Package org.jmol.jvxl.readers

Class Pmesh4Reader

java.lang.Object

org.jmol.jvxl.readers.SurfaceReader

org.jmol.jvxl.readers.SurfaceFileReader

org.jmol.jvxl.readers.PolygonFileReader

org.jmol.jvxl.readers.Pmesh4Reader

All Implemented Interfaces:

VertexDataServer

class Pmesh4Reader
extends PolygonFileReader

Field Summary

Fields

Modifier and Type	Field	Description
private int	color
private int	iToken
private int	nPolygons
private int	nX
private int	nY
private String	pmeshError
private String[]	tokens
(package private) float	transparency
private String	type

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
Pmesh4Reader()

Method Summary

Modifier and Type	Method	Description
private void	createMesh()
private float	getFloat()
private int	getInt()
(package private) void	getSurfaceData()
(package private) void	init2(SurfaceGenerator sg, BufferedReader br)
private String	nextToken()
private void	readColor()
private boolean	readVertices()
private boolean	readVerticesAndPolygons()

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

nPolygons

private int nPolygons

pmeshError

private String pmeshError

type

private String type

color

private int color

transparency

float transparency

nX

private int nX

nY

private int nY

tokens

private String[] tokens

iToken

private int iToken

Constructor Detail

Pmesh4Reader

Pmesh4Reader()

Method Detail

init2

void init2(SurfaceGenerator sg,
           BufferedReader br)

Overrides:

init2 in class SurfaceFileReader

getSurfaceData

void getSurfaceData()
             throws Exception

Specified by:

getSurfaceData in class PolygonFileReader

Throws:

Exception

readVerticesAndPolygons

private boolean readVerticesAndPolygons()

readColor

private void readColor()
                throws Exception

Throws:

Exception

readVertices

private boolean readVertices()
                      throws Exception

Throws:

Exception

createMesh

private void createMesh()

nextToken

private String nextToken()
                  throws Exception

Throws:

Exception

getInt

private int getInt()
            throws Exception

Throws:

Exception

getFloat

private float getFloat()
                throws Exception

Throws:

Exception