org.jmol.jvxl.readers

Class VolumeFileReader

class VolumeFileReader extends VoxelReader

Field Summary
protected intatomCount
protected BufferedReaderbr
protected booleancanDownsample
int[]downsampleRemainders
protected booleanendOfData
protected booleanisAngstroms
Stringline
protected booleannegativeAtomCount
int[]next
intnSurfaces
Constructor Summary
VolumeFileReader(SurfaceGenerator sg, BufferedReader br)
Method Summary
intcountData(String str)
static StringdetermineFileType(BufferedReader bufferedReader)
voiddiscardTempData(boolean discardAll)
protected floatgetNextVoxelValue(StringBuffer sb)
String[]getTokens()
protected voidgotoData(int n, int nPoints)
protected floatnextVoxel()
floatparseFloat()
floatparseFloat(String s)
floatparseFloatNext(String s)
intparseInt()
intparseInt(String s)
intparseInt(String s, int iStart)
intparseIntNext(String s)
protected voidreadAtomCountAndOrigin()
protected intreadExtraLine()
protected voidreadTitleLines()
voidreadVolumeData(boolean isMapData)
voidreadVolumeParameters()
protected intreadVolumetricHeader()
protected voidreadVoxelData(boolean isMapData)
protected voidreadVoxelVector(int voxelVectorIndex)
protected intskipComments(boolean addToHeader)
voidskipData(int nPoints)
voidskipVoxels(int n)

Field Detail

atomCount

protected int atomCount

br

protected BufferedReader br

canDownsample

protected boolean canDownsample

downsampleRemainders

private int[] downsampleRemainders

endOfData

protected boolean endOfData

isAngstroms

protected boolean isAngstroms

line

String line

negativeAtomCount

protected boolean negativeAtomCount

int[] next

nSurfaces

private int nSurfaces

Constructor Detail

VolumeFileReader

VolumeFileReader(SurfaceGenerator sg, BufferedReader br)

Method Detail

countData

private int countData(String str)

determineFileType

static String determineFileType(BufferedReader bufferedReader)

discardTempData

void discardTempData(boolean discardAll)

getNextVoxelValue

protected float getNextVoxelValue(StringBuffer sb)

getTokens

String[] getTokens()

gotoData

protected void gotoData(int n, int nPoints)

nextVoxel

protected float nextVoxel()

parseFloat

float parseFloat()

parseFloat

float parseFloat(String s)

parseFloatNext

float parseFloatNext(String s)

parseInt

int parseInt()

parseInt

int parseInt(String s)

parseInt

int parseInt(String s, int iStart)

parseIntNext

int parseIntNext(String s)

readAtomCountAndOrigin

protected void readAtomCountAndOrigin()

readExtraLine

protected int readExtraLine()

readTitleLines

protected void readTitleLines()

readVolumeData

void readVolumeData(boolean isMapData)

readVolumeParameters

void readVolumeParameters()

readVolumetricHeader

protected int readVolumetricHeader()

readVoxelData

protected void readVoxelData(boolean isMapData)

readVoxelVector

protected void readVoxelVector(int voxelVectorIndex)

skipComments

protected int skipComments(boolean addToHeader)

skipData

private void skipData(int nPoints)

skipVoxels

private void skipVoxels(int n)