org.jmol.shapesurface
Class Isosurface

java.lang.Object
  org.jmol.shape.Shape
      org.jmol.shape.MeshCollection
          org.jmol.shapesurface.MeshFileCollection
              org.jmol.shapesurface.Isosurface

All Implemented Interfaces:

MeshDataServer, VertexDataServer

Direct Known Subclasses:

LcaoCartoon, MolecularOrbital

public class Isosurface
extends MeshFileCollection
implements MeshDataServer

Field Summary

private boolean	associateNormals
private int	atomIndex
private javax.vecmath.Point3f	center
private ColorEncoder	colorEncoder
private short	defaultColix
private boolean	iHaveBitSets
private int	indexColorNegative
private int	indexColorPositive
private IsosurfaceMesh[]	isomeshes
private boolean	isPhaseColored
private JvxlData	jvxlData
private javax.vecmath.Point4f	lcaoDir
private int	lighting
private int	moNumber
private int	nLCAO
protected SurfaceGenerator	sg
private IsosurfaceMesh	thisMesh

Fields inherited from class org.jmol.shapesurface.MeshFileCollection

line, next

Fields inherited from class org.jmol.shape.MeshCollection

allowMesh, colix, currentMesh, explicitID, iHaveModelIndex, isFixed, linkedMesh, meshCount, meshes, modelCount, modelIndex, myType, nUnnamed, previousMeshID, script, title

Fields inherited from class org.jmol.shape.Shape

g3d, isBioShape, modelSet, myVisibilityFlag, shapeID, translucentAllowed, translucentLevel, viewer

Constructor Summary

Isosurface()

Method Summary

void	addTriangleCheck(int iA, int iB, int iC, int check, boolean isAbsolute) addTriangleCheck adds a triangle along with a 3-bit check indicating which edges to draw in mesh mode: 1 (iA-iB) + 2 (iB-iC) + 4 (iC-iA)
int	addVertexCopy(javax.vecmath.Point3f vertexXYZ, float value, int assocVertex) addVertexCopy is used by the Marching Squares algorithm to uniquely identify a new vertex when an edge is crossed in the 2D plane.
void	allocMesh(java.lang.String thisID)
javax.vecmath.Point3f[]	calculateGeodesicSurface(java.util.BitSet bsSelected, float envelopeRadius)
protected void	clearSg()
private void	createLcaoLobe(javax.vecmath.Vector3f lobeAxis, float factor)
private void	discardTempData(boolean discardAll)
private void	drawLcaoCartoon(javax.vecmath.Vector3f z, javax.vecmath.Vector3f x, javax.vecmath.Vector3f rotAxis)
void	fillMeshData(MeshData meshData, int mode)
private short	getDefaultColix()
java.lang.Object	getProperty(java.lang.String property, int index)
private boolean	getScriptBitSets(java.lang.String script, java.util.BitSet[] bsCmd)
java.util.Vector	getShapeDetail()
int	getSurfacePointIndex(float cutoff, boolean isCutoffAbsolute, int x, int y, int z, javax.vecmath.Point3i offset, int vA, int vB, float valueA, float valueB, javax.vecmath.Point3f pointA, javax.vecmath.Vector3f edgeVector, boolean isContourType) getSurfacePointIndex is used by the Marching Cubes algorithm and must return a unique integer identifier for a vertex created by the Marching Cube algorithm when it finds an edge.
private java.lang.String	getUserColorScheme(java.lang.String schemeName)
private void	initializeIsosurface()
void	initShape()
private void	initState()
void	invalidateTriangles()
void	notifySurfaceGenerationCompleted()
void	notifySurfaceMappingCompleted()
protected void	remapColors()
private void	setJvxlInfo()
private void	setModelIndex()
void	setProperty(java.lang.String propertyName, java.lang.Object value, java.util.BitSet bs)
private void	setPropertySuper(java.lang.String propertyName, java.lang.Object value, java.util.BitSet bs)
protected void	setScriptInfo()

Methods inherited from class org.jmol.shapesurface.MeshFileCollection

getTokens, parseFloat, parseFloat, parseFloatNext, parseInt, parseInt, parseInt, parseIntNext

Methods inherited from class org.jmol.shape.MeshCollection

deleteMesh, getIndexFromName, getModelIndex, getShapeState, setModelIndex, setVisibilityFlags

Methods inherited from class org.jmol.shape.Shape

appendCmd, checkBoundsMinMax, checkObjectClicked, checkObjectDragged, checkObjectHovered, findNearestAtomIndex, getColix, getColorCommand, getColorCommand, getFontCommand, getShapeCommands, getShapeCommands, getViewer, initializeShape, initModelSet, setColix, setColix, setModelClickability, setModelSet, setSize, setStateInfo, setStateInfo, wasClicked

Methods inherited from class java.lang.Object

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

Field Detail

isomeshes

private IsosurfaceMesh[] isomeshes

thisMesh

private IsosurfaceMesh thisMesh

lighting

private int lighting

iHaveBitSets

private boolean iHaveBitSets

atomIndex

private int atomIndex

moNumber

private int moNumber

defaultColix

private short defaultColix

center

private javax.vecmath.Point3f center

isPhaseColored

private boolean isPhaseColored

sg

protected SurfaceGenerator sg

jvxlData

private JvxlData jvxlData

colorEncoder

private ColorEncoder colorEncoder

indexColorPositive

private int indexColorPositive

indexColorNegative

private int indexColorNegative

nLCAO

private int nLCAO

lcaoDir

private javax.vecmath.Point4f lcaoDir

associateNormals

private boolean associateNormals

Constructor Detail

Isosurface

public Isosurface()

Method Detail

allocMesh

public void allocMesh(java.lang.String thisID)

Overrides:

allocMesh in class MeshCollection

initShape

public void initShape()

Overrides:

initShape in class MeshCollection

clearSg

protected void clearSg()

setProperty

public void setProperty(java.lang.String propertyName,
                        java.lang.Object value,
                        java.util.BitSet bs)

Overrides:

setProperty in class MeshCollection

setPropertySuper

private void setPropertySuper(java.lang.String propertyName,
                              java.lang.Object value,
                              java.util.BitSet bs)

getProperty

public java.lang.Object getProperty(java.lang.String property,
                                    int index)

Overrides:

getProperty in class MeshCollection

getScriptBitSets

private boolean getScriptBitSets(java.lang.String script,
                                 java.util.BitSet[] bsCmd)

initializeIsosurface

private void initializeIsosurface()

initState

private void initState()

discardTempData

private void discardTempData(boolean discardAll)

getDefaultColix

private short getDefaultColix()

drawLcaoCartoon

private void drawLcaoCartoon(javax.vecmath.Vector3f z,
                             javax.vecmath.Vector3f x,
                             javax.vecmath.Vector3f rotAxis)

createLcaoLobe

private void createLcaoLobe(javax.vecmath.Vector3f lobeAxis,
                            float factor)

invalidateTriangles

public void invalidateTriangles()

Specified by:

invalidateTriangles in interface MeshDataServer

fillMeshData

public void fillMeshData(MeshData meshData,
                         int mode)

Specified by:

fillMeshData in interface MeshDataServer

notifySurfaceGenerationCompleted

public void notifySurfaceGenerationCompleted()

Specified by:

notifySurfaceGenerationCompleted in interface MeshDataServer

notifySurfaceMappingCompleted

public void notifySurfaceMappingCompleted()

Specified by:

notifySurfaceMappingCompleted in interface MeshDataServer

calculateGeodesicSurface

public javax.vecmath.Point3f[] calculateGeodesicSurface(java.util.BitSet bsSelected,
                                                        float envelopeRadius)

Specified by:

calculateGeodesicSurface in interface MeshDataServer

getSurfacePointIndex

public int getSurfacePointIndex(float cutoff,
                                boolean isCutoffAbsolute,
                                int x,
                                int y,
                                int z,
                                javax.vecmath.Point3i offset,
                                int vA,
                                int vB,
                                float valueA,
                                float valueB,
                                javax.vecmath.Point3f pointA,
                                javax.vecmath.Vector3f edgeVector,
                                boolean isContourType)

Description copied from interface: MeshDataServer

getSurfacePointIndex is used by the Marching Cubes algorithm and must return a unique integer identifier for a vertex created by the Marching Cube algorithm when it finds an edge. If a vertex is discarded, then Integer.MAX_VALUE should be returned. the 3D coordinate of the point can be calculated using surfacePoint.scaleAdd(fraction, edgeVector, pointA); where fraction is generally calculated as: fraction = (cutoff - valueA) / (valueB - valueA); if (isCutoffAbsolute && (fraction < 0 || fraction > 1)) fraction = (-cutoff - valueA) / (valueB - valueA); This method is also used by MarchingCubes to deliver the appropriate oblique planar coordinate to MarchingSquares for later contouring.

Specified by:

getSurfacePointIndex in interface MeshDataServer

Specified by:

getSurfacePointIndex in interface VertexDataServer

vA - [0:7]

vB - [0:7]

edgeVector - vector from A to B

Returns:

new vertex index or Integer.MAX_VALUE

addVertexCopy

public int addVertexCopy(javax.vecmath.Point3f vertexXYZ,
                         float value,
                         int assocVertex)

Description copied from interface: MeshDataServer

addVertexCopy is used by the Marching Squares algorithm to uniquely identify a new vertex when an edge is crossed in the 2D plane. The implementing method should COPY the Point3f using Point3f.set(). The data consumer can use the association key to group this vertex with others near the same gridpoint.

Specified by:

addVertexCopy in interface MeshDataServer

Specified by:

addVertexCopy in interface VertexDataServer

assocVertex - unique association vertex or -1

Returns:

new vertex index

addTriangleCheck

public void addTriangleCheck(int iA,
                             int iB,
                             int iC,
                             int check,
                             boolean isAbsolute)

Description copied from interface: MeshDataServer

addTriangleCheck adds a triangle along with a 3-bit check indicating which edges to draw in mesh mode: 1 (iA-iB) + 2 (iB-iC) + 4 (iC-iA)

Specified by:

addTriangleCheck in interface MeshDataServer

Specified by:

addTriangleCheck in interface VertexDataServer

setModelIndex

private void setModelIndex()

setScriptInfo

protected void setScriptInfo()

setJvxlInfo

private void setJvxlInfo()

getShapeDetail

public java.util.Vector getShapeDetail()

Overrides:

getShapeDetail in class Shape

remapColors

protected void remapColors()

Overrides:

remapColors in class Shape

getUserColorScheme

private java.lang.String getUserColorScheme(java.lang.String schemeName)