Package 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	Description
protected javajs.util.BS	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 String	JVXL_VERSION
private String	jvxlColorEncodingRead
private String	strFractionTemp
protected int	surfaceDataCount
(package private) 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

ac, boundingBox, canDownsample, downsampleFactor, downsampleRemainders, endOfData, isAngstroms, nData, negativeAtomCount, nSkipX, nSkipY, nSkipZ, nSurfaces, readerClosed

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

binarydoc, br, line, next, 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
JvxlXmlReader()

Method Summary

Modifier and Type	Method	Description
private static int	getColor(String c)
private String	getData(String sdata, String name)
protected void	getEncodedVertexData()	retrieve Jvxl 2.0 format vertex/triangle/edge/color data found within <jvxlSurfaceData> element
private static String	getEncoding(String data)
private float	getNextValue()
protected float	getSurfacePointAndFraction(float cutoff, boolean isCutoffAbsolute, float valueA, float valueB, javajs.util.T3 pointA, javajs.util.V3 edgeVector, int x, int y, int z, int vA, int vB, float[] fReturn, javajs.util.T3 ptReturn)
protected javajs.util.BS	getVoxelBitSet(int nPoints)
protected boolean	gotoAndReadVoxelData(boolean isMapData)
protected void	gotoData(int n, int nPoints)
(package private) void	init2(SurfaceGenerator sg, BufferedReader br)
(package private) void	init2JXR(SurfaceGenerator sg, BufferedReader br)
protected void	jvxlDecodeContourData(JvxlData jvxlData, String data)
(package private) void	jvxlDecodeTriangleData(String tdata, String edgeData, String colorData)	decode triangle data found within <jvxlTriangleData> element as created with jvxlEncodeTriangleData (see above)
javajs.util.P3[]	jvxlDecodeVertexData(String data, boolean asArray)	decode vertex data found within <jvxlVertexData> element as created by jvxlEncodeVertexData (see above)
private float	jvxlGetNextFraction(int base, int range, float fracOffset)
protected String	jvxlReadFractionData(String type, int nPoints)	"edge" data includes two parts -- a compressed bitset indicating exactly which edges, in order or processing by Jmol, are crossed by the surface, and a set of fractions indicating how far along that edge (good to 1 part in 8100) that surface crosses that edge.
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 String	readColorData()
protected void	readParameters()
protected void	readSurfaceData(boolean isMapDataIgnored)
protected void	readSurfaceDataJXR()
protected boolean	readSurfaceDataXML()
protected void	readVector(int voxelVectorIndex)
protected boolean	readVolumeData(boolean isMapData)
private void	setValueMinMax()

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

checkAtomLine, closeReader, getNextVoxelValue, getPlane, getPlaneNCI, getSPFv, getValue, init2VFR, initializeSurfaceData, nextVoxel, readSurfaceDataVFR, readVolumeDataVFR, readVolumeParameters, readVoxelVector, recordData, skipComments, skipData, skipDataVFR, swapXZ

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

closeReaderSFR, discardTempData, getQuotedStringNext, getTokens, init, init2SFR, newBinaryDocument, parseFloat, parseFloatArray, parseFloatArrayStr, parseFloatRange, parseFloatStr, parseInt, parseIntNext, parseIntStr, rd, setOutputChannel, setStream, skipTo

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

addTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlaneSR, getSPF, getSurfaceAtomIndex, getSurfacePointIndexAndFraction, getValue2, getValueAtPoint, initializeMapping, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, readAndSetVolumeParameters, 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

JVXL_VERSION

protected 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

String tempDataXml

bsVoxelBitSet

protected javajs.util.BS 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 String strFractionTemp

haveReadColorData

boolean haveReadColorData

jvxlColorEncodingRead

private String jvxlColorEncodingRead

Constructor Detail

JvxlXmlReader

JvxlXmlReader()

Method Detail

init2

void init2(SurfaceGenerator sg,
           BufferedReader br)

Overrides:

init2 in class VolumeFileReader

init2JXR

void init2JXR(SurfaceGenerator sg,
              BufferedReader br)

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 Exception

Specified by:

readParameters in class VolumeFileReader

Throws:

Exception

readVector

protected void readVector(int voxelVectorIndex)
                   throws Exception

Throws:

Exception

gotoData

protected void gotoData(int n,
                        int nPoints)
                 throws Exception

Overrides:

gotoData in class VolumeFileReader

Throws:

Exception

jvxlSkipData

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

Throws:

Exception

jvxlReadSurfaceInfo

protected void jvxlReadSurfaceInfo()
                            throws Exception

Throws:

Exception

jvxlSetColorRanges

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

readSurfaceData

protected void readSurfaceData(boolean isMapDataIgnored)
                        throws Exception

Overrides:

readSurfaceData in class VolumeFileReader

Throws:

Exception

readSurfaceDataXML

protected boolean readSurfaceDataXML()
                              throws Exception

Throws:

Exception

readSurfaceDataJXR

protected void readSurfaceDataJXR()
                           throws Exception

Throws:

Exception

jvxlReadFractionData

protected String jvxlReadFractionData(String type,
                                      int nPoints)

"edge" data includes two parts -- a compressed bitset indicating exactly which edges, in order or processing by Jmol, are crossed by the surface, and a set of fractions indicating how far along that edge (good to 1 part in 8100) that surface crosses that edge. We are just reading he fractions here. "color" data comprises the corresponding sequence of data mapping values, again stored to a precision of 1 part in 8100, relative to a range of values.

Parameters:

type -

nPoints -

Returns:

data

getVoxelBitSet

protected javajs.util.BS getVoxelBitSet(int nPoints)
                                 throws Exception

Overrides:

getVoxelBitSet in class VolumeFileReader

Returns:

JVXL bitset

Throws:

Exception

getSurfacePointAndFraction

protected float getSurfacePointAndFraction(float cutoff,
                                           boolean isCutoffAbsolute,
                                           float valueA,
                                           float valueB,
                                           javajs.util.T3 pointA,
                                           javajs.util.V3 edgeVector,
                                           int x,
                                           int y,
                                           int z,
                                           int vA,
                                           int vB,
                                           float[] fReturn,
                                           javajs.util.T3 ptReturn)

Overrides:

getSurfacePointAndFraction in class VolumeFileReader

getNextValue

private float getNextValue()

setValueMinMax

private void setValueMinMax()

jvxlGetNextFraction

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

readColorData

protected String readColorData()

Overrides:

readColorData in class SurfaceReader

getColor

private static int getColor(String c)

getEncodedVertexData

protected void getEncodedVertexData()
                             throws Exception

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

Throws:

Exception

getData

private String getData(String sdata,
                       String name)
                throws Exception

Throws:

Exception

getEncoding

private static String getEncoding(String data)

jvxlDecodeVertexData

public javajs.util.P3[] jvxlDecodeVertexData(String data,
                                             boolean asArray)
                                      throws Exception

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

Parameters:

data - tag and contents

asArray - or just addVertexCopy

Returns:

Point3f[] if desired

Throws:

Exception

jvxlDecodeTriangleData

void jvxlDecodeTriangleData(String tdata,
                            String edgeData,
                            String colorData)
                     throws Exception

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

Parameters:

tdata - tag and contents

edgeData -

colorData -

Throws:

Exception

jvxlDecodeContourData

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

Throws:

Exception

postProcessVertices

protected void postProcessVertices()

Overrides:

postProcessVertices in class SurfaceReader