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 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

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 and Description

JvxlXmlReader()

Constructors
Constructor and Description
`JvxlXmlReader()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and 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 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 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 element as created with jvxlEncodeTriangleData (see above)
`javajs.util.P3[]`	`jvxlDecodeVertexData(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 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 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 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 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 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 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 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

Class JvxlXmlReader

Field Summary

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

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

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

Constructor Summary

Method Summary

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

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

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

Methods inherited from class java.lang.Object

Field Detail

JVXL_VERSION

surfaceDataCount

edgeDataCount

colorDataCount

excludedTriangleCount

excludedVertexCount

invalidatedVertexCount

haveContourData

xr

isXmlFile

thisInside

tempDataXml

bsVoxelBitSet

includeValueNaN

valueCount

valueMin

valueRange

fractionPtr

colorPtr

strFractionTemp

haveReadColorData

jvxlColorEncodingRead

Constructor Detail

JvxlXmlReader

Method Detail

init2

init2JXR

readVolumeData

gotoAndReadVoxelData

readParameters

readVector

gotoData

jvxlSkipData

jvxlReadSurfaceInfo

jvxlSetColorRanges

readSurfaceData

readSurfaceDataXML

readSurfaceDataJXR

jvxlReadFractionData

getVoxelBitSet

getSurfacePointAndFraction

getNextValue

setValueMinMax

jvxlGetNextFraction

readColorData

getColor

getEncodedVertexData

getData

getEncoding

jvxlDecodeVertexData

jvxlDecodeTriangleData

jvxlDecodeContourData

postProcessVertices