|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectorg.jmol.util.MeshSurface
org.jmol.shape.Mesh
org.jmol.shapesurface.IsosurfaceMesh
public class IsosurfaceMesh
Field Summary | |
---|---|
private java.util.Map<java.lang.Integer,java.lang.Integer> |
assocGridPointMap
|
private java.util.Map<java.lang.Integer,javax.vecmath.Vector3f> |
assocGridPointNormals
|
(package private) java.util.BitSet |
bsVdw
|
(package private) java.lang.Object |
calculatedArea
|
(package private) java.lang.Object |
calculatedVolume
|
(package private) javax.vecmath.Point3f[] |
centers
|
(package private) ColorEncoder |
colorEncoder
|
(package private) short[] |
contourColixes
|
(package private) float[] |
contourValues
|
(package private) int |
dataType
|
(package private) int |
firstRealVertex
|
(package private) boolean |
hasGridPoints
|
(package private) java.lang.Object |
info
|
(package private) JvxlData |
jvxlData
|
private int |
mergeAssociatedNormalCount
|
(package private) int |
thisSet
|
(package private) int |
vertexIncrement
|
(package private) float |
volumeRenderPointSize
|
Fields inherited from class org.jmol.shape.Mesh |
---|
atomIndex, cappingObject, checkByteCount, color, colorCommand, colorDensity, connections, diameter, drawTriangles, fillTriangles, frontOnly, havePlanarContours, haveXyPoints, index, insideOut, isPolygonSet, isTwoSided, isValid, lattice, lighting, lineData, linkedMesh, meshColix, modelIndex, normixes, PREVIOUS_MESH_ID, ptCenter, q, recalcAltVertices, scale, scriptCommand, showContourLines, showPoints, showTriangles, slabbingObject, thisID, title, vAB, vAC, vertexColorMap, visibilityFlags, visible, vTemp, width, 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 | |
---|---|
IsosurfaceMesh(java.lang.String thisID,
Graphics3D g3d,
short colix,
int index)
|
Method Summary | |
---|---|
private static void |
addColorToMap(java.util.Map<java.lang.String,java.util.BitSet> colorMap,
java.lang.String color,
java.util.BitSet bs)
adds a set of specifically-colored vertices to the map, ensuring that no vertex is in two maps. |
static void |
addContourPoints(java.util.List<java.lang.Object> v,
java.util.BitSet bsContour,
int i,
java.lang.StringBuffer fData,
javax.vecmath.Point3f[] vertices,
float[] vertexValues,
int iA,
int iB,
int iC,
float value)
|
(package private) int |
addVertexCopy(javax.vecmath.Point3f vertex,
float value,
int assocVertex,
boolean associateNormals)
|
(package private) void |
allocVertexColixes()
|
private static float |
checkPt(float[] vertexValues,
int i,
int j,
float v)
two values -- v1, and v2, which need not be ordered v1 < v2. |
(package private) void |
clear(java.lang.String meshType,
boolean iAddGridPoints)
|
(package private) void |
colorAtoms(short colix,
java.util.BitSet bs)
color a specific set of vertices based on a set of atoms |
(package private) void |
colorVertices(short colix,
java.util.BitSet bs)
color a specific set of vertices |
private void |
colorVertices(short colix,
java.util.BitSet bs,
boolean isAtoms)
color a specific set of vertices a specific color |
(package private) void |
deleteContours()
|
private void |
get3dContour(java.util.List<java.lang.Object> v,
float value,
short colix)
|
javax.vecmath.Point3f[] |
getBoundingBox()
|
(package private) javax.vecmath.Point3f[] |
getCenters()
|
(package private) java.util.Map<java.lang.String,java.lang.Object> |
getContourList(Viewer viewer)
|
private static javax.vecmath.Point3f |
getContourPoint(javax.vecmath.Point3f[] vertices,
int i,
int j,
float f)
|
(package private) java.util.List<java.lang.Object>[] |
getContours()
create a set of contour data. |
(package private) javax.vecmath.Point4f |
getFacePlane(int i,
javax.vecmath.Vector3f vNorm)
|
protected void |
merge(MeshData m)
|
private static int |
mergePolygons(MeshSurface m,
int ipt,
int vertexCount,
int[][] newPolygons)
|
void |
reinitializeLightingAndColor()
|
(package private) void |
remapColors(ColorEncoder ce,
float translucentLevel)
remaps colors based on a new color scheme or translucency level |
(package private) void |
setColorCommand()
just sets the color command for this isosurface. |
(package private) void |
setColorsFromJvxlData(int colorRgb)
from Isosurface.notifySurfaceGenerationCompleted() starting with Jmol 12.1.50, JVXL files contain color, translucency, color scheme information, and vertex color mappings (as from COLOR ISOSURFACE {hydrophobic} WHITE), returning these settings when the JVXL file is opened. |
static void |
setContourVector(java.util.List<java.lang.Object> v,
int nPolygons,
java.util.BitSet bsContour,
float value,
short colix,
int color,
java.lang.StringBuffer fData)
|
void |
setDiscreteColixes(float[] values,
short[] colixes)
|
(package private) void |
setJvxlColorMap(boolean isAll)
set up the jvxlData fields needed for either just the header (isAll = false) or the full file (isAll = true) |
void |
setMerged(boolean TF)
|
void |
setTranslucent(boolean isTranslucent,
float iLevel)
|
protected void |
sumVertexNormals(javax.vecmath.Point3f[] vertices,
javax.vecmath.Vector3f[] vectorSums)
|
Methods inherited from class org.jmol.shape.Mesh |
---|
checkWithin, clear, getNormals, getOffsetVertices, getRendering, getState, getVertexIndexFromNumber, initialize, setLighting, setShowWithin, setTokenProperty, setVisibilityFlags, updateCoordinates |
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 |
---|
JvxlData jvxlData
int vertexIncrement
int firstRealVertex
int dataType
boolean hasGridPoints
java.lang.Object calculatedArea
java.lang.Object calculatedVolume
java.lang.Object info
private java.util.Map<java.lang.Integer,java.lang.Integer> assocGridPointMap
private java.util.Map<java.lang.Integer,javax.vecmath.Vector3f> assocGridPointNormals
int thisSet
private int mergeAssociatedNormalCount
javax.vecmath.Point3f[] centers
float[] contourValues
short[] contourColixes
ColorEncoder colorEncoder
float volumeRenderPointSize
java.util.BitSet bsVdw
Constructor Detail |
---|
IsosurfaceMesh(java.lang.String thisID, Graphics3D g3d, short colix, int index)
Method Detail |
---|
void clear(java.lang.String meshType, boolean iAddGridPoints)
void allocVertexColixes()
int addVertexCopy(javax.vecmath.Point3f vertex, float value, int assocVertex, boolean associateNormals)
public void setTranslucent(boolean isTranslucent, float iLevel)
setTranslucent
in class Mesh
public void setMerged(boolean TF)
protected void sumVertexNormals(javax.vecmath.Point3f[] vertices, javax.vecmath.Vector3f[] vectorSums)
sumVertexNormals
in class Mesh
javax.vecmath.Point3f[] getCenters()
javax.vecmath.Point4f getFacePlane(int i, javax.vecmath.Vector3f vNorm)
java.util.List<java.lang.Object>[] getContours()
private void get3dContour(java.util.List<java.lang.Object> v, float value, short colix)
public static void setContourVector(java.util.List<java.lang.Object> v, int nPolygons, java.util.BitSet bsContour, float value, short colix, int color, java.lang.StringBuffer fData)
public static void addContourPoints(java.util.List<java.lang.Object> v, java.util.BitSet bsContour, int i, java.lang.StringBuffer fData, javax.vecmath.Point3f[] vertices, float[] vertexValues, int iA, int iB, int iC, float value)
private static float checkPt(float[] vertexValues, int i, int j, float v)
vertexValues
- i
- j
- v
-
private static javax.vecmath.Point3f getContourPoint(javax.vecmath.Point3f[] vertices, int i, int j, float f)
public void setDiscreteColixes(float[] values, short[] colixes)
java.util.Map<java.lang.String,java.lang.Object> getContourList(Viewer viewer)
viewer
-
void deleteContours()
void colorAtoms(short colix, java.util.BitSet bs)
colix
- bs
- void colorVertices(short colix, java.util.BitSet bs)
colix
- bs
- private void colorVertices(short colix, java.util.BitSet bs, boolean isAtoms)
colix
- bs
- isAtoms
- private static void addColorToMap(java.util.Map<java.lang.String,java.util.BitSet> colorMap, java.lang.String color, java.util.BitSet bs)
colorMap
- color
- bs
- void setJvxlColorMap(boolean isAll)
isAll
- void setColorCommand()
void setColorsFromJvxlData(int colorRgb)
colorRgb
- void remapColors(ColorEncoder ce, float translucentLevel)
ce
- translucentLevel
- public void reinitializeLightingAndColor()
public javax.vecmath.Point3f[] getBoundingBox()
getBoundingBox
in class Mesh
protected void merge(MeshData m)
private static int mergePolygons(MeshSurface m, int ipt, int vertexCount, int[][] newPolygons)
|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |