org.jmol.jvxl.readers
public class JvxlXmlReader extends VolumeFileReader
Modifier and Type | Field and Description |
---|---|
protected BitSet |
bsVoxelBitSet |
protected int |
colorDataCount |
private int |
colorPtr |
protected int |
edgeDataCount |
private int |
excludedTriangleCount |
private int |
excludedVertexCount |
private int |
fractionPtr |
protected boolean |
haveContourData |
(package private) boolean |
haveReadColorData |
private boolean |
includeValueNaN |
private int |
invalidatedVertexCount |
protected boolean |
isXmlFile |
protected String |
JVXL_VERSION |
private String |
strFractionTemp |
protected int |
surfaceDataCount |
(package private) String |
tempDataXml |
protected boolean |
thisInside |
private int |
valueCount |
private float |
valueMin |
private float |
valueRange |
private XmlReader |
xr |
atomCount, boundingBox, canDownsample, downsampleFactor, endOfData, isAngstroms, negativeAtomCount, nSurfaces, readerClosed, thePlane
allowSigma, ANGSTROMS_PER_BOHR, anisotropy, center, cJvxlEdgeNaN, colorFractionBase, colorFractionRange, contourVertexCount, dataMax, dataMean, dataMin, defaultCutoff, defaultMappedDataMax, defaultMappedDataMin, eccentricityMatrix, eccentricityMatrixInverse, eccentricityRatio, eccentricityScale, edgeFractionBase, edgeFractionRange, fractionData, hasColorData, haveSurfaceAtoms, isAnisotropic, isEccentric, isJvxl, isProgressive, isQuiet, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorDensity, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, jvxlVoxelBitSet, marchingCubes, marchingSquares, meshData, meshDataServer, minMax, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, qpc, sg, vertexDataOnly, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData, xyzMax, xyzMin, yzCount, yzPlanes
Constructor and Description |
---|
JvxlXmlReader(SurfaceGenerator sg,
BufferedReader br) |
Modifier and Type | Method and Description |
---|---|
protected void |
getEncodedVertexData()
retrieve Jvxl 2.0 format vertex/triangle/edge/color data found
within
|
private float |
getNextValue() |
protected float |
getSurfacePointAndFraction(float cutoff,
boolean isCutoffAbsolute,
float valueA,
float valueB,
Point3f pointA,
Vector3f edgeVector,
int x,
int y,
int z,
int vA,
int vB,
float[] fReturn,
Point3f ptReturn) |
protected BitSet |
getVoxelBitSet(int nPoints) |
protected boolean |
gotoAndReadVoxelData(boolean isMapData) |
protected void |
gotoData(int n,
int nPoints) |
protected void |
jvxlDecodeContourData(JvxlData jvxlData,
String data) |
(package private) int[][] |
jvxlDecodeTriangleData(String data,
String edgeData,
String colorData)
decode triangle data found within
|
Point3f[] |
jvxlDecodeVertexData(String data,
boolean asArray)
decode vertex data found within
|
private float |
jvxlGetNextFraction(int base,
int range,
float fracOffset) |
protected String |
jvxlReadData(String type,
int nPoints) |
protected void |
jvxlReadSurfaceInfo() |
protected void |
jvxlSetColorRanges(float dataMin,
float dataMax,
float red,
float blue,
boolean insideOut) |
protected void |
jvxlSkipData(int nPoints,
boolean doSkipColorData) |
protected void |
postProcessVertices() |
protected String |
readColorData() |
protected void |
readParameters() |
protected boolean |
readSurfaceData() |
protected void |
readSurfaceData(boolean isMapDataIgnored) |
protected void |
readVector(int voxelVectorIndex) |
protected boolean |
readVolumeData(boolean isMapData) |
protected void |
readVolumeFileSurfaceData() |
private void |
setValueMinMax() |
checkAtomLine, closeReader, getNextVoxelValue, getPlane, getPlaneProcessed, getValue, initializeSurfaceData, nextVoxel, readVolumeParameters, readVoxelVector, recordData, skipComments, skipData
discardTempData, getNextQuotedString, getTokens, parseFloat, parseFloat, parseFloatArray, parseFloatArray, parseInt, parseInt, parseIntNext, readLine, setOutputStream, skipTo
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getSurfaceAtomIndex, getSurfacePointIndexAndFraction, getValueAtPoint, initializeMapping, initializeVolumetricData, initPlanes, jvxlUpdateInfo, newVoxelDataCube, readAndSetVolumeParameters, resetIsosurface, selectPocket, setBoundingBox, setVectorAnisotropy, setVertexAnisotropy, setVolumeData, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles
protected String JVXL_VERSION
protected int surfaceDataCount
protected int edgeDataCount
protected int colorDataCount
private int excludedTriangleCount
private int excludedVertexCount
private int invalidatedVertexCount
protected boolean haveContourData
private XmlReader xr
protected boolean isXmlFile
protected boolean thisInside
String tempDataXml
protected BitSet bsVoxelBitSet
private boolean includeValueNaN
private int valueCount
private float valueMin
private float valueRange
private int fractionPtr
private int colorPtr
private String strFractionTemp
boolean haveReadColorData
JvxlXmlReader(SurfaceGenerator sg, BufferedReader br)
protected boolean readVolumeData(boolean isMapData)
readVolumeData
in class VolumeFileReader
protected boolean gotoAndReadVoxelData(boolean isMapData)
gotoAndReadVoxelData
in class SurfaceReader
protected void readParameters() throws Exception
readParameters
in class VolumeFileReader
Exception
protected void gotoData(int n, int nPoints) throws Exception
gotoData
in class VolumeFileReader
Exception
protected void jvxlSkipData(int nPoints, boolean doSkipColorData) throws Exception
Exception
protected void jvxlSetColorRanges(float dataMin, float dataMax, float red, float blue, boolean insideOut)
protected void readSurfaceData(boolean isMapDataIgnored) throws Exception
readSurfaceData
in class VolumeFileReader
Exception
protected void readVolumeFileSurfaceData() throws Exception
Exception
protected BitSet getVoxelBitSet(int nPoints) throws Exception
getVoxelBitSet
in class VolumeFileReader
Exception
protected float getSurfacePointAndFraction(float cutoff, boolean isCutoffAbsolute, float valueA, float valueB, Point3f pointA, Vector3f edgeVector, int x, int y, int z, int vA, int vB, float[] fReturn, Point3f ptReturn)
getSurfacePointAndFraction
in class VolumeFileReader
x
- TODOy
- TODOz
- TODOprivate float getNextValue()
private void setValueMinMax()
private float jvxlGetNextFraction(int base, int range, float fracOffset)
protected String readColorData()
readColorData
in class SurfaceReader
protected void getEncodedVertexData() throws Exception
Exception
public Point3f[] jvxlDecodeVertexData(String data, boolean asArray) throws Exception
data
- tag and contentsasArray
- or just addVertexCopyException
int[][] jvxlDecodeTriangleData(String data, String edgeData, String colorData) throws Exception
data
- tag and contentsedgeData
- colorData
- Exception
protected void jvxlDecodeContourData(JvxlData jvxlData, String data) throws Exception
Exception
protected void postProcessVertices()
postProcessVertices
in class SurfaceReader