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, JaguarReader, JvxlXmlReader, MapFileReader, PltFormattedReader
abstract class VolumeFileReader
- extends SurfaceFileReader
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, 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 |
Method Summary |
protected static boolean |
checkAtomLine(boolean isXLowToHigh,
boolean isAngstroms,
String strAtomCount,
String atomLine,
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(String str)
|
protected float |
getNextVoxelValue()
|
void |
getPlane(int x)
|
float |
getValue(int x,
int y,
int z,
int ptyz)
for readers only |
protected 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 String |
skipComments(boolean allowBlankLines)
|
protected void |
skipData(int nPoints)
|
private void |
skipVoxels(int n)
|
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, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValueAtPoint, gotoAndReadVoxelData, initializeMapping, initializeVolumetricData, jvxlUpdateInfo, readAndSetVolumeParameters, readColorData, readTheVolumeData, resetIsosurface, selectPocket, setBoundingBox, setMappingPlane, 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 |
endOfData
protected boolean endOfData
negativeAtomCount
protected boolean negativeAtomCount
atomCount
protected int atomCount
nSurfaces
protected int nSurfaces
isAngstroms
protected boolean isAngstroms
canDownsample
protected boolean canDownsample
downsampleRemainders
private int[] downsampleRemainders
readerClosed
boolean readerClosed
thePlane
Point4f thePlane
downsampleFactor
private int downsampleFactor
nSkipX
private int nSkipX
nSkipY
private int nSkipY
nSkipZ
private int nSkipZ
yzPlanes
private float[][] yzPlanes
yzCount
private int yzCount
boundingBox
protected Point3f[] boundingBox
VolumeFileReader
VolumeFileReader(SurfaceGenerator sg,
BufferedReader br)
recordData
protected float recordData(float value)
closeReader
protected void closeReader()
- Overrides:
closeReader
in class SurfaceFileReader
readVolumeParameters
protected boolean readVolumeParameters()
- Specified by:
readVolumeParameters
in class SurfaceReader
readVolumeData
protected boolean readVolumeData(boolean isMapData)
- Specified by:
readVolumeData
in class SurfaceReader
readVolumetricHeader
private int readVolumetricHeader()
readParameters
protected abstract void readParameters()
throws Exception
- Throws:
Exception
skipComments
protected String skipComments(boolean allowBlankLines)
throws Exception
- Throws:
Exception
readVoxelVector
protected void readVoxelVector(int voxelVectorIndex)
throws Exception
- Throws:
Exception
readSurfaceData
protected void readSurfaceData(boolean isMapData)
throws Exception
- Specified by:
readSurfaceData
in class SurfaceReader
- Throws:
Exception
getPlane
public void getPlane(int x)
- Specified by:
getPlane
in interface VertexDataServer
- Overrides:
getPlane
in class SurfaceReader
getValue
public float getValue(int x,
int y,
int z,
int ptyz)
- Description copied from interface:
VertexDataServer
- for readers only
- Specified by:
getValue
in interface VertexDataServer
- Overrides:
getValue
in class SurfaceReader
- Returns:
- value[x][y][z]
skipVoxels
private void skipVoxels(int n)
throws Exception
- Throws:
Exception
getVoxelBitSet
protected BitSet getVoxelBitSet(int nPoints)
throws Exception
- Throws:
Exception
getNextVoxelValue
protected float getNextVoxelValue()
throws Exception
- Throws:
Exception
nextVoxel
protected float nextVoxel()
throws Exception
- Throws:
Exception
gotoData
protected void gotoData(int n,
int nPoints)
throws Exception
- Overrides:
gotoData
in class SurfaceReader
- Throws:
Exception
skipData
protected void skipData(int nPoints)
throws Exception
- Throws:
Exception
countData
private int countData(String str)
checkAtomLine
protected static boolean checkAtomLine(boolean isXLowToHigh,
boolean isAngstroms,
String strAtomCount,
String atomLine,
StringBuffer 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