abstract class VolumeFileReader extends SurfaceFileReader
Modifier and Type | Field and Description |
---|---|
protected int |
atomCount |
protected javax.vecmath.Point3f[] |
boundingBox |
protected boolean |
canDownsample |
private int |
downsampleFactor |
private int[] |
downsampleRemainders |
protected boolean |
endOfData |
protected boolean |
isAngstroms |
protected boolean |
negativeAtomCount |
private int |
nSkipX |
private int |
nSkipY |
private int |
nSkipZ |
protected int |
nSurfaces |
(package private) boolean |
readerClosed |
(package private) javax.vecmath.Point4f |
thePlane |
private int |
yzCount |
private float[][] |
yzPlanes |
allowSigma, ANGSTROMS_PER_BOHR, anisotropy, center, cJvxlEdgeNaN, colorFractionBase, colorFractionRange, contourVertexCount, dataMax, dataMean, dataMin, defaultCutoff, defaultMappedDataMax, defaultMappedDataMin, eccentricityMatrix, eccentricityMatrixInverse, eccentricityRatio, eccentricityScale, edgeFractionBase, edgeFractionRange, fractionData, hasColorData, isAnisotropic, isEccentric, isJvxl, isProgressive, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, jvxlVoxelBitSet, mappingPlane, marchingSquares, meshData, meshDataServer, minMax, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, sg, vertexDataOnly, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData, xyzMax, xyzMin
Constructor and Description |
---|
VolumeFileReader(SurfaceGenerator sg,
java.io.BufferedReader br) |
Modifier and Type | Method and Description |
---|---|
protected static boolean |
checkAtomLine(boolean isXLowToHigh,
boolean isAngstroms,
java.lang.String strAtomCount,
java.lang.String atomLine,
java.lang.StringBuffer bs)
checks an atom line for "ANGSTROMS", possibly overriding the data's natural
units, BOHR (similar to Gaussian CUBE files).
|
protected void |
closeReader() |
private int |
countData(java.lang.String str) |
protected float |
getNextVoxelValue() |
void |
getPlane(int x) |
float |
getValue(int x,
int y,
int z,
int ptyz)
for readers only
|
protected java.util.BitSet |
getVoxelBitSet(int nPoints) |
protected void |
gotoData(int n,
int nPoints) |
protected float |
nextVoxel() |
protected abstract void |
readParameters() |
protected void |
readSurfaceData(boolean isMapData) |
protected boolean |
readVolumeData(boolean isMapData) |
protected boolean |
readVolumeParameters() |
private int |
readVolumetricHeader() |
protected void |
readVoxelVector(int voxelVectorIndex) |
protected float |
recordData(float value) |
protected java.lang.String |
skipComments(boolean allowBlankLines) |
protected void |
skipData(int nPoints) |
private void |
skipVoxels(int n) |
discardTempData, getNextQuotedString, getTokens, parseFloat, parseFloat, parseFloatArray, parseFloatArray, parseInt, parseInt, parseIntNext, readLine, setOutputStream, skipTo
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValueAtPoint, gotoAndReadVoxelData, initializeMapping, initializeVolumetricData, jvxlUpdateInfo, readAndSetVolumeParameters, readColorData, readTheVolumeData, resetIsosurface, selectPocket, setBoundingBox, setMappingPlane, setVectorAnisotropy, setVertexAnisotropy, setVolumeData, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles
protected boolean endOfData
protected boolean negativeAtomCount
protected int atomCount
protected int nSurfaces
protected boolean isAngstroms
protected boolean canDownsample
private int[] downsampleRemainders
boolean readerClosed
javax.vecmath.Point4f thePlane
private int downsampleFactor
private int nSkipX
private int nSkipY
private int nSkipZ
private float[][] yzPlanes
private int yzCount
protected javax.vecmath.Point3f[] boundingBox
VolumeFileReader(SurfaceGenerator sg, java.io.BufferedReader br)
protected float recordData(float value)
protected void closeReader()
closeReader
in class SurfaceFileReader
protected boolean readVolumeParameters()
readVolumeParameters
in class SurfaceReader
protected boolean readVolumeData(boolean isMapData)
readVolumeData
in class SurfaceReader
private int readVolumetricHeader()
protected abstract void readParameters() throws java.lang.Exception
java.lang.Exception
protected java.lang.String skipComments(boolean allowBlankLines) throws java.lang.Exception
java.lang.Exception
protected void readVoxelVector(int voxelVectorIndex) throws java.lang.Exception
java.lang.Exception
protected void readSurfaceData(boolean isMapData) throws java.lang.Exception
readSurfaceData
in class SurfaceReader
java.lang.Exception
public void getPlane(int x)
getPlane
in interface VertexDataServer
getPlane
in class SurfaceReader
public float getValue(int x, int y, int z, int ptyz)
VertexDataServer
getValue
in interface VertexDataServer
getValue
in class SurfaceReader
private void skipVoxels(int n) throws java.lang.Exception
java.lang.Exception
protected java.util.BitSet getVoxelBitSet(int nPoints) throws java.lang.Exception
java.lang.Exception
protected float getNextVoxelValue() throws java.lang.Exception
java.lang.Exception
protected float nextVoxel() throws java.lang.Exception
java.lang.Exception
protected void gotoData(int n, int nPoints) throws java.lang.Exception
gotoData
in class SurfaceReader
java.lang.Exception
protected void skipData(int nPoints) throws java.lang.Exception
java.lang.Exception
private int countData(java.lang.String str)
protected static boolean checkAtomLine(boolean isXLowToHigh, boolean isAngstroms, java.lang.String strAtomCount, java.lang.String atomLine, java.lang.StringBuffer bs)
isXLowToHigh
- isAngstroms
- strAtomCount
- atomLine
- bs
-