org.jmol.jvxl.readers
Class PmeshReader

java.lang.Object
  extended by org.jmol.jvxl.readers.SurfaceReader
      extended by org.jmol.jvxl.readers.SurfaceFileReader
          extended by org.jmol.jvxl.readers.PolygonFileReader
              extended by org.jmol.jvxl.readers.PmeshReader
All Implemented Interfaces:
VertexDataServer
Direct Known Subclasses:
KinemageReader, MsmsReader, ObjReader

 class PmeshReader
extends PolygonFileReader


Field Summary
protected  int fixedCount
           
private  boolean isBinary
           
protected  boolean isClosedFace
           
protected  int iToken
           
protected  int nPolygons
           
protected  boolean onePerLine
           
(package private) static java.lang.String PMESH_BINARY_MAGIC_NUMBER
           
protected  java.lang.String pmeshError
           
protected  java.lang.String[] tokens
           
protected  java.lang.String type
           
protected  int vertexBase
           
protected  int[] vertexMap
           
 
Fields inherited from class org.jmol.jvxl.readers.PolygonFileReader
nTriangles, nVertices
 
Fields inherited from class org.jmol.jvxl.readers.SurfaceFileReader
binarydoc, br, line, next, os
 
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, isProgressive, isQuiet, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, 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
PmeshReader(SurfaceGenerator sg, java.io.BufferedReader br)
           
PmeshReader(SurfaceGenerator sg, java.lang.String fileName, java.io.BufferedReader br)
           
 
Method Summary
 int addTriangleCheck(int iA, int iB, int iC, int check, int check2, boolean isAbsolute, int color)
          addTriangleCheck adds a triangle along with a 3-bit check indicating which edges to draw in mesh mode: 1 (iA-iB) + 2 (iB-iC) + 4 (iC-iA)
protected  boolean checkBinary(java.lang.String fileName)
           
private  float getFloat()
           
private  int getInt()
           
(package private)  void getSurfaceData()
           
private  java.lang.String nextToken()
           
(package private)  boolean readBinaryHeader()
           
protected  boolean readPolygons()
           
protected  boolean readVertices()
           
protected  boolean readVerticesAndPolygons()
           
protected  void setHeader()
           
 
Methods inherited from class org.jmol.jvxl.readers.PolygonFileReader
readSurfaceData, readVolumeData, readVolumeParameters
 
Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader
closeReader, discardTempData, getNextQuotedString, getTokens, parseFloat, parseFloat, parseFloatArray, parseFloatArray, parseInt, parseInt, parseIntNext, readLine, setOutputStream, skipTo
 
Methods inherited from class org.jmol.jvxl.readers.SurfaceReader
addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getSurfaceAtomIndex, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValueAtPoint, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, initPlanes, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBoundingBox, setVectorAnisotropy, setVertexAnisotropy, setVolumeData, 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

PMESH_BINARY_MAGIC_NUMBER

static final java.lang.String PMESH_BINARY_MAGIC_NUMBER
See Also:
Constant Field Values

isBinary

private boolean isBinary

nPolygons

protected int nPolygons

pmeshError

protected java.lang.String pmeshError

type

protected java.lang.String type

isClosedFace

protected boolean isClosedFace

fixedCount

protected int fixedCount

onePerLine

protected boolean onePerLine

vertexBase

protected int vertexBase

vertexMap

protected int[] vertexMap

tokens

protected java.lang.String[] tokens

iToken

protected int iToken
Constructor Detail

PmeshReader

PmeshReader(SurfaceGenerator sg,
            java.io.BufferedReader br)

PmeshReader

PmeshReader(SurfaceGenerator sg,
            java.lang.String fileName,
            java.io.BufferedReader br)
Method Detail

setHeader

protected void setHeader()

checkBinary

protected boolean checkBinary(java.lang.String fileName)

getSurfaceData

void getSurfaceData()
              throws java.lang.Exception
Specified by:
getSurfaceData in class PolygonFileReader
Throws:
java.lang.Exception

readVerticesAndPolygons

protected boolean readVerticesAndPolygons()

readBinaryHeader

boolean readBinaryHeader()

readVertices

protected boolean readVertices()
                        throws java.lang.Exception
Throws:
java.lang.Exception

readPolygons

protected boolean readPolygons()
                        throws java.lang.Exception
Throws:
java.lang.Exception

addTriangleCheck

public int addTriangleCheck(int iA,
                            int iB,
                            int iC,
                            int check,
                            int check2,
                            boolean isAbsolute,
                            int color)
Description copied from interface: VertexDataServer
addTriangleCheck adds a triangle along with a 3-bit check indicating which edges to draw in mesh mode: 1 (iA-iB) + 2 (iB-iC) + 4 (iC-iA)

Specified by:
addTriangleCheck in interface VertexDataServer
Overrides:
addTriangleCheck in class SurfaceReader
check2 - TODO
Returns:
polygon index or -1

nextToken

private java.lang.String nextToken()
                            throws java.lang.Exception
Throws:
java.lang.Exception

getInt

private int getInt()
            throws java.lang.Exception
Throws:
java.lang.Exception

getFloat

private float getFloat()
                throws java.lang.Exception
Throws:
java.lang.Exception