public class JvxlXmlReader extends VolumeFileReader
| Modifier and Type | Field and Description |
|---|---|
protected javajs.util.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 java.lang.String |
JVXL_VERSION |
private java.lang.String |
jvxlColorEncodingRead |
private java.lang.String |
strFractionTemp |
protected int |
surfaceDataCount |
(package private) java.lang.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, readerClosedallowSigma, 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(java.lang.String c) |
private java.lang.String |
getData(java.lang.String sdata,
java.lang.String name) |
protected void |
getEncodedVertexData()
retrieve Jvxl 2.0 format vertex/triangle/edge/color data found
within
|
private static java.lang.String |
getEncoding(java.lang.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 javajs.util.BS |
getVoxelBitSet(int nPoints) |
protected boolean |
gotoAndReadVoxelData(boolean isMapData) |
protected void |
gotoData(int n,
int nPoints) |
(package private) void |
init2(SurfaceGenerator sg,
java.io.BufferedReader br) |
(package private) void |
init2JXR(SurfaceGenerator sg,
java.io.BufferedReader br) |
protected void |
jvxlDecodeContourData(JvxlData jvxlData,
java.lang.String data) |
(package private) void |
jvxlDecodeTriangleData(java.lang.String tdata,
java.lang.String edgeData,
java.lang.String colorData)
decode triangle data found within
|
javajs.util.P3[] |
jvxlDecodeVertexData(java.lang.String data,
boolean asArray)
decode vertex data found within
|
private float |
jvxlGetNextFraction(int base,
int range,
float fracOffset) |
protected java.lang.String |
jvxlReadFractionData(java.lang.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 java.lang.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, swapXZcloseReaderSFR, discardTempData, getQuotedStringNext, getTokens, init, init2SFR, newBinaryDocument, parseFloat, parseFloatArray, parseFloatArrayStr, parseFloatRange, parseFloatStr, parseInt, parseIntNext, parseIntStr, rd, setOutputChannel, setStream, skipToaddTriangleCheck, 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, updateTrianglesprotected java.lang.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
java.lang.String tempDataXml
protected javajs.util.BS bsVoxelBitSet
private boolean includeValueNaN
private int valueCount
private float valueMin
private float valueRange
private int fractionPtr
private int colorPtr
private java.lang.String strFractionTemp
boolean haveReadColorData
private java.lang.String jvxlColorEncodingRead
void init2(SurfaceGenerator sg, java.io.BufferedReader br)
init2 in class VolumeFileReadervoid init2JXR(SurfaceGenerator sg, java.io.BufferedReader br)
protected boolean readVolumeData(boolean isMapData)
readVolumeData in class VolumeFileReaderprotected boolean gotoAndReadVoxelData(boolean isMapData)
gotoAndReadVoxelData in class SurfaceReaderprotected void readParameters()
throws java.lang.Exception
readParameters in class VolumeFileReaderjava.lang.Exceptionprotected void readVector(int voxelVectorIndex)
throws java.lang.Exception
java.lang.Exceptionprotected void gotoData(int n,
int nPoints)
throws java.lang.Exception
gotoData in class VolumeFileReaderjava.lang.Exceptionprotected void jvxlSkipData(int nPoints,
boolean doSkipColorData)
throws java.lang.Exception
java.lang.Exceptionprotected void jvxlReadSurfaceInfo()
throws java.lang.Exception
java.lang.Exceptionprotected void jvxlSetColorRanges(float dataMin,
float dataMax,
float red,
float blue,
boolean insideOut)
protected void readSurfaceData(boolean isMapDataIgnored)
throws java.lang.Exception
readSurfaceData in class VolumeFileReaderjava.lang.Exceptionprotected boolean readSurfaceDataXML()
throws java.lang.Exception
java.lang.Exceptionprotected void readSurfaceDataJXR()
throws java.lang.Exception
java.lang.Exceptionprotected java.lang.String jvxlReadFractionData(java.lang.String type,
int nPoints)
type - nPoints - protected javajs.util.BS getVoxelBitSet(int nPoints)
throws java.lang.Exception
getVoxelBitSet in class VolumeFileReaderjava.lang.Exceptionprotected 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 VolumeFileReaderprivate float getNextValue()
private void setValueMinMax()
private float jvxlGetNextFraction(int base,
int range,
float fracOffset)
protected java.lang.String readColorData()
readColorData in class SurfaceReaderprivate static int getColor(java.lang.String c)
protected void getEncodedVertexData()
throws java.lang.Exception
java.lang.Exceptionprivate java.lang.String getData(java.lang.String sdata,
java.lang.String name)
throws java.lang.Exception
java.lang.Exceptionprivate static java.lang.String getEncoding(java.lang.String data)
public javajs.util.P3[] jvxlDecodeVertexData(java.lang.String data,
boolean asArray)
throws java.lang.Exception
data - tag and contentsasArray - or just addVertexCopyjava.lang.Exceptionvoid jvxlDecodeTriangleData(java.lang.String tdata,
java.lang.String edgeData,
java.lang.String colorData)
throws java.lang.Exception
tdata - tag and contentsedgeData - colorData - java.lang.Exceptionprotected void jvxlDecodeContourData(JvxlData jvxlData, java.lang.String data) throws java.lang.Exception
java.lang.Exceptionprotected void postProcessVertices()
postProcessVertices in class SurfaceReader