org.jmol.jvxl.readers
Class JvxlXmlReader
java.lang.Object
org.jmol.jvxl.readers.SurfaceReader
org.jmol.jvxl.readers.SurfaceFileReader
org.jmol.jvxl.readers.VolumeFileReader
org.jmol.jvxl.readers.JvxlXmlReader
- All Implemented Interfaces:
- VertexDataServer
- Direct Known Subclasses:
- JvxlReader
public class JvxlXmlReader
- extends VolumeFileReader
Fields inherited from class org.jmol.jvxl.readers.SurfaceReader |
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, 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 |
Method Summary |
protected void |
getEncodedVertexData()
retrieve Jvxl 2.0 format vertex/triangle/edge/color data found
within element |
private float |
getNextValue()
|
protected float |
getSurfacePointAndFraction(float cutoff,
boolean isCutoffAbsolute,
float valueA,
float valueB,
javax.vecmath.Point3f pointA,
javax.vecmath.Vector3f edgeVector,
int x,
int y,
int z,
int vA,
int vB,
float[] fReturn,
javax.vecmath.Point3f ptReturn)
|
protected java.util.BitSet |
getVoxelBitSet(int nPoints)
|
protected boolean |
gotoAndReadVoxelData(boolean isMapData)
|
protected void |
gotoData(int n,
int nPoints)
|
protected void |
jvxlDecodeContourData(JvxlData jvxlData,
java.lang.String data)
|
(package private) int[][] |
jvxlDecodeTriangleData(java.lang.String data,
java.lang.String edgeData,
java.lang.String colorData)
decode triangle data found within element as created
with jvxlEncodeTriangleData (see above) |
javax.vecmath.Point3f[] |
jvxlDecodeVertexData(java.lang.String data,
boolean asArray)
decode vertex data found within element
as created by jvxlEncodeVertexData (see above) |
private float |
jvxlGetNextFraction(int base,
int range,
float fracOffset)
|
protected java.lang.String |
jvxlReadData(java.lang.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 java.lang.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()
|
Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader |
checkAtomLine, closeReader, getNextVoxelValue, getPlane, getPlaneProcessed, getValue, initializeSurfaceData, nextVoxel, readVolumeParameters, readVoxelVector, recordData, skipComments, skipData |
Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader |
discardTempData, getNextQuotedString, getTokens, parseFloat, parseFloat, parseFloatArray, parseFloatArray, parseInt, parseInt, parseIntNext, readLine, setOutputStream, skipTo |
Methods inherited from class org.jmol.jvxl.readers.SurfaceReader |
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 |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
JVXL_VERSION
protected java.lang.String JVXL_VERSION
surfaceDataCount
protected int surfaceDataCount
edgeDataCount
protected int edgeDataCount
colorDataCount
protected int colorDataCount
excludedTriangleCount
private int excludedTriangleCount
excludedVertexCount
private int excludedVertexCount
invalidatedVertexCount
private int invalidatedVertexCount
haveContourData
protected boolean haveContourData
xr
private XmlReader xr
isXmlFile
protected boolean isXmlFile
thisInside
protected boolean thisInside
tempDataXml
java.lang.String tempDataXml
bsVoxelBitSet
protected java.util.BitSet bsVoxelBitSet
includeValueNaN
private boolean includeValueNaN
valueCount
private int valueCount
valueMin
private float valueMin
valueRange
private float valueRange
fractionPtr
private int fractionPtr
colorPtr
private int colorPtr
strFractionTemp
private java.lang.String strFractionTemp
haveReadColorData
boolean haveReadColorData
JvxlXmlReader
JvxlXmlReader(SurfaceGenerator sg,
java.io.BufferedReader br)
readVolumeData
protected boolean readVolumeData(boolean isMapData)
- Overrides:
readVolumeData
in class VolumeFileReader
gotoAndReadVoxelData
protected boolean gotoAndReadVoxelData(boolean isMapData)
- Overrides:
gotoAndReadVoxelData
in class SurfaceReader
readParameters
protected void readParameters()
throws java.lang.Exception
- Specified by:
readParameters
in class VolumeFileReader
- Throws:
java.lang.Exception
readVector
protected void readVector(int voxelVectorIndex)
throws java.lang.Exception
- Throws:
java.lang.Exception
gotoData
protected void gotoData(int n,
int nPoints)
throws java.lang.Exception
- Overrides:
gotoData
in class VolumeFileReader
- Throws:
java.lang.Exception
jvxlSkipData
protected void jvxlSkipData(int nPoints,
boolean doSkipColorData)
throws java.lang.Exception
- Throws:
java.lang.Exception
jvxlReadSurfaceInfo
protected void jvxlReadSurfaceInfo()
throws java.lang.Exception
- Throws:
java.lang.Exception
jvxlSetColorRanges
protected void jvxlSetColorRanges(float dataMin,
float dataMax,
float red,
float blue,
boolean insideOut)
readSurfaceData
protected void readSurfaceData(boolean isMapDataIgnored)
throws java.lang.Exception
- Overrides:
readSurfaceData
in class VolumeFileReader
- Throws:
java.lang.Exception
readSurfaceData
protected boolean readSurfaceData()
throws java.lang.Exception
- Throws:
java.lang.Exception
readVolumeFileSurfaceData
protected void readVolumeFileSurfaceData()
throws java.lang.Exception
- Throws:
java.lang.Exception
jvxlReadData
protected java.lang.String jvxlReadData(java.lang.String type,
int nPoints)
getVoxelBitSet
protected java.util.BitSet getVoxelBitSet(int nPoints)
throws java.lang.Exception
- Overrides:
getVoxelBitSet
in class VolumeFileReader
- Returns:
- JVXL bitset
- Throws:
java.lang.Exception
getSurfacePointAndFraction
protected float getSurfacePointAndFraction(float cutoff,
boolean isCutoffAbsolute,
float valueA,
float valueB,
javax.vecmath.Point3f pointA,
javax.vecmath.Vector3f edgeVector,
int x,
int y,
int z,
int vA,
int vB,
float[] fReturn,
javax.vecmath.Point3f ptReturn)
- Overrides:
getSurfacePointAndFraction
in class VolumeFileReader
x
- TODOy
- TODOz
- TODO
- Returns:
- fractional distance from A to B
getNextValue
private float getNextValue()
setValueMinMax
private void setValueMinMax()
jvxlGetNextFraction
private float jvxlGetNextFraction(int base,
int range,
float fracOffset)
readColorData
protected java.lang.String readColorData()
- Overrides:
readColorData
in class SurfaceReader
getEncodedVertexData
protected void getEncodedVertexData()
throws java.lang.Exception
- retrieve Jvxl 2.0 format vertex/triangle/edge/color data found
within element
- Throws:
java.lang.Exception
jvxlDecodeVertexData
public javax.vecmath.Point3f[] jvxlDecodeVertexData(java.lang.String data,
boolean asArray)
throws java.lang.Exception
- decode vertex data found within element
as created by jvxlEncodeVertexData (see above)
- Parameters:
data
- tag and contentsasArray
- or just addVertexCopy
- Returns:
- Point3f[] if desired
- Throws:
java.lang.Exception
jvxlDecodeTriangleData
int[][] jvxlDecodeTriangleData(java.lang.String data,
java.lang.String edgeData,
java.lang.String colorData)
throws java.lang.Exception
- decode triangle data found within element as created
with jvxlEncodeTriangleData (see above)
- Parameters:
data
- tag and contentsedgeData
- colorData
-
- Returns:
- int[][] if desired
- Throws:
java.lang.Exception
jvxlDecodeContourData
protected void jvxlDecodeContourData(JvxlData jvxlData,
java.lang.String data)
throws java.lang.Exception
- Throws:
java.lang.Exception
postProcessVertices
protected void postProcessVertices()
- Overrides:
postProcessVertices
in class SurfaceReader