org.jmol.shape
Class Mesh

java.lang.Object
  extended by org.jmol.util.MeshSurface
      extended by org.jmol.shape.Mesh
Direct Known Subclasses:
DrawMesh, IsosurfaceMesh

public class Mesh
extends MeshSurface


Field Summary
 int atomIndex
           
 java.lang.Object cappingObject
           
 int checkByteCount
           
 int color
           
 java.lang.String colorCommand
           
 boolean colorDensity
           
 int[] connections
           
 int diameter
           
 boolean drawTriangles
           
 boolean fillTriangles
           
 boolean frontOnly
           
 boolean havePlanarContours
           
 boolean haveXyPoints
           
 int index
           
 boolean insideOut
           
 boolean isPolygonSet
           
 boolean isTwoSided
           
 boolean isValid
           
 javax.vecmath.Point3f lattice
           
 int lighting
           
 java.util.List<javax.vecmath.Point3f[]> lineData
           
 Mesh linkedMesh
           
(package private)  javax.vecmath.Matrix4f mat4
           
 short meshColix
           
 int modelIndex
           
private  int normixCount
           
 short[] normixes
           
static java.lang.String PREVIOUS_MESH_ID
           
 javax.vecmath.Point3f ptCenter
           
 Quaternion q
           
 boolean recalcAltVertices
           
 float scale
           
 java.lang.String scriptCommand
           
 boolean showContourLines
           
 boolean showPoints
           
 boolean showTriangles
           
 java.lang.Object slabbingObject
           
 java.lang.String thisID
           
 java.lang.String[] title
           
 javax.vecmath.Vector3f vAB
           
 javax.vecmath.Vector3f vAC
           
 java.util.Map<java.lang.String,java.util.BitSet> vertexColorMap
           
 int visibilityFlags
           
 boolean visible
           
 javax.vecmath.Vector3f vTemp
           
 float width
           
 java.util.List<java.lang.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(java.lang.String thisID, JmolRendererInterface g3d, short colix, int index)
           
 
Method Summary
static boolean checkWithin(javax.vecmath.Point3f pti, java.util.List<javax.vecmath.Point3f> withinPoints, float withinDistance2, boolean isWithinNot)
           
 void clear(java.lang.String meshType)
           
private  void flipLighting(int lighting)
           
 javax.vecmath.Point3f[] getBoundingBox()
           
(package private)  java.lang.Object getInfo()
           
 javax.vecmath.Vector3f[] getNormals(javax.vecmath.Point3f[] vertices, javax.vecmath.Point4f plane)
           
 javax.vecmath.Point3f[] getOffsetVertices(javax.vecmath.Point4f thePlane)
           
protected  java.lang.String getRendering()
           
 java.lang.String getState(java.lang.String type)
           
 int getVertexIndexFromNumber(int vertexIndex)
           
(package private)  java.util.BitSet getVisibleGhostBitSet()
           
(package private)  java.util.BitSet getVisibleVertexBitSet()
           
 void initialize(int lighting, javax.vecmath.Point3f[] vertices, javax.vecmath.Point4f plane)
           
private  void invertNormixes()
           
 void setLighting(int lighting)
           
 void setShowWithin(java.util.List<javax.vecmath.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(javax.vecmath.Point3f[] vertices, javax.vecmath.Vector3f[] normals)
           
 void updateCoordinates(javax.vecmath.Matrix4f m, java.util.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 java.lang.String PREVIOUS_MESH_ID
See Also:
Constant Field Values

title

public java.lang.String[] title

meshColix

public short meshColix

normixes

public short[] normixes

normixCount

private int normixCount

lineData

public java.util.List<javax.vecmath.Point3f[]> lineData

thisID

public java.lang.String thisID

isValid

public boolean isValid

scriptCommand

public java.lang.String scriptCommand

colorCommand

public java.lang.String colorCommand

lattice

public javax.vecmath.Point3f lattice

visible

public boolean visible

lighting

public int lighting

q

public Quaternion q

scale

public float scale

haveXyPoints

public boolean haveXyPoints

isPolygonSet

public boolean isPolygonSet

diameter

public int diameter

width

public float width

ptCenter

public javax.vecmath.Point3f ptCenter

linkedMesh

public Mesh linkedMesh

vertexColorMap

public java.util.Map<java.lang.String,java.util.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 javax.vecmath.Vector3f vAB

vAC

public final javax.vecmath.Vector3f vAC

vTemp

public final javax.vecmath.Vector3f vTemp

xmlProperties

public java.util.List<java.lang.Object> xmlProperties

colorDensity

public boolean colorDensity

cappingObject

public java.lang.Object cappingObject

slabbingObject

public java.lang.Object slabbingObject

connections

public int[] connections

recalcAltVertices

public boolean recalcAltVertices

mat4

javax.vecmath.Matrix4f mat4

color

public int color
Constructor Detail

Mesh

public Mesh(java.lang.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(java.lang.String meshType)

initialize

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

getNormals

public javax.vecmath.Vector3f[] getNormals(javax.vecmath.Point3f[] vertices,
                                           javax.vecmath.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(javax.vecmath.Point3f[] vertices,
                                javax.vecmath.Vector3f[] normals)

getState

public java.lang.String getState(java.lang.String type)

getRendering

protected java.lang.String getRendering()

getOffsetVertices

public javax.vecmath.Point3f[] getOffsetVertices(javax.vecmath.Point4f thePlane)

setShowWithin

public void setShowWithin(java.util.List<javax.vecmath.Point3f> showWithinPoints,
                          float showWithinDistance2,
                          boolean isWithinNot)
Parameters:
showWithinPoints -
showWithinDistance2 -
isWithinNot -

checkWithin

public static boolean checkWithin(javax.vecmath.Point3f pti,
                                  java.util.List<javax.vecmath.Point3f> withinPoints,
                                  float withinDistance2,
                                  boolean isWithinNot)

getVertexIndexFromNumber

public int getVertexIndexFromNumber(int vertexIndex)

updateCoordinates

public void updateCoordinates(javax.vecmath.Matrix4f m,
                              java.util.BitSet bs)

getVisibleVertexBitSet

java.util.BitSet getVisibleVertexBitSet()

getVisibleGhostBitSet

java.util.BitSet getVisibleGhostBitSet()

setTokenProperty

public void setTokenProperty(int tokProp,
                             boolean bProp)

getInfo

java.lang.Object getInfo()

getBoundingBox

public javax.vecmath.Point3f[] getBoundingBox()