Package org.jmol.jvxl.readers

Class SurfaceFileReader

java.lang.Object

org.jmol.jvxl.readers.SurfaceReader

org.jmol.jvxl.readers.SurfaceFileReader

All Implemented Interfaces:

VertexDataServer

Direct Known Subclasses:

PolygonFileReader, VolumeFileReader

abstract class SurfaceFileReader
extends SurfaceReader

PolygonFileReader or VolumeFileReader

Field Summary

Fields

Modifier and Type	Field	Description
protected javajs.api.GenericBinaryDocument	binarydoc
protected BufferedReader	br
protected String	line
protected int[]	next
protected javajs.util.OC	out

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, 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

Constructor Summary

Constructors

Constructor	Description
SurfaceFileReader()

Method Summary

Modifier and Type	Method	Description
protected void	closeReader()
protected void	closeReaderSFR()
(package private) void	discardTempData(boolean discardAll)
protected String	getQuotedStringNext()
protected String[]	getTokens()
(package private) void	init(SurfaceGenerator sg)	implemented in SurfaceFileReader and
(package private) void	init2(SurfaceGenerator sg, BufferedReader br)
(package private) void	init2SFR(SurfaceGenerator sg, BufferedReader br)
(package private) javajs.api.GenericBinaryDocument	newBinaryDocument()
protected float	parseFloat()
protected float[]	parseFloatArray(float[] a, String strStart, String strEnd)
protected float[]	parseFloatArrayStr(String s)
protected float	parseFloatRange(String s, int iStart, int iEnd)
protected float	parseFloatStr(String s)
protected int	parseInt()
protected int	parseIntNext(String s)
protected int	parseIntStr(String s)
protected String	rd()
protected void	setOutputChannel(javajs.util.OC out)
protected void	setStream(String fileName, boolean isBigEndian)
protected void	skipTo(String info, String what)

Methods inherited from class org.jmol.jvxl.readers.SurfaceReader

addTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getPlaneSR, getSPF, getSurfaceAtomIndex, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValue2, getValueAtPoint, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, readSurfaceData, readVolumeData, readVolumeParameters, resetIsosurface, selectPocket, setBBox, setVectorAnisotropy, setVertexAnisotropy, setVolumeDataV, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

br

protected BufferedReader br

binarydoc

protected javajs.api.GenericBinaryDocument binarydoc

out

protected javajs.util.OC out

line

protected String line

next

protected int[] next

Constructor Detail

SurfaceFileReader

SurfaceFileReader()

Method Detail

setStream

protected void setStream(String fileName,
                         boolean isBigEndian)

init

void init(SurfaceGenerator sg)

Description copied from class: SurfaceReader

implemented in SurfaceFileReader and

Specified by:

init in class SurfaceReader

init2

void init2(SurfaceGenerator sg,
           BufferedReader br)

init2SFR

void init2SFR(SurfaceGenerator sg,
              BufferedReader br)

newBinaryDocument

javajs.api.GenericBinaryDocument newBinaryDocument()

setOutputChannel

protected void setOutputChannel(javajs.util.OC out)

Overrides:

setOutputChannel in class SurfaceReader

closeReader

protected void closeReader()

Specified by:

closeReader in class SurfaceReader

closeReaderSFR

protected void closeReaderSFR()

discardTempData

void discardTempData(boolean discardAll)

Overrides:

discardTempData in class SurfaceReader

getTokens

protected String[] getTokens()

parseFloat

protected float parseFloat()

parseFloatStr

protected float parseFloatStr(String s)

parseFloatRange

protected float parseFloatRange(String s,
                                int iStart,
                                int iEnd)

parseInt

protected int parseInt()

parseIntStr

protected int parseIntStr(String s)

parseIntNext

protected int parseIntNext(String s)

parseFloatArrayStr

protected float[] parseFloatArrayStr(String s)

parseFloatArray

protected float[] parseFloatArray(float[] a,
                                  String strStart,
                                  String strEnd)

getQuotedStringNext

protected String getQuotedStringNext()

skipTo

protected void skipTo(String info,
                      String what)
               throws Exception

Throws:

Exception

rd

protected String rd()
             throws Exception

Throws:

Exception