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 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 java.lang.String strFractionTemp

• haveReadColorData

  boolean haveReadColorData

• jvxlColorEncodingRead

  private java.lang.String jvxlColorEncodingRead

Constructor Detail

• JvxlXmlReader

  JvxlXmlReader()

Method Detail

• init2

  void init2​(SurfaceGenerator sg,
             java.io.BufferedReader br)

  Overrides:

  init2 in class VolumeFileReader

• init2JXR

  void init2JXR​(SurfaceGenerator sg,
                java.io.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 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

• readSurfaceDataXML

  protected boolean readSurfaceDataXML()
                                throws java.lang.Exception

  Throws:

  java.lang.Exception

• readSurfaceDataJXR

  protected void readSurfaceDataJXR()
                             throws java.lang.Exception

  Throws:

  java.lang.Exception

• jvxlReadFractionData

  protected java.lang.String jvxlReadFractionData​(java.lang.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 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,
                                             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 java.lang.String readColorData()

  Overrides:

  readColorData in class SurfaceReader

• getColor

  private static int getColor​(java.lang.String c)

• 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

• getData

  private java.lang.String getData​(java.lang.String sdata,
                                   java.lang.String name)
                            throws java.lang.Exception

  Throws:

  java.lang.Exception

• getEncoding

  private static java.lang.String getEncoding​(java.lang.String data)

• jvxlDecodeVertexData

  public javajs.util.P3[] 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

  void jvxlDecodeTriangleData​(java.lang.String tdata,
                              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:

  tdata - tag and contents

  edgeData -

  colorData -

  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