Package 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

PMESH format created for Jmol. This is not the "pmesh" format from Edinburgh: see http://i-sight.sourceforge.net/docs/GridView/MeshFileReader.html#ReadPMeshFile(java.lang.String,%20GridView.OutputPanel,%20javax.swing.JProgressBar) That format is read by the ObjReader.

Author:

Bob Hanson hansonr@stolaf.edu

Field Summary

Fields

Modifier and Type	Field	Description
protected int	fixedCount
private boolean	isBinary
protected boolean	isClosedFace
protected int	iToken
protected int	nPolygons
protected boolean	onePerLine
protected String	pmeshError
protected String[]	tokens
protected 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, 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, 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
PmeshReader()

Method Summary

Modifier and Type	Method	Description
protected boolean	checkBinary(String fileName)
private float	getFloat()
private int	getInt()
(package private) void	getSurfaceData()
(package private) void	init2(SurfaceGenerator sg, BufferedReader br)
protected void	init2PR(SurfaceGenerator sg, BufferedReader br)
private String	nextToken()
(package private) boolean	readBinaryHeader()
protected boolean	readPolygons()
protected boolean	readPolygonsPM()
protected boolean	readVertices()
protected boolean	readVerticesAndPolygons()
protected boolean	readVerticesPM()
protected void	setHeader()

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

init2PFR, readSurfaceData, readVolumeData, readVolumeParameters

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

closeReader, 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, getPlane, getPlaneSR, getSPF, getSurfaceAtomIndex, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValue2, getValueAtPoint, gotoAndReadVoxelData, gotoData, 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 Detail

isBinary

private boolean isBinary

nPolygons

protected int nPolygons

pmeshError

protected String pmeshError

type

protected String type

isClosedFace

protected boolean isClosedFace

fixedCount

protected int fixedCount

onePerLine

protected boolean onePerLine

vertexBase

protected int vertexBase

vertexMap

protected int[] vertexMap

tokens

protected String[] tokens

iToken

protected int iToken

Constructor Detail

PmeshReader

PmeshReader()

Method Detail

init2

void init2(SurfaceGenerator sg,
           BufferedReader br)

Overrides:

init2 in class SurfaceFileReader

init2PR

protected void init2PR(SurfaceGenerator sg,
                       BufferedReader br)

setHeader

protected void setHeader()

checkBinary

protected boolean checkBinary(String fileName)

getSurfaceData

void getSurfaceData()
             throws Exception

Specified by:

getSurfaceData in class PolygonFileReader

Throws:

Exception

readVerticesAndPolygons

protected boolean readVerticesAndPolygons()

readBinaryHeader

boolean readBinaryHeader()

readVertices

protected boolean readVertices()
                        throws Exception

Throws:

Exception

readVerticesPM

protected boolean readVerticesPM()
                          throws Exception

Throws:

Exception

readPolygons

protected boolean readPolygons()
                        throws Exception

Throws:

Exception

readPolygonsPM

protected boolean readPolygonsPM()
                          throws Exception

Throws:

Exception

nextToken

private String nextToken()
                  throws Exception

Throws:

Exception

getInt

private int getInt()
            throws Exception

Throws:

Exception

getFloat

private float getFloat()
                throws Exception

Throws:

Exception