MeshSurface

java.lang.Object
- org.jmol.util.MeshSurface

public class MeshSurface
extends java.lang.Object

Field Summary

Fields
Modifier and Type	Field	Description
`Tuple3f[]`	`altVertices`
`BitSet`	`bsDisplay`
`BitSet`	`bsPolygons`
`BitSet`	`bsSlabDisplay`
`BitSet`	`bsSlabGhost`
`short`	`colix`
`short`	`colixBack`
`boolean`	`haveQuads`
`protected int`	`iA`
`protected int`	`iB`
`protected int`	`iC`
`boolean`	`isColorSolid`
`boolean`	`isMerged`
`boolean`	`isTriangleSet`
`Matrix4f`	`mat4`
`int`	`mergePolygonCount0`
`int`	`mergeVertexCount0`
`java.lang.String`	`meshType`
`int`	`normalCount`
`Tuple3f[]`	`normals`
`Vector3f[]`	`normalsTemp`
`int`	`normixCount`
`int`	`nSets`
`Point3f`	`offset`
`short[]`	`polygonColixes`
`int`	`polygonCount`
`int`	`polygonCount0`
`int[][]`	`polygonIndexes`
`protected static int`	`SEED_COUNT`
`short`	`slabColix`
`int`	`slabMeshType`
`StringXBuilder`	`slabOptions`
`Vector3f[]`	`spanningVectors`
`BitSet[]`	`surfaceSet`
`short[]`	`vertexColixes`
`int`	`vertexCount`
`int`	`vertexCount0`
`int[]`	`vertexSets`
`int[]`	`vertexSource`
`float[]`	`vertexValues`
`Point3f[]`	`vertices`

Constructor Summary

Constructors
Constructor Description

MeshSurface()

Constructors
Constructor	Description
`MeshSurface()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected int`	`addIntersectionVertex(Point3f vertex, float value, int source, int set, java.util.Map<java.lang.String,java.lang.Integer> mapEdge, int i1, int i2)`
`protected int`	`addPolygonC(int[] polygon, int color, BitSet bs)`
`void`	`addQuad(int vertexA, int vertexB, int vertexC, int vertexD)`
`void`	`addTriangle(int vertexA, int vertexB, int vertexC)`
`int`	`addTriangleCheck(int vertexA, int vertexB, int vertexC, int check, int check2, int color)`
`int`	`addVertexCopy(Point3f vertex)`
`protected int`	`addVertexCopy(Point3f vertex, float value, boolean assocNormals, int iNormal)`
`int`	`addVertexCopyVal(Point3f vertex, float value)`
`static java.lang.Object[]`	`getCapSlabObject(java.lang.String s, boolean isCap)`	legacy -- for some scripts with early isosurface slabbing
`int[][]`	`getFaces()`
`void`	`getIntersection(float distance, Point4f plane, Point3f[] ptCenters, java.util.List<Point3f[]> vData, float[] fData, BitSet bsSource, MeshSurface meshSurface, boolean andCap, boolean doClean, int tokType, boolean isGhost)`
`java.lang.String`	`getSlabColor()`
`static java.lang.Object[]`	`getSlabObject(int tok, java.lang.Object data, boolean isCap, java.lang.Object colorData)`
`java.lang.String`	`getSlabTranslucency()`
`java.lang.String`	`getSlabType()`
`static java.lang.Object[]`	`getSlabWithinRange(float min, float max)`
`static MeshSurface`	`getSphereData(int lvl)`	Calculates the data (faces, vertices, normals) for a sphere.
`static float`	`getSphericalInterpolationFraction(double r, double valueA, double valueB, double d)`
`Tuple3f[]`	`getVertices()`
`void`	`invalidatePolygons()`
`static MeshSurface`	`newMesh(boolean isAlt, Tuple3f[] vertices, int vertexCount, int[][] polygonIndexes, Tuple3f[] normals, int nNormals)`
`static MeshSurface`	`newSlab(Point3f[] vertices, int vertexCount, float[] vertexValues, int[][] polygonIndexes, int polygonCount, int checkCount)`
`void`	`resetSlab()`
`protected boolean`	`setABC(int i)`
`void`	`setColix(short colix)`
`void`	`setColixBack(short colix)`
`void`	`setPolygonCount(int polygonCount)`
`void`	`setSlab(BitSet bsDisplay, BitSet bsGhost, java.lang.String type, java.lang.String color, float translucency)`
`protected void`	`slabBrillouin(Point3f[] unitCellVectors)`
`boolean`	`slabPolygons(java.lang.Object[] slabObject, boolean allowCap)`
`void`	`slabPolygonsList(java.util.List<java.lang.Object[]> slabInfo, boolean allowCap)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

SEED_COUNT
```
protected static final int SEED_COUNT
```
See Also:

Constant Field Values

spanningVectors
```
public Vector3f[] spanningVectors
```

meshType
```
public java.lang.String meshType
```

vertexCount
```
public int vertexCount
```

vertices
```
public Point3f[] vertices
```

vertexValues
```
public float[] vertexValues
```

vertexSource
```
public int[] vertexSource
```

polygonCount
```
public int polygonCount
```

polygonIndexes
```
public int[][] polygonIndexes
```

isTriangleSet
```
public boolean isTriangleSet
```

haveQuads
```
public boolean haveQuads
```

colix
```
public short colix
```

colixBack
```
public short colixBack
```

isColorSolid
```
public boolean isColorSolid
```

offset
```
public Point3f offset
```

altVertices
```
public Tuple3f[] altVertices
```

polygonColixes
```
public short[] polygonColixes
```

vertexColixes
```
public short[] vertexColixes
```

normals
```
public Tuple3f[] normals
```

normalsTemp
```
public Vector3f[] normalsTemp
```

normalCount
```
public int normalCount
```

normixCount
```
public int normixCount
```

bsPolygons
```
public BitSet bsPolygons
```

mat4
```
public Matrix4f mat4
```

surfaceSet
```
public BitSet[] surfaceSet
```

vertexSets
```
public int[] vertexSets
```

nSets
```
public int nSets
```

iA
```
protected int iA
```

iB
```
protected int iB
```

iC
```
protected int iC
```

polygonCount0
```
public int polygonCount0
```

vertexCount0
```
public int vertexCount0
```

bsSlabDisplay
```
public BitSet bsSlabDisplay
```

bsSlabGhost
```
public BitSet bsSlabGhost
```

slabMeshType
```
public int slabMeshType
```

slabColix
```
public short slabColix
```

bsDisplay
```
public BitSet bsDisplay
```

slabOptions
```
public StringXBuilder slabOptions
```

mergeVertexCount0
```
public int mergeVertexCount0
```

mergePolygonCount0
```
public int mergePolygonCount0
```

isMerged
```
public boolean isMerged
```

Constructor Detail
- MeshSurface
```
public MeshSurface()
```

Method Detail

newMesh

public static MeshSurface newMesh(boolean isAlt,
                                  Tuple3f[] vertices,
                                  int vertexCount,
                                  int[][] polygonIndexes,
                                  Tuple3f[] normals,
                                  int nNormals)

newSlab

public static MeshSurface newSlab(Point3f[] vertices,
                                  int vertexCount,
                                  float[] vertexValues,
                                  int[][] polygonIndexes,
                                  int polygonCount,
                                  int checkCount)

getVertices
```
public Tuple3f[] getVertices()
```
Returns:

The vertices.

getFaces
```
public int[][] getFaces()
```
Returns:

faces, if defined (in exporter), otherwise polygonIndexes

setColix
```
public void setColix(short colix)
```

setColixBack

public void setColixBack(short colix)

addVertexCopy

public int addVertexCopy(Point3f vertex)

addTriangle

public void addTriangle(int vertexA,
                        int vertexB,
                        int vertexC)

addQuad

public void addQuad(int vertexA,
                    int vertexB,
                    int vertexC,
                    int vertexD)

setPolygonCount

public void setPolygonCount(int polygonCount)

addVertexCopyVal

public int addVertexCopyVal(Point3f vertex,
                            float value)

addTriangleCheck

public int addTriangleCheck(int vertexA,
                            int vertexB,
                            int vertexC,
                            int check,
                            int check2,
                            int color)

addPolygonC

protected int addPolygonC(int[] polygon,
                          int color,
                          BitSet bs)

invalidatePolygons
```
public void invalidatePolygons()
```

setABC
```
protected boolean setABC(int i)
```

setSlab

public void setSlab(BitSet bsDisplay,
                    BitSet bsGhost,
                    java.lang.String type,
                    java.lang.String color,
                    float translucency)

getSlabColor

public java.lang.String getSlabColor()

getSlabTranslucency

public java.lang.String getSlabTranslucency()

getSlabType

public java.lang.String getSlabType()

getSlabWithinRange

public static java.lang.Object[] getSlabWithinRange(float min,
                                                    float max)

resetSlab
```
public void resetSlab()
```

getSlabObject

public static java.lang.Object[] getSlabObject(int tok,
                                               java.lang.Object data,
                                               boolean isCap,
                                               java.lang.Object colorData)

getCapSlabObject

public static java.lang.Object[] getCapSlabObject(java.lang.String s,
                                                  boolean isCap)

legacy -- for some scripts with early isosurface slabbing

Parameters:: s -; isCap -
Returns:: slabInfo object

slabPolygonsList

public void slabPolygonsList(java.util.List<java.lang.Object[]> slabInfo,
                             boolean allowCap)

slabPolygons

public boolean slabPolygons(java.lang.Object[] slabObject,
                            boolean allowCap)

slabBrillouin

protected void slabBrillouin(Point3f[] unitCellVectors)

Parameters:: unitCellVectors -

addIntersectionVertex

protected int addIntersectionVertex(Point3f vertex,
                                    float value,
                                    int source,
                                    int set,
                                    java.util.Map<java.lang.String,java.lang.Integer> mapEdge,
                                    int i1,
                                    int i2)

addVertexCopy

protected int addVertexCopy(Point3f vertex,
                            float value,
                            boolean assocNormals,
                            int iNormal)

Parameters:: vertex -; value -; assocNormals -; iNormal -
Returns:: new vertex index

getIntersection

public void getIntersection(float distance,
                            Point4f plane,
                            Point3f[] ptCenters,
                            java.util.List<Point3f[]> vData,
                            float[] fData,
                            BitSet bsSource,
                            MeshSurface meshSurface,
                            boolean andCap,
                            boolean doClean,
                            int tokType,
                            boolean isGhost)

Parameters:: distance - a distance from a plane or point; plane - a slabbing plane; ptCenters - a set of atoms to measure distance from; vData - when not null, this is a query, not an actual slabbing; fData - vertex values or other data to overlay; bsSource - TODO; meshSurface - second surface; not implemented -- still some problems there; andCap - to cap this off, crudely only; doClean - compact set - draw only; tokType - type of slab; isGhost - translucent slab, so we mark slabbed triangles

getSphericalInterpolationFraction

public static float getSphericalInterpolationFraction(double r,
                                                      double valueA,
                                                      double valueB,
                                                      double d)

getSphereData
```
public static MeshSurface getSphereData(int lvl)
```
Calculates the data (faces, vertices, normals) for a sphere.

Returns:

The data.

Class MeshSurface

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

SEED_COUNT

spanningVectors

meshType

vertexCount

vertices

vertexValues

vertexSource

polygonCount

polygonIndexes

isTriangleSet

haveQuads

colix

colixBack

isColorSolid

offset

altVertices

polygonColixes

vertexColixes

normals

normalsTemp

normalCount

normixCount

bsPolygons

mat4

surfaceSet

vertexSets

nSets

iA

iB

iC

polygonCount0

vertexCount0

bsSlabDisplay

bsSlabGhost

slabMeshType

slabColix

bsDisplay

slabOptions

mergeVertexCount0

mergePolygonCount0

isMerged

Constructor Detail

MeshSurface

Method Detail

newMesh

newSlab

getVertices

getFaces

setColix

setColixBack

addVertexCopy

addTriangle

addQuad

setPolygonCount

addVertexCopyVal

addTriangleCheck

addPolygonC

invalidatePolygons

setABC

setSlab

getSlabColor

getSlabTranslucency

getSlabType

getSlabWithinRange

resetSlab

getSlabObject

getCapSlabObject

slabPolygonsList

slabPolygons

slabBrillouin

addIntersectionVertex

addVertexCopy

getIntersection

getSphericalInterpolationFraction