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

Field Summary

Fields

Modifier and Type	Field and Description
protected BinaryDocument	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(SurfaceGenerator sg, java.io.BufferedReader br)

Method Summary

Methods

Modifier and Type	Method and Description
protected void	closeReader()
(package private) void	discardTempData(boolean discardAll)
protected java.lang.String	getNextQuotedString()
protected java.lang.String[]	getTokens()
protected float	parseFloat()
protected float	parseFloat(java.lang.String s)
protected float[]	parseFloatArray()
protected float[]	parseFloatArray(java.lang.String s)
protected int	parseInt()
protected int	parseInt(java.lang.String s)
protected int	parseIntNext(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, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getSurfaceAtomIndex, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValueAtPoint, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, initPlanes, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, readSurfaceData, readVolumeData, readVolumeParameters, resetIsosurface, selectPocket, setBoundingBox, 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

Field Detail

br

protected java.io.BufferedReader br

binarydoc

protected BinaryDocument binarydoc

os

protected java.io.OutputStream os

line

protected java.lang.String line

next

protected int[] next

Constructor Detail

SurfaceFileReader

SurfaceFileReader(SurfaceGenerator sg,
                 java.io.BufferedReader br)

Method Detail

setOutputStream

protected void setOutputStream(java.io.OutputStream os)

Overrides:

setOutputStream in class SurfaceReader

closeReader

protected void closeReader()

Specified by:

closeReader in class SurfaceReader

discardTempData

void discardTempData(boolean discardAll)

Overrides:

discardTempData in class SurfaceReader

getTokens

protected java.lang.String[] getTokens()

parseFloat

protected float parseFloat()

parseFloat

protected float parseFloat(java.lang.String s)

parseInt

protected int parseInt()

parseInt

protected int parseInt(java.lang.String s)

parseIntNext

protected int parseIntNext(java.lang.String s)

parseFloatArray

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

parseFloatArray

protected float[] parseFloatArray()

getNextQuotedString

protected java.lang.String getNextQuotedString()

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