Package org.jmol.jvxl.readers
Class VolumeFileReader
java.lang.Object
org.jmol.jvxl.readers.SurfaceReader
org.jmol.jvxl.readers.SurfaceFileReader
org.jmol.jvxl.readers.VolumeFileReader
- All Implemented Interfaces:
VertexDataServer
- Direct Known Subclasses:
ApbsReader
,CubeReader
,DelPhiBinaryReader
,IsoIntersectGridReader
,JaguarReader
,JvxlXmlReader
,MapFileReader
,PeriodicVolumeFileReader
,PltFormattedReader
,UhbdReader
,XsfReader
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected int
protected javajs.util.P3[]
protected boolean
protected int
protected int[]
protected boolean
private boolean
private int
protected boolean
private boolean
protected int
protected boolean
protected int
protected int
protected int
protected int
protected boolean
private float[][]
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, isPeriodic, isProgressive, isQuiet, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlCutoffRange, 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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected static boolean
checkAtomLine
(boolean isXLowToHigh, boolean isAngstroms, String strAtomCount, String atomLine, javajs.util.SB bs) checks an atom line for "ANGSTROMS", possibly overriding the data's natural units, BOHR (similar to Gaussian CUBE files).protected void
private int
protected float
protected float
float[]
getPlane
(int x) float[]
getPlaneNCI
(int x) Retrieve raw file planes and pass them to the calculation object for processing into new data.private void
getPlaneVFR
(float[] plane, boolean doRecord) protected float
getSPFv
(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 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) float
getValue
(int x, int y, int z, int ptyz) for readers onlyprotected javajs.util.BS
getVoxelBitSet
(int nPoints) protected void
gotoData
(int n, int nPoints) (package private) void
init2
(SurfaceGenerator sg, BufferedReader br) (package private) void
init2VFR
(SurfaceGenerator sg, BufferedReader br) (package private) void
protected float
protected abstract void
protected void
readSurfaceData
(boolean isMapData) protected void
readSurfaceDataVFR
(boolean isMapData) protected boolean
readVolumeData
(boolean isMapData) protected boolean
readVolumeDataVFR
(boolean isMapData) protected boolean
readVolumeParameters
(boolean isMapData) private int
protected void
readVoxelVector
(int voxelVectorIndex) protected float
recordData
(float value) private void
scaleIsosurface
(float scale) protected String
skipComments
(boolean allowBlankLines) protected void
skipData
(int nPoints) protected void
skipDataVFR
(int nPoints) private void
skipVoxels
(int n) protected void
swapXZ()
Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader
closeReaderSFR, discardTempData, getQuotedStringNext, getTokens, init, init2SFR, newBinaryDocument, parseFloat, parseFloatArray, parseFloatArrayStr, parseFloatRange, parseFloatStr, parseInt, parseIntNext, parseIntStr, rd, setOutputChannel, setStream, skipTo
Methods inherited from class org.jmol.jvxl.readers.SurfaceReader
addTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlaneSR, getSPF, getSurfaceAtomIndex, getSurfacePointIndexAndFraction, getValue2, getValueAtPoint, gotoAndReadVoxelData, initializeMapping, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBBox, setVectorAnisotropy, setVertexAnisotropy, setVolumeDataV, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles
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Field Details
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endOfData
protected boolean endOfData -
negativeAtomCount
protected boolean negativeAtomCount -
ac
protected int ac -
nSurfaces
protected int nSurfaces -
isAngstroms
protected boolean isAngstroms -
canDownsample
protected boolean canDownsample -
downsampleRemainders
protected int[] downsampleRemainders -
getNCIPlanes
private boolean getNCIPlanes -
nData
protected int nData -
readerClosed
protected boolean readerClosed -
downsampleFactor
protected int downsampleFactor -
nSkipX
protected int nSkipX -
nSkipY
protected int nSkipY -
nSkipZ
protected int nSkipZ -
yzPlanesRaw
private float[][] yzPlanesRaw -
iPlaneNCI
private int iPlaneNCI -
boundingBox
protected javajs.util.P3[] boundingBox -
isScaledAlready
private boolean isScaledAlready
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Constructor Details
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VolumeFileReader
VolumeFileReader()
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Method Details
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init2
- Overrides:
init2
in classSurfaceFileReader
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init2VFR
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recordData
protected float recordData(float value) -
closeReader
protected void closeReader()- Overrides:
closeReader
in classSurfaceFileReader
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readVolumeParameters
protected boolean readVolumeParameters(boolean isMapData) - Specified by:
readVolumeParameters
in classSurfaceReader
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readVolumeData
protected boolean readVolumeData(boolean isMapData) - Specified by:
readVolumeData
in classSurfaceReader
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readVolumeDataVFR
protected boolean readVolumeDataVFR(boolean isMapData) -
readVolumetricHeader
private int readVolumetricHeader() -
readParameters
- Throws:
Exception
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skipComments
- Throws:
Exception
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readVoxelVector
- Throws:
Exception
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initializeSurfaceData
void initializeSurfaceData() -
getJVXLCutoff
protected float getJVXLCutoff() -
readSurfaceData
- Specified by:
readSurfaceData
in classSurfaceReader
- Throws:
Exception
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readSurfaceDataVFR
- Throws:
Exception
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getPlane
public float[] getPlane(int x) - Specified by:
getPlane
in interfaceVertexDataServer
- Overrides:
getPlane
in classSurfaceReader
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getPlaneNCI
public float[] getPlaneNCI(int x) Retrieve raw file planes and pass them to the calculation object for processing into new data. Bob Hanson hansonr@stolaf.edu 6/7/2011- Parameters:
x
-- Returns:
- plane (for testing)
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getPlaneVFR
private void getPlaneVFR(float[] plane, boolean doRecord) -
getValue
public float getValue(int x, int y, int z, int ptyz) Description copied from interface:VertexDataServer
for readers only- Specified by:
getValue
in interfaceVertexDataServer
- Overrides:
getValue
in classSurfaceReader
- Parameters:
x
-y
-z
-ptyz
-- Returns:
- value[x][y][z]
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skipVoxels
- Throws:
Exception
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getVoxelBitSet
- Parameters:
nPoints
-- Returns:
- JVXL bitset
- Throws:
Exception
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getNextVoxelValue
- Throws:
Exception
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nextVoxel
- Throws:
Exception
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gotoData
- Overrides:
gotoData
in classSurfaceReader
- Parameters:
n
-nPoints
-- Throws:
Exception
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skipData
- Throws:
Exception
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skipDataVFR
- Throws:
Exception
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countData
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checkAtomLine
protected static boolean checkAtomLine(boolean isXLowToHigh, boolean isAngstroms, String strAtomCount, String atomLine, javajs.util.SB bs) checks an atom line for "ANGSTROMS", possibly overriding the data's natural units, BOHR (similar to Gaussian CUBE files).- Parameters:
isXLowToHigh
-isAngstroms
-strAtomCount
-atomLine
-bs
-- Returns:
- isAngstroms
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getSurfacePointAndFraction
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) - Overrides:
getSurfacePointAndFraction
in classSurfaceReader
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getSPFv
protected float getSPFv(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) -
scaleIsosurface
private void scaleIsosurface(float scale) -
swapXZ
protected void swapXZ()
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