public class JvxlXmlReader extends VolumeFileReader
Modifier and Type | Field and Description |
---|---|
protected BS |
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 |
jvxlColorEncodingRead |
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 |
ac, boundingBox, canDownsample, downsampleFactor, downsampleRemainders, endOfData, isAngstroms, nData, negativeAtomCount, nSkipX, nSkipY, nSkipZ, nSurfaces
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, isPeriodic, 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() |
Modifier and Type | Method and Description |
---|---|
private static int |
getColor(String c) |
private String |
getData(String sdata,
String name) |
protected void |
getEncodedVertexData()
retrieve Jvxl 2.0 format vertex/triangle/edge/color data found
within
|
private static String |
getEncoding(String data) |
private float |
getNextValue() |
protected float |
getSurfacePointAndFraction(float cutoff,
boolean isCutoffAbsolute,
float valueA,
float valueB,
javajs.util.T3 pointA,
javajs.util.V3 edgeVector,
int x,
int y,
int z,
int vA,
int vB,
float[] fReturn,
javajs.util.T3 ptReturn) |
protected BS |
getVoxelBitSet(int nPoints) |
protected boolean |
gotoAndReadVoxelData(boolean isMapData) |
protected void |
gotoData(int n,
int nPoints) |
(package private) void |
init2(SurfaceGenerator sg,
BufferedReader br) |
(package private) void |
init2JXR(SurfaceGenerator sg,
BufferedReader br) |
protected void |
jvxlDecodeContourData(JvxlData jvxlData,
String data) |
(package private) void |
jvxlDecodeTriangleData(String tdata,
String edgeData,
String colorData)
decode triangle data found within
|
javajs.util.P3[] |
jvxlDecodeVertexData(String data,
boolean asArray)
decode vertex data found within
|
private float |
jvxlGetNextFraction(int base,
int range,
float fracOffset) |
protected String |
jvxlReadFractionData(String type,
int nPoints)
"edge" data includes two parts -- a compressed bitset indicating exactly which edges,
in order or processing by Jmol, are crossed by the surface, and a set of fractions
indicating how far along that edge (good to 1 part in 8100) that surface crosses that edge.
|
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 void |
readSurfaceData(boolean isMapDataIgnored) |
protected void |
readSurfaceDataJXR() |
protected boolean |
readSurfaceDataXML() |
protected void |
readVector(int voxelVectorIndex) |
protected boolean |
readVolumeData(boolean isMapData) |
private void |
setValueMinMax() |
checkAtomLine, closeReader, getNextVoxelValue, getPlane, getPlaneNCI, getSPFv, getValue, init2VFR, initializeSurfaceData, nextVoxel, readSurfaceDataVFR, readVolumeDataVFR, readVolumeParameters, readVoxelVector, recordData, skipComments, skipData, skipDataVFR, swapXZ
closeReaderSFR, discardTempData, getQuotedStringNext, getTokens, init, init2SFR, newBinaryDocument, parseFloat, parseFloatArray, parseFloatArrayStr, parseFloatRange, parseFloatStr, parseInt, parseIntNext, parseIntStr, rd, setOutputChannel, setStream, skipTo
addTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlaneSR, getSPF, getSurfaceAtomIndex, getSurfacePointIndexAndFraction, getValue2, getValueAtPoint, initializeMapping, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, readAndSetVolumeParameters, resetIsosurface, selectPocket, setBBox, setVectorAnisotropy, setVertexAnisotropy, setVolumeDataV, 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 BS bsVoxelBitSet
private boolean includeValueNaN
private int valueCount
private float valueMin
private float valueRange
private int fractionPtr
private int colorPtr
private String strFractionTemp
boolean haveReadColorData
private String jvxlColorEncodingRead
void init2(SurfaceGenerator sg, BufferedReader br)
init2
in class VolumeFileReader
void init2JXR(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 String jvxlReadFractionData(String type, int nPoints)
type
- nPoints
- protected BS getVoxelBitSet(int nPoints) throws Exception
getVoxelBitSet
in class VolumeFileReader
Exception
protected float getSurfacePointAndFraction(float cutoff, boolean isCutoffAbsolute, float valueA, float valueB, javajs.util.T3 pointA, javajs.util.V3 edgeVector, int x, int y, int z, int vA, int vB, float[] fReturn, javajs.util.T3 ptReturn)
getSurfacePointAndFraction
in class VolumeFileReader
private float getNextValue()
private void setValueMinMax()
private float jvxlGetNextFraction(int base, int range, float fracOffset)
protected String readColorData()
readColorData
in class SurfaceReader
private static int getColor(String c)
protected void getEncodedVertexData() throws Exception
Exception
public javajs.util.P3[] jvxlDecodeVertexData(String data, boolean asArray) throws Exception
data
- tag and contentsasArray
- or just addVertexCopyException
void jvxlDecodeTriangleData(String tdata, String edgeData, String colorData) throws Exception
tdata
- tag and contentsedgeData
- colorData
- Exception
protected void jvxlDecodeContourData(JvxlData jvxlData, String data) throws Exception
Exception
protected void postProcessVertices()
postProcessVertices
in class SurfaceReader