org.jmol.shapesurface
Class IsosurfaceMesh
java.lang.Object
org.jmol.shape.Mesh
org.jmol.shapesurface.IsosurfaceMesh
public class IsosurfaceMesh
- extends Mesh
Fields inherited from class org.jmol.shape.Mesh |
atomIndex, bitsets, colix, colorCommand, data1, data2, diameter, drawTriangles, fillTriangles, frontOnly, haveCheckByte, havePlanarContours, haveXyPoints, index, insideOut, isColorSolid, isTwoSided, isValid, lighting, linkedMesh, meshType, modelIndex, normixes, polygonCount, polygonIndexes, PREVIOUS_MESH_ID, ptCenter, scale, scriptCommand, SEED_COUNT, showContourLines, showPoints, showTriangles, thisID, title, vAB, vAC, vertexCount, vertices, visibilityFlags, visible, vTemp, width |
Method Summary |
(package private) void |
addTriangleCheck(int vertexA,
int vertexB,
int vertexC,
int check,
int color)
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(package private) int |
addVertexCopy(javax.vecmath.Point3f vertex,
float value)
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(package private) int |
addVertexCopy(javax.vecmath.Point3f vertex,
float value,
int assocVertex,
boolean associateNormals)
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(package private) void |
allocVertexColixes()
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(package private) java.lang.Object |
calculateArea()
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(package private) java.lang.Object |
calculateVolume()
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private float |
checkPt(int i,
int j,
float f)
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(package private) void |
clear(java.lang.String meshType,
boolean iAddGridPoints)
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private void |
dumpData()
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private void |
get3dContour(java.util.Vector v,
float value,
int color)
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(package private) javax.vecmath.Point3f[] |
getCenters()
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static javax.vecmath.Point3f |
getContourPoint(javax.vecmath.Point3f[] vertices,
int i,
int j,
float f)
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(package private) java.util.Vector[] |
getContours()
create a set of contour data. |
(package private) javax.vecmath.Point4f |
getFacePlane(int i,
javax.vecmath.Vector3f vNorm)
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(package private) void |
invalidateTriangles()
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private boolean |
setABC(int i)
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static void |
setContourVector(java.util.Vector v,
int nPolygons,
java.util.BitSet bsContour,
float value,
int color,
java.lang.StringBuffer fData)
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void |
setTranslucent(boolean isTranslucent,
float iLevel)
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void |
sumVertexNormals(javax.vecmath.Vector3f[] vectorSums)
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Methods inherited from class org.jmol.shape.Mesh |
addQuad, addTriangle, addVertexCopy, clear, getState, getVertexNormals, initialize, initializeNormixes, setColix, setLighting, setPolygonCount, setVisibilityFlags |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
jvxlData
JvxlData jvxlData
vertexIncrement
int vertexIncrement
firstRealVertex
int firstRealVertex
dataType
int dataType
hasGridPoints
boolean hasGridPoints
calculatedArea
java.lang.Object calculatedArea
calculatedVolume
java.lang.Object calculatedVolume
isSolvent
public boolean isSolvent
vertexValues
public float[] vertexValues
vertexColixes
public short[] vertexColixes
assocGridPointMap
java.util.Hashtable assocGridPointMap
assocGridPointNormals
java.util.Hashtable assocGridPointNormals
polygonColixes
public short[] polygonColixes
lastColor
private int lastColor
lastColix
private short lastColix
iA
private int iA
iB
private int iB
iC
private int iC
surfaceSet
java.util.BitSet[] surfaceSet
vertexSets
int[] vertexSets
nSets
int nSets
thisSet
int thisSet
centers
javax.vecmath.Point3f[] centers
CONTOUR_NPOLYGONS
public static final int CONTOUR_NPOLYGONS
- See Also:
- Constant Field Values
CONTOUR_BITSET
public static final int CONTOUR_BITSET
- See Also:
- Constant Field Values
CONTOUR_VALUE
public static final int CONTOUR_VALUE
- See Also:
- Constant Field Values
CONTOUR_COLOR
public static final int CONTOUR_COLOR
- See Also:
- Constant Field Values
CONTOUR_FDATA
public static final int CONTOUR_FDATA
- See Also:
- Constant Field Values
CONTOUR_POINTS
public static final int CONTOUR_POINTS
- See Also:
- Constant Field Values
IsosurfaceMesh
IsosurfaceMesh(java.lang.String thisID,
Graphics3D g3d,
short colix,
int index)
clear
void clear(java.lang.String meshType,
boolean iAddGridPoints)
allocVertexColixes
void allocVertexColixes()
addVertexCopy
int addVertexCopy(javax.vecmath.Point3f vertex,
float value,
int assocVertex,
boolean associateNormals)
addVertexCopy
int addVertexCopy(javax.vecmath.Point3f vertex,
float value)
setTranslucent
public void setTranslucent(boolean isTranslucent,
float iLevel)
- Overrides:
setTranslucent
in class Mesh
addTriangleCheck
void addTriangleCheck(int vertexA,
int vertexB,
int vertexC,
int check,
int color)
invalidateTriangles
void invalidateTriangles()
setABC
private boolean setABC(int i)
calculateArea
java.lang.Object calculateArea()
calculateVolume
java.lang.Object calculateVolume()
sumVertexNormals
public void sumVertexNormals(javax.vecmath.Vector3f[] vectorSums)
- Overrides:
sumVertexNormals
in class Mesh
getCenters
javax.vecmath.Point3f[] getCenters()
getFacePlane
javax.vecmath.Point4f getFacePlane(int i,
javax.vecmath.Vector3f vNorm)
getContours
java.util.Vector[] getContours()
- create a set of contour data. Each contour is a
Vector containing:
0 Integer number of polygons (length of BitSet)
1 BitSet of critical triangles
2 Float value
3 int[] [colorArgb]
4 StringBuffer containing encoded data for each segment:
char type ('3', '6', '5') indicating which two edges
of the triangle are connected:
'3' 0x011 AB-BC
'5' 0x101 AB-CA
'6' 0x110 BC-CA
char fraction along first edge (jvxlFractionToCharacter)
char fraction along second edge (jvxlFractionToCharacter)
5- stream of pairs of points for rendering
- Returns:
- contour vector set
setContourVector
public static void setContourVector(java.util.Vector v,
int nPolygons,
java.util.BitSet bsContour,
float value,
int color,
java.lang.StringBuffer fData)
get3dContour
private void get3dContour(java.util.Vector v,
float value,
int color)
checkPt
private float checkPt(int i,
int j,
float f)
getContourPoint
public static javax.vecmath.Point3f getContourPoint(javax.vecmath.Point3f[] vertices,
int i,
int j,
float f)
dumpData
private void dumpData()