org.jmol.jvxl.readers.VolumeFileReader

All Implemented Interfaces:: VertexDataServer

Direct Known Subclasses:: ApbsReader, CubeReader, DelPhiBinaryReader, IsoIntersectGridReader, JaguarReader, JvxlXmlReader, MapFileReader, PeriodicVolumeFileReader, PltFormattedReader, UhbdReader, XsfReader

abstract class VolumeFileReader extends SurfaceFileReader

Field Summary

Fields

Modifier and Type

Field

Description

protected int

ac

protected javajs.util.P3[]

boundingBox

protected boolean

canDownsample

protected int

downsampleFactor

protected int[]

downsampleRemainders

protected boolean

endOfData

private boolean

getNCIPlanes

private int

iPlaneNCI

protected boolean

isAngstroms

private boolean

isScaledAlready

protected int

nData

protected boolean

negativeAtomCount

protected int

nSkipX

protected int

nSkipY

protected int

nSkipZ

protected int

nSurfaces

protected boolean

readerClosed

private float[][]

yzPlanesRaw

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, jvxlCutoffRange, 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

VolumeFileReader()
Method Summary

Modifier and Type

Method

Description

protected static boolean

checkAtomLine(boolean isXLowToHigh, boolean isAngstroms, String strAtomCount, String atomLine, javajs.util.SB bs)

checks an atom line for "ANGSTROMS", possibly overriding the data's natural units, BOHR (similar to Gaussian CUBE files).

protected void

closeReader()

private int

countData(String str)

protected float

getJVXLCutoff()

protected float

getNextVoxelValue()

float[]

getPlane(int x)

float[]

getPlaneNCI(int x)

Retrieve raw file planes and pass them to the calculation object for processing into new data.

private void

getPlaneVFR(float[] plane, boolean doRecord)

protected float

getSPFv(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 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)

float

getValue(int x, int y, int z, int ptyz)

for readers only

protected javajs.util.BS

getVoxelBitSet(int nPoints)

protected void

gotoData(int n, int nPoints)

(package private) void

init2(SurfaceGenerator sg, BufferedReader br)

(package private) void

init2VFR(SurfaceGenerator sg, BufferedReader br)

(package private) void

initializeSurfaceData()

protected float

nextVoxel()

protected abstract void

readParameters()

protected void

readSurfaceData(boolean isMapData)

protected void

readSurfaceDataVFR(boolean isMapData)

protected boolean

readVolumeData(boolean isMapData)

protected boolean

readVolumeDataVFR(boolean isMapData)

protected boolean

readVolumeParameters(boolean isMapData)

private int

readVolumetricHeader()

protected void

readVoxelVector(int voxelVectorIndex)

protected float

recordData(float value)

private void

scaleIsosurface(float scale)

protected String

skipComments(boolean allowBlankLines)

protected void

skipData(int nPoints)

protected void

skipDataVFR(int nPoints)

private void

skipVoxels(int n)

protected void

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, gotoAndReadVoxelData, initializeMapping, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, 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 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
- getNCIPlanes
  
  private boolean getNCIPlanes
- nData
  
  protected int nData
- readerClosed
  
  protected boolean readerClosed
- downsampleFactor
  
  protected int downsampleFactor
- nSkipX
  
  protected int nSkipX
- nSkipY
  
  protected int nSkipY
- nSkipZ
  
  protected int nSkipZ
- yzPlanesRaw
  
  private float[][] yzPlanesRaw
- iPlaneNCI
  
  private int iPlaneNCI
- boundingBox
  
  protected javajs.util.P3[] boundingBox
- isScaledAlready
  
  private boolean isScaledAlready
Constructor Details
- VolumeFileReader
  
  VolumeFileReader()
Method Details
- init2
  
  void init2(SurfaceGenerator sg, BufferedReader br)
  
  Overrides:
  
  init2 in class SurfaceFileReader
- init2VFR
  
  void init2VFR(SurfaceGenerator sg, BufferedReader br)
- recordData
  
  protected float recordData(float value)
- closeReader
  
  protected void closeReader()
  
  Overrides:
  
  closeReader in class SurfaceFileReader
- readVolumeParameters
  
  protected boolean readVolumeParameters(boolean isMapData)
  
  Specified by:
  
  readVolumeParameters in class SurfaceReader
- readVolumeData
  
  protected boolean readVolumeData(boolean isMapData)
  
  Specified by:
  
  readVolumeData in class SurfaceReader
- readVolumeDataVFR
  
  protected boolean readVolumeDataVFR(boolean isMapData)
- readVolumetricHeader
  
  private int readVolumetricHeader()
- readParameters
  
  protected abstract void readParameters() throws Exception
  
  Throws:
  
  Exception
- skipComments
  
  protected String skipComments(boolean allowBlankLines) throws Exception
  
  Throws:
  
  Exception
- readVoxelVector
  
  protected void readVoxelVector(int voxelVectorIndex) throws Exception
  
  Throws:
  
  Exception
- initializeSurfaceData
  
  void initializeSurfaceData()
- getJVXLCutoff
  
  protected float getJVXLCutoff()
- readSurfaceData
  
  protected void readSurfaceData(boolean isMapData) throws Exception
  
  Specified by:
  
  readSurfaceData in class SurfaceReader
  
  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)
- getPlaneVFR
  
  private void getPlaneVFR(float[] plane, boolean doRecord)
- 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
  
  Returns:
  
  value[x][y][z]
- skipVoxels
  
  private void skipVoxels(int n) throws Exception
  
  Throws:
  
  Exception
- getVoxelBitSet
  
  protected javajs.util.BS getVoxelBitSet(int nPoints) throws Exception
  
  Parameters:
  
  nPoints -
  
  Returns:
  
  JVXL bitset
  
  Throws:
  
  Exception
- getNextVoxelValue
  
  protected float getNextVoxelValue() throws Exception
  
  Throws:
  
  Exception
- nextVoxel
  
  protected float nextVoxel() throws Exception
  
  Throws:
  
  Exception
- gotoData
  
  protected void gotoData(int n, int nPoints) throws Exception
  
  Overrides:
  
  gotoData in class SurfaceReader
  
  Throws:
  
  Exception
- skipData
  
  protected void skipData(int nPoints) throws Exception
  
  Throws:
  
  Exception
- skipDataVFR
  
  protected void skipDataVFR(int nPoints) throws Exception
  
  Throws:
  
  Exception
- countData
  
  private int countData(String str)
- checkAtomLine
  
  protected static boolean checkAtomLine(boolean isXLowToHigh, boolean isAngstroms, String strAtomCount, String atomLine, javajs.util.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
- 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 SurfaceReader
- getSPFv
  
  protected float getSPFv(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)
- scaleIsosurface
  
  private void scaleIsosurface(float scale)
- swapXZ
  
  protected void swapXZ()

Class VolumeFileReader

Field Summary

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.SurfaceFileReader

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

Methods inherited from class java.lang.Object

Field Details

endOfData

negativeAtomCount

ac

nSurfaces

isAngstroms

canDownsample

downsampleRemainders

getNCIPlanes

nData

readerClosed

downsampleFactor

nSkipX

nSkipY

nSkipZ

yzPlanesRaw

iPlaneNCI

boundingBox

isScaledAlready

Constructor Details

VolumeFileReader

Method Details

init2

init2VFR

recordData

closeReader

readVolumeParameters

readVolumeData

readVolumeDataVFR

readVolumetricHeader

readParameters

skipComments

readVoxelVector

initializeSurfaceData

getJVXLCutoff

readSurfaceData

readSurfaceDataVFR

getPlane

getPlaneNCI

getPlaneVFR

getValue

skipVoxels

getVoxelBitSet

getNextVoxelValue

nextVoxel

gotoData

skipData

skipDataVFR

countData

checkAtomLine

getSurfacePointAndFraction

getSPFv

scaleIsosurface

swapXZ