org.jmol.jvxl.readers

Class JvxlReader

java.lang.Object

org.jmol.jvxl.readers.SurfaceReader

org.jmol.jvxl.readers.SurfaceFileReader

org.jmol.jvxl.readers.VolumeFileReader

org.jmol.jvxl.readers.JvxlXmlReader

org.jmol.jvxl.readers.JvxlReader

All Implemented Interfaces:

VertexDataServer

public class JvxlReader
extends JvxlXmlReader

Field Summary

Fields inherited from class org.jmol.jvxl.readers.JvxlXmlReader

bsVoxelBitSet, colorDataCount, edgeDataCount, haveContourData, haveReadColorData, isXmlFile, JVXL_VERSION, surfaceDataCount, tempDataXml, thisInside

Fields inherited from class org.jmol.jvxl.readers.VolumeFileReader

atomCount, boundingBox, canDownsample, downsampleFactor, endOfData, isAngstroms, negativeAtomCount, nSurfaces, readerClosed, thePlane

Fields inherited from class org.jmol.jvxl.readers.SurfaceFileReader

binarydoc, br, line, next, 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
JvxlReader(SurfaceGenerator sg, java.io.BufferedReader br)

Method Summary

Methods

Modifier and Type	Method and Description
private int	countData(java.lang.String str)
protected void	gotoData(int n, int nPoints)
protected java.lang.String	jvxlReadData(java.lang.String type, int nPoints)
private void	jvxlReadDefinitionLine(boolean showMsg)
protected void	jvxlSkipData(int nPoints, boolean doSkipColorData)
private void	jvxlSkipDataBlock(int nPoints, boolean isInt)
protected void	readParameters()
protected void	readSurfaceData(boolean isMapDataIgnored)

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

getEncodedVertexData, getSurfacePointAndFraction, getVoxelBitSet, gotoAndReadVoxelData, jvxlDecodeContourData, jvxlDecodeTriangleData, jvxlDecodeVertexData, jvxlReadSurfaceInfo, jvxlSetColorRanges, postProcessVertices, readColorData, readSurfaceData, readVector, readVolumeData, readVolumeFileSurfaceData

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

checkAtomLine, closeReader, getNextVoxelValue, getPlane, getPlaneProcessed, getValue, initializeSurfaceData, nextVoxel, readVolumeParameters, readVoxelVector, recordData, skipComments, skipData

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

discardTempData, getNextQuotedString, getTokens, parseFloat, parseFloat, parseFloatArray, parseFloatArray, parseInt, parseInt, parseIntNext, readLine, setOutputStream, skipTo

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

addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getSurfaceAtomIndex, getSurfacePointIndexAndFraction, getValueAtPoint, initializeMapping, initializeVolumetricData, initPlanes, jvxlUpdateInfo, newVoxelDataCube, readAndSetVolumeParameters, 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

Constructor Detail

JvxlReader

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

Method Detail

readParameters

protected void readParameters()
                       throws java.lang.Exception

Overrides:

readParameters in class JvxlXmlReader

Throws:

java.lang.Exception

jvxlReadData

protected java.lang.String jvxlReadData(java.lang.String type,
                            int nPoints)

Overrides:

jvxlReadData in class JvxlXmlReader

gotoData

protected void gotoData(int n,
            int nPoints)
                 throws java.lang.Exception

Overrides:

gotoData in class JvxlXmlReader

Throws:

java.lang.Exception

jvxlReadDefinitionLine

private void jvxlReadDefinitionLine(boolean showMsg)
                             throws java.lang.Exception

Throws:

java.lang.Exception

readSurfaceData

protected void readSurfaceData(boolean isMapDataIgnored)
                        throws java.lang.Exception

Overrides:

readSurfaceData in class JvxlXmlReader

Throws:

java.lang.Exception

jvxlSkipData

protected void jvxlSkipData(int nPoints,
                boolean doSkipColorData)
                     throws java.lang.Exception

Overrides:

jvxlSkipData in class JvxlXmlReader

Throws:

java.lang.Exception

jvxlSkipDataBlock

private void jvxlSkipDataBlock(int nPoints,
                     boolean isInt)
                        throws java.lang.Exception

Throws:

java.lang.Exception

countData

private int countData(java.lang.String str)