org.jmol.jvxl.readers

Class JvxlXmlReader

java.lang.Object

org.jmol.jvxl.readers.SurfaceReader

org.jmol.jvxl.readers.SurfaceFileReader

org.jmol.jvxl.readers.VolumeFileReader

org.jmol.jvxl.readers.JvxlXmlReader

All Implemented Interfaces:

VertexDataServer

Direct Known Subclasses:

JvxlReader

public class JvxlXmlReader
extends VolumeFileReader

Field Summary

Fields

Modifier and Type	Field and Description
protected java.util.BitSet	bsVoxelBitSet
protected int	colorDataCount
private int	colorPtr
protected int	edgeDataCount
private int	excludedTriangleCount
private int	excludedVertexCount
private int	fractionPtr
protected boolean	haveContourData
(package private) boolean	haveReadColorData
private boolean	includeValueNaN
private int	invalidatedVertexCount
protected boolean	isXmlFile
protected java.lang.String	JVXL_VERSION
private java.lang.String	strFractionTemp
protected int	surfaceDataCount
(package private) java.lang.String	tempDataXml
protected boolean	thisInside
private int	valueCount
private float	valueMin
private float	valueRange
private XmlReader	xr

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

Method Summary

Methods

Modifier and Type	Method and Description
protected void	getEncodedVertexData() retrieve Jvxl 2.0 format vertex/triangle/edge/color data found within element
private float	getNextValue()
protected float	getSurfacePointAndFraction(float cutoff, boolean isCutoffAbsolute, float valueA, float valueB, javax.vecmath.Point3f pointA, javax.vecmath.Vector3f edgeVector, int x, int y, int z, int vA, int vB, float[] fReturn, javax.vecmath.Point3f ptReturn)
protected java.util.BitSet	getVoxelBitSet(int nPoints)
protected boolean	gotoAndReadVoxelData(boolean isMapData)
protected void	gotoData(int n, int nPoints)
protected void	jvxlDecodeContourData(JvxlData jvxlData, java.lang.String data)
(package private) int[][]	jvxlDecodeTriangleData(java.lang.String data, java.lang.String edgeData, java.lang.String colorData) decode triangle data found within element as created with jvxlEncodeTriangleData (see above)
javax.vecmath.Point3f[]	jvxlDecodeVertexData(java.lang.String data, boolean asArray) decode vertex data found within element as created by jvxlEncodeVertexData (see above)
private float	jvxlGetNextFraction(int base, int range, float fracOffset)
protected java.lang.String	jvxlReadData(java.lang.String type, int nPoints)
protected void	jvxlReadSurfaceInfo()
protected void	jvxlSetColorRanges(float dataMin, float dataMax, float red, float blue, boolean insideOut)
protected void	jvxlSkipData(int nPoints, boolean doSkipColorData)
protected void	postProcessVertices()
protected java.lang.String	readColorData()
protected void	readParameters()
protected boolean	readSurfaceData()
protected void	readSurfaceData(boolean isMapDataIgnored)
protected void	readVector(int voxelVectorIndex)
protected boolean	readVolumeData(boolean isMapData)
protected void	readVolumeFileSurfaceData()
private void	setValueMinMax()

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

Field Detail

JVXL_VERSION

protected java.lang.String JVXL_VERSION

surfaceDataCount

protected int surfaceDataCount

edgeDataCount

protected int edgeDataCount

colorDataCount

protected int colorDataCount

excludedTriangleCount

private int excludedTriangleCount

excludedVertexCount

private int excludedVertexCount

invalidatedVertexCount

private int invalidatedVertexCount

haveContourData

protected boolean haveContourData

xr

private XmlReader xr

isXmlFile

protected boolean isXmlFile

thisInside

protected boolean thisInside

tempDataXml

java.lang.String tempDataXml

bsVoxelBitSet

protected java.util.BitSet bsVoxelBitSet

includeValueNaN

private boolean includeValueNaN

valueCount

private int valueCount

valueMin

private float valueMin

valueRange

private float valueRange

fractionPtr

private int fractionPtr

colorPtr

private int colorPtr

strFractionTemp

private java.lang.String strFractionTemp

haveReadColorData

boolean haveReadColorData

Constructor Detail

JvxlXmlReader

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

Method Detail

readVolumeData

protected boolean readVolumeData(boolean isMapData)

Overrides:

readVolumeData in class VolumeFileReader

gotoAndReadVoxelData

protected boolean gotoAndReadVoxelData(boolean isMapData)

Overrides:

gotoAndReadVoxelData in class SurfaceReader

readParameters

protected void readParameters()
                       throws java.lang.Exception

Specified by:

readParameters in class VolumeFileReader

Throws:

java.lang.Exception

readVector

protected void readVector(int voxelVectorIndex)
                   throws java.lang.Exception

Throws:

java.lang.Exception

gotoData

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

Overrides:

gotoData in class VolumeFileReader

Throws:

java.lang.Exception

jvxlSkipData

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

Throws:

java.lang.Exception

jvxlReadSurfaceInfo

protected void jvxlReadSurfaceInfo()
                            throws java.lang.Exception

Throws:

java.lang.Exception

jvxlSetColorRanges

protected void jvxlSetColorRanges(float dataMin,
                      float dataMax,
                      float red,
                      float blue,
                      boolean insideOut)

readSurfaceData

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

Overrides:

readSurfaceData in class VolumeFileReader

Throws:

java.lang.Exception

readSurfaceData

protected boolean readSurfaceData()
                           throws java.lang.Exception

Throws:

java.lang.Exception

readVolumeFileSurfaceData

protected void readVolumeFileSurfaceData()
                                  throws java.lang.Exception

Throws:

java.lang.Exception

jvxlReadData

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

getVoxelBitSet

protected java.util.BitSet getVoxelBitSet(int nPoints)
                                   throws java.lang.Exception

Overrides:

getVoxelBitSet in class VolumeFileReader

Returns:

JVXL bitset

Throws:

java.lang.Exception

getSurfacePointAndFraction

protected float getSurfacePointAndFraction(float cutoff,
                               boolean isCutoffAbsolute,
                               float valueA,
                               float valueB,
                               javax.vecmath.Point3f pointA,
                               javax.vecmath.Vector3f edgeVector,
                               int x,
                               int y,
                               int z,
                               int vA,
                               int vB,
                               float[] fReturn,
                               javax.vecmath.Point3f ptReturn)

Overrides:

getSurfacePointAndFraction in class VolumeFileReader

x - TODO

y - TODO

z - TODO

Returns:

fractional distance from A to B

getNextValue

private float getNextValue()

setValueMinMax

private void setValueMinMax()

jvxlGetNextFraction

private float jvxlGetNextFraction(int base,
                        int range,
                        float fracOffset)

readColorData

protected java.lang.String readColorData()

Overrides:

readColorData in class SurfaceReader

getEncodedVertexData

protected void getEncodedVertexData()
                             throws java.lang.Exception

retrieve Jvxl 2.0 format vertex/triangle/edge/color data found within element

Throws:

java.lang.Exception

jvxlDecodeVertexData

public javax.vecmath.Point3f[] jvxlDecodeVertexData(java.lang.String data,
                                           boolean asArray)
                                             throws java.lang.Exception

decode vertex data found within element as created by jvxlEncodeVertexData (see above)

Parameters:

data - tag and contents

asArray - or just addVertexCopy

Returns:

Point3f[] if desired

Throws:

java.lang.Exception

jvxlDecodeTriangleData

int[][] jvxlDecodeTriangleData(java.lang.String data,
                             java.lang.String edgeData,
                             java.lang.String colorData)
                         throws java.lang.Exception

decode triangle data found within element as created with jvxlEncodeTriangleData (see above)

Parameters:

data - tag and contents

edgeData -

colorData -

Returns:

int[][] if desired

Throws:

java.lang.Exception

jvxlDecodeContourData

protected void jvxlDecodeContourData(JvxlData jvxlData,
                         java.lang.String data)
                              throws java.lang.Exception

Throws:

java.lang.Exception

postProcessVertices

protected void postProcessVertices()

Overrides:

postProcessVertices in class SurfaceReader