,
                      short bgcolix,
                      int width,
                      int height)

setFontFid

public void setFontFid(byte fid)

Overrides:

setFontFid in class GData

setFont

public void setFont(JmolFont font3d)

Overrides:

setFont in class GData

getFont3DCurrent

public JmolFont getFont3DCurrent()

Overrides:

getFont3DCurrent in class GData

drawPixel

public void drawPixel(int x,
                      int y,
                      int z)

drawPoints

public void drawPoints(int count,
                       int[] coordinates,
                       int scale)

drawDashedLine

public void drawDashedLine(int run,
                           int rise,
                           Point3i pointA,
                           Point3i pointB)

drawDottedLine

public void drawDottedLine(Point3i pointA,
                           Point3i pointB)

drawLineXYZ

public void drawLineXYZ(int x1,
                        int y1,
                        int z1,
                        int x2,
                        int y2,
                        int z2)

drawLine

public void drawLine(short colixA,
                     short colixB,
                     int x1,
                     int y1,
                     int z1,
                     int x2,
                     int y2,
                     int z2)

drawLineAB

public void drawLineAB(Point3i pointA,
                       Point3i pointB)

fillCylinderXYZ

public void fillCylinderXYZ(short colixA,
                            short colixB,
                            byte endcaps,
                            int diameter,
                            int xA,
                            int yA,
                            int zA,
                            int xB,
                            int yB,
                            int zB)

fillCylinderScreen

public void fillCylinderScreen(byte endcaps,
                               int diameter,
                               int xA,
                               int yA,
                               int zA,
                               int xB,
                               int yB,
                               int zB)

fillCylinderScreen3I

public void fillCylinderScreen3I(byte endcaps,
                                 int diameter,
                                 Point3i screenA,
                                 Point3i screenB,
                                 Point3f pt0f,
                                 Point3f pt1f,
                                 float radius)

fillCylinder

public void fillCylinder(byte endcaps,
                         int diameter,
                         Point3i screenA,
                         Point3i screenB)

fillCylinderBits

public void fillCylinderBits(byte endcaps,
                             int diameter,
                             Point3f screenA,
                             Point3f screenB)

fillConeScreen

public void fillConeScreen(byte endcap,
                           int screenDiameter,
                           Point3i screenBase,
                           Point3i screenTip,
                           boolean isBarb)

fillConeSceen3f

public void fillConeSceen3f(byte endcap,
                            int screenDiameter,
                            Point3f screenBase,
                            Point3f screenTip)

drawHermite4

public void drawHermite4(int tension,
                         Point3i s0,
                         Point3i s1,
                         Point3i s2,
                         Point3i s3)

drawHermite7

public void drawHermite7(boolean fill,
                         boolean border,
                         int tension,
                         Point3i s0,
                         Point3i s1,
                         Point3i s2,
                         Point3i s3,
                         Point3i s4,
                         Point3i s5,
                         Point3i s6,
                         Point3i s7,
                         int aspectRatio,
                         short colixBack)

fillHermite

public void fillHermite(int tension,
                        int diameterBeg,
                        int diameterMid,
                        int diameterEnd,
                        Point3i s0,
                        Point3i s1,
                        Point3i s2,
                        Point3i s3)

drawTriangle3C

public void drawTriangle3C(Point3i screenA,
                           short colixA,
                           Point3i screenB,
                           short colixB,
                           Point3i screenC,
                           short colixC,
                           int check)

drawTriangle3I

public void drawTriangle3I(Point3i screenA,
                           Point3i screenB,
                           Point3i screenC,
                           int check)

fillTriangleTwoSided

public void fillTriangleTwoSided(short normix,
                                 int xScreenA,
                                 int yScreenA,
                                 int zScreenA,
                                 int xScreenB,
                                 int yScreenB,
                                 int zScreenB,
                                 int xScreenC,
                                 int yScreenC,
                                 int zScreenC)

fillTriangle3f

public void fillTriangle3f(Point3f screenA,
                           Point3f screenB,
                           Point3f screenC,
                           boolean setNoisy)

fillTriangle3i

public void fillTriangle3i(Point3i screenA,
                           Point3i screenB,
                           Point3i screenC,
                           Point3f ptA,
                           Point3f ptB,
                           Point3f ptC)

fillTriangle

public void fillTriangle(Point3i screenA,
                         short colixA,
                         short normixA,
                         Point3i screenB,
                         short colixB,
                         short normixB,
                         Point3i screenC,
                         short colixC,
                         short normixC,
                         float factor)

fillTriangle3CN

public void fillTriangle3CN(Point3i screenA,
                            short colixA,
                            short normixA,
                            Point3i screenB,
                            short colixB,
                            short normixB,
                            Point3i screenC,
                            short colixC,
                            short normixC)

drawQuadrilateral

public void drawQuadrilateral(short colix,
                              Point3i screenA,
                              Point3i screenB,
                              Point3i screenC,
                              Point3i screenD)

fillQuadrilateral

public void fillQuadrilateral(Point3f screenA,
                              Point3f screenB,
                              Point3f screenC,
                              Point3f screenD)

fillQuadrilateral3i

public void fillQuadrilateral3i(Point3i screenA,
                                short colixA,
                                short normixA,
                                Point3i screenB,
                                short colixB,
                                short normixB,
                                Point3i screenC,
                                short colixC,
                                short normixC,
                                Point3i screenD,
                                short colixD,
                                short normixD)

drawSurface

public void drawSurface(MeshSurface meshSurface,
                        short colix)

plotPixelClippedP3i

public void plotPixelClippedP3i(Point3i screen)

plotImagePixel

public void plotImagePixel(int argb,
                           int x,
                           int y,
                           int z,
                           int shade,
                           int bgargb)

setNoisySurfaceShade

public void setNoisySurfaceShade(Point3i screenA,
                                 Point3i screenB,
                                 Point3i screenC)

used by CartoonRenderer (DNA surface) and GeoSurfaceRenderer (face) to assign a noisy shade to the surface it will render

Overrides:

setNoisySurfaceShade in class GData

Parameters:

screenA -

screenB -

screenC -

renderBackground

public void renderBackground(Graphics3D jmolRenderer)

Overrides:

renderBackground in class GData

getExportType

public int getExportType()

getExportName

public java.lang.String getExportName()

canDoTriangles

public boolean canDoTriangles()

isCartesianExport

public boolean isCartesianExport()

finalizeOutput

public java.lang.String finalizeOutput()

drawBond

public void drawBond(Point3f atomA,
                     Point3f atomB,
                     short colixA,
                     short colixB,
                     byte endcaps,
                     short mad,
                     int bondOrder)

drawEllipse

public boolean drawEllipse(Point3f ptAtom,
                           Point3f ptX,
                           Point3f ptY,
                           boolean fillArc,
                           boolean wireframeOnly)

getPrivateKey

public double getPrivateKey()

clearFontCache

public void clearFontCache()

Overrides:

clearFontCache in class GData

getTransformedVertexVectors

public Vector3f[] getTransformedVertexVectors()

Overrides:

getTransformedVertexVectors in class GData

isDirectedTowardsCamera

public boolean isDirectedTowardsCamera(short normix)

Overrides:

isDirectedTowardsCamera in class GData

Returns:

true if front

setRotationMatrix

public void setRotationMatrix(Matrix3f rotationMatrix)

getShadeIndex

public int getShadeIndex(short normix)

renderCrossHairs

public void renderCrossHairs(int[] minMax,
                             int screenWidth,
                             int screenHeight,
                             Point3f navOffset,
                             float navDepth)

Parameters:

minMax -

screenWidth -

screenHeight -

navOffset -

navDepth -