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 and Description
protected JmolDocument	binarydoc
protected java.io.BufferedReader	br
protected java.lang.String	line
protected int[]	next
protected java.io.OutputStream	os

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, 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 and Description
SurfaceFileReader()

Method Summary

Methods

Modifier and Type	Method and Description
protected void	closeReader()
protected void	closeReaderSFR()
(package private) void	discardTempData(boolean discardAll)
protected java.lang.String	getQuotedStringNext()
protected java.lang.String[]	getTokens()
(package private) void	init(SurfaceGenerator sg) implemented in SurfaceFileReader and
(package private) void	init2(SurfaceGenerator sg, java.io.BufferedReader br)
(package private) void	init2SFR(SurfaceGenerator sg, java.io.BufferedReader br)
(package private) JmolDocument	newBinaryDocument()
protected float	parseFloat()
protected float[]	parseFloatArray(float[] a, java.lang.String strStart, java.lang.String strEnd)
protected float[]	parseFloatArrayStr(java.lang.String s)
protected float	parseFloatRange(java.lang.String s, int iStart, int iEnd)
protected float	parseFloatStr(java.lang.String s)
protected int	parseInt()
protected int	parseIntNext(java.lang.String s)
protected int	parseIntStr(java.lang.String s)
protected java.lang.String	readLine()
protected void	setOutputStream(java.io.OutputStream os)
protected void	skipTo(java.lang.String info, java.lang.String what)

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

addTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getPlane2, getSpanningVectors, 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 java.io.BufferedReader br

binarydoc

protected JmolDocument binarydoc

os

protected java.io.OutputStream os

line

protected java.lang.String line

next

protected int[] next

Constructor Detail

SurfaceFileReader

SurfaceFileReader()

Method Detail

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,
         java.io.BufferedReader br)

init2SFR

void init2SFR(SurfaceGenerator sg,
            java.io.BufferedReader br)

newBinaryDocument

JmolDocument newBinaryDocument()

setOutputStream

protected void setOutputStream(java.io.OutputStream os)

Overrides:

setOutputStream 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 java.lang.String[] getTokens()

parseFloat

protected float parseFloat()

parseFloatStr

protected float parseFloatStr(java.lang.String s)

parseFloatRange

protected float parseFloatRange(java.lang.String s,
                    int iStart,
                    int iEnd)

parseInt

protected int parseInt()

parseIntStr

protected int parseIntStr(java.lang.String s)

parseIntNext

protected int parseIntNext(java.lang.String s)

parseFloatArrayStr

protected float[] parseFloatArrayStr(java.lang.String s)

parseFloatArray

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

getQuotedStringNext

protected java.lang.String getQuotedStringNext()

skipTo

protected void skipTo(java.lang.String info,
          java.lang.String what)
               throws java.lang.Exception

Throws:

java.lang.Exception

readLine

protected java.lang.String readLine()
                             throws java.lang.Exception

Throws:

java.lang.Exception