org.jmol.jvxl.readers

Class PmeshReader

java.lang.Object

org.jmol.jvxl.readers.SurfaceReader

org.jmol.jvxl.readers.SurfaceFileReader

org.jmol.jvxl.readers.PolygonFileReader

org.jmol.jvxl.readers.PmeshReader

All Implemented Interfaces:

VertexDataServer

Direct Known Subclasses:

KinemageReader, MsmsReader, ObjReader

 class PmeshReader
extends PolygonFileReader

Field Summary

Fields

Modifier and Type	Field and Description
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, 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
PmeshReader(SurfaceGenerator sg, java.io.BufferedReader br)
PmeshReader(SurfaceGenerator sg, java.lang.String fileName, java.io.BufferedReader br)

Method Summary

Methods

Modifier and Type	Method and Description
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