Package org.jmol.jvxl.readers

Class JvxlReader

java.lang.Object
org.jmol.jvxl.readers.SurfaceReader
org.jmol.jvxl.readers.JvxlXmlReader
org.jmol.jvxl.readers.JvxlReader
All Implemented Interfaces:
VertexDataServer
public class JvxlReader extends JvxlXmlReader

  • Field Details

    • endOfData

      protected boolean endOfData

    • negativeAtomCount

      protected boolean negativeAtomCount

    • ac

      protected int ac

    • nSurfaces

      protected int nSurfaces

    • isAngstroms

      protected boolean isAngstroms

    • canDownsample

      protected boolean canDownsample

    • downsampleRemainders

      protected int[] downsampleRemainders

    • nData

      protected int nData

    • readerClosed

      protected boolean readerClosed

    • downsampleFactor

      protected int downsampleFactor

    • nSkipX

      protected int nSkipX

    • nSkipY

      protected int nSkipY

    • nSkipZ

      protected int nSkipZ

    • boundingBox

      protected P3[] boundingBox

    • br

      protected BufferedReader br

    • binarydoc

      protected GenericBinaryDocument binarydoc

    • out

      protected OC out

    • line

      protected String line

    • next

      protected int[] next

  • Method Details

    • readParameters

      protected void readParameters() throws Exception
      Overrides:
      readParameters in class JvxlXmlReader
      Throws:
      Exception

    • jvxlReadFractionData

      protected String jvxlReadFractionData(String type, int nPoints)
      Description copied from class: JvxlXmlReader
      "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.
      Overrides:
      jvxlReadFractionData in class JvxlXmlReader
      Parameters:
      type -
      nPoints -
      Returns:
      data

    • gotoData

      protected void gotoData(int n, int nPoints) throws Exception
      Overrides:
      gotoData in class JvxlXmlReader
      Parameters:
      n -
      nPoints -
      Throws:
      Exception

    • readSurfaceData

      protected void readSurfaceData(boolean isMapDataIgnored) throws Exception
      Overrides:
      readSurfaceData in class JvxlXmlReader
      Throws:
      Exception

    • jvxlSkipData

      protected void jvxlSkipData(int nPoints, boolean doSkipColorData) throws Exception
      Overrides:
      jvxlSkipData in class JvxlXmlReader
      Throws:
      Exception

    • recordData

      protected float recordData(float value)

    • closeReader

      protected void closeReader()

    • readVolumeParameters

      protected boolean readVolumeParameters(boolean isMapData)
      Specified by:
      readVolumeParameters in class SurfaceReader

    • readVolumeDataVFR

      protected boolean readVolumeDataVFR(boolean isMapData)

    • skipComments

      protected String skipComments(boolean allowBlankLines) throws Exception
      Throws:
      Exception

    • readVoxelVector

      protected void readVoxelVector(int voxelVectorIndex) throws Exception
      Throws:
      Exception

    • readSurfaceDataVFR

      protected void readSurfaceDataVFR(boolean isMapData) throws Exception
      Throws:
      Exception

    • getPlane

      public float[] getPlane(int x)
      Specified by:
      getPlane in interface VertexDataServer
      Overrides:
      getPlane in class SurfaceReader

    • getPlaneNCI

      public float[] getPlaneNCI(int x)
      Retrieve raw file planes and pass them to the calculation object for processing into new data. Bob Hanson hansonr@stolaf.edu 6/7/2011
      Parameters:
      x -
      Returns:
      plane (for testing)

    • getValue

      public float getValue(int x, int y, int z, int ptyz)
      Description copied from interface: VertexDataServer
      for readers only
      Specified by:
      getValue in interface VertexDataServer
      Overrides:
      getValue in class SurfaceReader
      Parameters:
      x -
      y -
      z -
      ptyz -
      Returns:
      value[x][y][z]

    • getNextVoxelValue

      protected float getNextVoxelValue() throws Exception
      Throws:
      Exception

    • nextVoxel

      protected float nextVoxel() throws Exception
      Throws:
      Exception

    • skipData

      protected void skipData(int nPoints) throws Exception
      Throws:
      Exception

    • skipDataVFR

      protected void skipDataVFR(int nPoints) throws Exception
      Throws:
      Exception

    • checkAtomLine

      protected static boolean checkAtomLine(boolean isXLowToHigh, boolean isAngstroms, String strAtomCount, String atomLine, SB bs)
      checks an atom line for "ANGSTROMS", possibly overriding the data's natural units, BOHR (similar to Gaussian CUBE files).
      Parameters:
      isXLowToHigh -
      isAngstroms -
      strAtomCount -
      atomLine -
      bs -
      Returns:
      isAngstroms

    • getSPFv

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

    • swapXZ

      protected void swapXZ()

    • setStream

      protected void setStream(String fileName, boolean isBigEndian)

    • setOutputChannel

      protected void setOutputChannel(OC out)
      Overrides:
      setOutputChannel in class SurfaceReader
      Parameters:
      out -

    • closeReaderSFR

      protected void closeReaderSFR()

    • getTokens

      protected String[] getTokens()

    • parseFloat

      protected float parseFloat()

    • parseFloatStr

      protected float parseFloatStr(String s)

    • parseFloatRange

      protected float parseFloatRange(String s, int iStart, int iEnd)

    • parseInt

      protected int parseInt()

    • parseIntStr

      protected int parseIntStr(String s)

    • parseIntNext

      protected int parseIntNext(String s)

    • parseFloatArrayStr

      protected float[] parseFloatArrayStr(String s)

    • parseFloatArray

      protected float[] parseFloatArray(float[] a, String strStart, String strEnd)

    • getQuotedStringNext

      protected String getQuotedStringNext()

    • skipTo

      protected void skipTo(String info, String what) throws Exception
      Throws:
      Exception

    • rd

      protected String rd() throws Exception
      Throws:
      Exception