org.jmol.shape
Class Mesh

java.lang.Object
  org.jmol.util.MeshSurface
      org.jmol.shape.Mesh

Direct Known Subclasses:

DrawMesh, IsosurfaceMesh

public class Mesh
extends MeshSurface

Field Summary

int	atomIndex
Object	cappingObject
int	checkByteCount
int	color
String	colorCommand
boolean	colorDensity
int[]	connections
int	diameter
boolean	drawTriangles
boolean	fillTriangles
boolean	frontOnly
boolean	havePlanarContours
boolean	haveXyPoints
int	index
boolean	insideOut
boolean	isTriangleSet
boolean	isTwoSided
boolean	isValid
Point3f	lattice
int	lighting
List<Point3f[]>	lineData
Mesh	linkedMesh
(package private) Matrix4f	mat4
short	meshColix
int	modelIndex
private int	normixCount
short[]	normixes
static String	PREVIOUS_MESH_ID
Point3f	ptCenter
Quaternion	q
boolean	recalcAltVertices
float	scale
String	scriptCommand
boolean	showContourLines
boolean	showPoints
boolean	showTriangles
Object	slabbingObject
String	thisID
String[]	title
Vector3f	vAB
Vector3f	vAC
Map<String,BitSet>	vertexColorMap
int	visibilityFlags
boolean	visible
Vector3f	vTemp
float	width
List<Object>	xmlProperties

Fields inherited from class org.jmol.util.MeshSurface

altVertices, bsDisplay, bsPolygons, bsSlabDisplay, bsSlabGhost, colix, haveQuads, iA, iB, iC, isColorSolid, isMerged, mergePolygonCount0, mergeVertexCount0, meshType, normalCount, normals, nSets, offset, polygonColixes, polygonCount, polygonCount0, polygonIndexes, ptOffset, scale3d, SEED_COUNT, slabColix, slabMeshType, slabOptions, surfaceSet, vertexColixes, vertexCount, vertexCount0, vertexSets, vertexSource, vertexValues, vertices

Constructor Summary

Mesh(String thisID, JmolRendererInterface g3d, short colix, int index)

Method Summary

static boolean	checkWithin(Point3f pti, List<Point3f> withinPoints, float withinDistance2, boolean isWithinNot)
void	clear(String meshType)
private void	flipLighting(int lighting)
Point3f[]	getBoundingBox()
(package private) Object	getInfo()
Vector3f[]	getNormals(Point3f[] vertices, Point4f plane)
Point3f[]	getOffsetVertices(Point4f thePlane)
protected String	getRendering()
String	getState(String type)
int	getVertexIndexFromNumber(int vertexIndex)
(package private) BitSet	getVisibleGhostBitSet()
(package private) BitSet	getVisibleVertexBitSet()
void	initialize(int lighting, Point3f[] vertices, Point4f plane)
private void	invertNormixes()
void	setLighting(int lighting)
void	setShowWithin(List<Point3f> showWithinPoints, float showWithinDistance2, boolean isWithinNot)
void	setTokenProperty(int tokProp, boolean bProp)
void	setTranslucent(boolean isTranslucent, float iLevel)
void	setVisibilityFlags(int n)
protected void	sumVertexNormals(Point3f[] vertices, Vector3f[] normals)
void	updateCoordinates(Matrix4f m, BitSet bs)

Methods inherited from class org.jmol.util.MeshSurface

addQuad, addTriangle, addTriangleCheck, addVertexCopy, addVertexCopy, getCapSlabObject, getFaces, getIntersection, getSlabColor, getSlabObject, getSlabTranslucency, getSlabType, getSlabWithinRange, getSphericalInterpolationFraction, getVertices, invalidatePolygons, resetSlab, setABC, setColix, setPolygonCount, setSlab, slabPolygons, slabPolygons

Methods inherited from class java.lang.Object

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

Field Detail

PREVIOUS_MESH_ID

public static final String PREVIOUS_MESH_ID

See Also:

Constant Field Values

title

public String[] title

meshColix

public short meshColix

normixes

public short[] normixes

normixCount

private int normixCount

lineData

public List<Point3f[]> lineData

thisID

public String thisID

isValid

public boolean isValid

scriptCommand

public String scriptCommand

colorCommand

public String colorCommand

lattice

public Point3f lattice

visible

public boolean visible

lighting

public int lighting

q

public Quaternion q

scale

public float scale

haveXyPoints

public boolean haveXyPoints

isTriangleSet

public boolean isTriangleSet

diameter

public int diameter

width

public float width

ptCenter

public Point3f ptCenter

linkedMesh

public Mesh linkedMesh

vertexColorMap

public Map<String,BitSet> vertexColorMap

index

public int index

atomIndex

public int atomIndex

modelIndex

public int modelIndex

visibilityFlags

public int visibilityFlags

insideOut

public boolean insideOut

checkByteCount

public int checkByteCount

showContourLines

public boolean showContourLines

showPoints

public boolean showPoints

drawTriangles

public boolean drawTriangles

fillTriangles

public boolean fillTriangles

showTriangles

public boolean showTriangles

frontOnly

public boolean frontOnly

isTwoSided

public boolean isTwoSided

havePlanarContours

public boolean havePlanarContours

vAB

public final Vector3f vAB

vAC

public final Vector3f vAC

vTemp

public final Vector3f vTemp

xmlProperties

public List<Object> xmlProperties

colorDensity

public boolean colorDensity

cappingObject

public Object cappingObject

slabbingObject

public Object slabbingObject

connections

public int[] connections

recalcAltVertices

public boolean recalcAltVertices

mat4

Matrix4f mat4

color

public int color

Constructor Detail

Mesh

public Mesh(String thisID,
            JmolRendererInterface g3d,
            short colix,
            int index)

Parameters:

thisID -

g3d - IGNORED

colix -

index -

Method Detail

setVisibilityFlags

public void setVisibilityFlags(int n)

clear

public void clear(String meshType)

initialize

public void initialize(int lighting,
                       Point3f[] vertices,
                       Point4f plane)

getNormals

public Vector3f[] getNormals(Point3f[] vertices,
                             Point4f plane)

setLighting

public void setLighting(int lighting)

flipLighting

private void flipLighting(int lighting)

invertNormixes

private void invertNormixes()

setTranslucent

public void setTranslucent(boolean isTranslucent,
                           float iLevel)

sumVertexNormals

protected void sumVertexNormals(Point3f[] vertices,
                                Vector3f[] normals)

getState

public String getState(String type)

getRendering

protected String getRendering()

getOffsetVertices

public Point3f[] getOffsetVertices(Point4f thePlane)

setShowWithin

public void setShowWithin(List<Point3f> showWithinPoints,
                          float showWithinDistance2,
                          boolean isWithinNot)

Parameters:

showWithinPoints -

showWithinDistance2 -

isWithinNot -

checkWithin

public static boolean checkWithin(Point3f pti,
                                  List<Point3f> withinPoints,
                                  float withinDistance2,
                                  boolean isWithinNot)

getVertexIndexFromNumber

public int getVertexIndexFromNumber(int vertexIndex)

updateCoordinates

public void updateCoordinates(Matrix4f m,
                              BitSet bs)

getVisibleVertexBitSet

BitSet getVisibleVertexBitSet()

getVisibleGhostBitSet

BitSet getVisibleGhostBitSet()

setTokenProperty

public void setTokenProperty(int tokProp,
                             boolean bProp)

getInfo

Object getInfo()

getBoundingBox

public Point3f[] getBoundingBox()