org.jmol.jvxl.readers
Class VoxelReader
public abstract
class
VoxelReader
extends Object
implements VertexDataServer
Method Summary |
void | addTriangleCheck(int iA, int iB, int iC, int check, boolean isAbsolute) |
int | addVertexCopy(Point3f vertexXYZ, float value, int assocVertex) |
void | applyColorScale() |
void | colorData() |
void | colorIsosurface() |
boolean | createIsosurface(boolean justForPlane) |
void | discardTempData(boolean discardAll) |
void | excludeMaximumSet() |
void | excludeMinimumSet() |
void | generateSurfaceData() |
void | getCalcPoint(Point3f pt) |
protected short | getColorIndexFromPalette(float value) |
static int | getColorPhaseIndex(String color) |
float | getMaxMappedValue() |
float | getMinMappedValue() |
float | getPhase(Point3f pt) |
int | getSurfacePointIndex(float cutoff, boolean isCutoffAbsolute, int x, int y, int z, Point3i offset, int vA, int vB, float valueA, float valueB, Point3f pointA, Vector3f edgeVector, boolean isContourType) |
protected void | gotoAndReadVoxelData(boolean isMapData) |
protected void | gotoData(int n, int nPoints) |
protected void | initializeVolumetricData() |
protected static boolean | isInside(float voxelValue, float max, boolean isAbsolute) |
void | jvxlUpdateInfo() |
protected String | readColorData() |
protected float | readSurfacePoint(float cutoff, boolean isCutoffAbsolute, float valueA, float valueB, Point3f pointA, Vector3f edgeVector, float[] fReturn, Point3f ptReturn) |
abstract void | readVolumeData(boolean isMapData) |
abstract void | readVolumeParameters() |
protected abstract void | readVoxelData(boolean isMapData) |
void | resetIsosurface() |
void | selectPocket(boolean doExclude) |
void | setVolumeData(VolumeData v) |
void | updateSurfaceData() |
void | updateTriangles() |
static final float ANGSTROMS_PER_BOHR
private float assocCutoff
protected char cJvxlEdgeNaN
protected int colorFractionBase
protected int colorFractionRange
private static final String[] colorPhases
protected int contourVertexCount
static final int defaultColorFractionBase
static final int defaultColorFractionRange
static final float defaultCutoff
static final int defaultEdgeFractionBase
static final int defaultEdgeFractionRange
static final float defaultMappedDataMax
static final float defaultMappedDataMin
private int edgeCount
protected int edgeFractionBase
protected int edgeFractionRange
protected StringBuffer fractionData
final float[] fReturn
protected boolean isApbsDx
protected boolean isJvxl
protected boolean isProgressive
protected boolean isXLowToHigh
protected String jvxlColorDataRead
protected float jvxlCutoff
protected boolean jvxlDataIs2dContour
protected boolean jvxlDataIsColorMapped
protected boolean jvxlDataIsPrecisionColor
protected String jvxlEdgeDataRead
protected StringBuffer jvxlFileHeaderBuffer
protected int jvxlNSurfaceInts
protected int nBytes
protected int nDataPoints
protected int nPointsX
protected int nPointsY
protected int nPointsZ
protected final Point3f ptTemp
protected Point3f volumetricOrigin
protected Vector3f[] volumetricVectors
protected int[] voxelCounts
protected float[][][] voxelData
public void addTriangleCheck(int iA, int iB, int iC, int check, boolean isAbsolute)
public int addVertexCopy(Point3f vertexXYZ, float value, int assocVertex)
void applyColorScale()
private void colorData()
void colorIsosurface()
boolean createIsosurface(boolean justForPlane)
void discardTempData(boolean discardAll)
void excludeMaximumSet()
void excludeMinimumSet()
private void generateSurfaceData()
public void getCalcPoint(Point3f pt)
protected short getColorIndexFromPalette(float value)
static int getColorPhaseIndex(String color)
float getMaxMappedValue()
float getMinMappedValue()
private float getPhase(Point3f pt)
public int getSurfacePointIndex(float cutoff, boolean isCutoffAbsolute, int x, int y, int z, Point3i offset, int vA, int vB, float valueA, float valueB, Point3f pointA, Vector3f edgeVector, boolean isContourType)
protected void gotoAndReadVoxelData(boolean isMapData)
protected void gotoData(int n, int nPoints)
protected void initializeVolumetricData()
protected static boolean isInside(float voxelValue, float max, boolean isAbsolute)
void jvxlUpdateInfo()
protected String readColorData()
protected float readSurfacePoint(float cutoff, boolean isCutoffAbsolute, float valueA, float valueB, Point3f pointA, Vector3f edgeVector, float[] fReturn, Point3f ptReturn)
abstract void readVolumeData(boolean isMapData)
abstract void readVolumeParameters()
protected abstract void readVoxelData(boolean isMapData)
void resetIsosurface()
public void selectPocket(boolean doExclude)
void updateSurfaceData()
void updateTriangles()