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, JvxlReader, MapFileReader, PltFormattedReader
abstract class VolumeFileReader
- extends SurfaceFileReader
Fields inherited from class org.jmol.jvxl.readers.SurfaceReader |
ANGSTROMS_PER_BOHR, cJvxlEdgeNaN, colorEncoder, colorFractionBase, colorFractionRange, contourVertexCount, defaultCutoff, defaultMappedDataMax, defaultMappedDataMin, edgeFractionBase, edgeFractionRange, fractionData, hasColorData, isApbsDx, isJvxl, isProgressive, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, jvxlVoxelBitSet, marchingSquares, meshData, meshDataServer, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, sg, vContours, vertexDataOnly, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData |
Methods inherited from class org.jmol.jvxl.readers.SurfaceReader |
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, excludeMaximumSet, excludeMinimumSet, getArgbFromPalette, getColorIndexFromPalette, getColorPhaseIndex, getMaxMappedValue, getMinMappedValue, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, gotoAndReadVoxelData, initializeVolumetricData, jvxlUpdateInfo, readColorData, resetIsosurface, selectPocket, setVolumeData, 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
private int nSurfaces
isAngstroms
protected boolean isAngstroms
canDownsample
protected boolean canDownsample
downsampleRemainders
protected int[] downsampleRemainders
VolumeFileReader
VolumeFileReader(SurfaceGenerator sg,
java.io.BufferedReader br)
readVolumeParameters
boolean readVolumeParameters()
- Specified by:
readVolumeParameters
in class SurfaceReader
readVolumeData
boolean readVolumeData(boolean isMapData)
- Specified by:
readVolumeData
in class SurfaceReader
readVolumetricHeader
protected int readVolumetricHeader()
readTitleLines
protected void readTitleLines()
throws java.lang.Exception
- Throws:
java.lang.Exception
skipComments
protected java.lang.String skipComments(boolean allowBlankLines)
throws java.lang.Exception
- Throws:
java.lang.Exception
readAtomCountAndOrigin
protected void readAtomCountAndOrigin()
throws java.lang.Exception
- Throws:
java.lang.Exception
readVoxelVector
protected void readVoxelVector(int voxelVectorIndex)
throws java.lang.Exception
- Throws:
java.lang.Exception
readExtraLine
protected int readExtraLine()
throws java.lang.Exception
- Throws:
java.lang.Exception
readSurfaceData
protected void readSurfaceData(boolean isMapData)
throws java.lang.Exception
- Specified by:
readSurfaceData
in class SurfaceReader
- Throws:
java.lang.Exception
skipVoxels
private void skipVoxels(int n)
throws java.lang.Exception
- Throws:
java.lang.Exception
getVoxelBitSet
protected java.util.BitSet getVoxelBitSet(int nPoints)
throws java.lang.Exception
- Throws:
java.lang.Exception
getNextVoxelValue
protected float getNextVoxelValue()
throws java.lang.Exception
- Throws:
java.lang.Exception
nextVoxel
protected float nextVoxel()
throws java.lang.Exception
- Throws:
java.lang.Exception
gotoData
protected void gotoData(int n,
int nPoints)
throws java.lang.Exception
- Overrides:
gotoData
in class SurfaceReader
- Throws:
java.lang.Exception
skipData
protected void skipData(int nPoints)
throws java.lang.Exception
- Throws:
java.lang.Exception
countData
private int countData(java.lang.String str)