META-INF/MANIFEST.MF
META-INF/SELFSIGN.SF
META-INF/SELFSIGN.RSA
META-INF/
org/
org/jmol/
org/jmol/jvxl/
org/jmol/jvxl/api/
org/jmol/jvxl/calc/
org/jmol/jvxl/data/
org/jmol/jvxl/readers/
org/jmol/shapesurface/
org/jmol/jvxl/api/MeshDataServer.class
<Unknown>
package org.jmol.jvxl.api
public abstract org.jmol.jvxl.api.MeshDataServer extends java.lang.Object implements org.jmol.jvxl.api.VertexDataServer  {
	public abstract void invalidateTriangles () 
	public abstract void fillMeshData (org.jmol.jvxl.data.MeshData, int) 
	public abstract void notifySurfaceGenerationCompleted () 
	public abstract void notifySurfaceMappingCompleted () 
	public abstract javax.vecmath.Point3f[] calculateGeodesicSurface (java.util.BitSet, float) 
	public abstract int getColixArgb (short) 
}

org/jmol/jvxl/api/VertexDataServer.class
<Unknown>
package org.jmol.jvxl.api
public abstract org.jmol.jvxl.api.VertexDataServer extends java.lang.Object {
	public abstract int getSurfacePointIndexAndFraction (float, boolean, int, int, int, javax.vecmath.Point3i, int, int, float, float, javax.vecmath.Point3f, javax.vecmath.Vector3f, boolean, float[]) 
	public abstract int addVertexCopy (javax.vecmath.Point3f, float, int) 
	public abstract void addTriangleCheck (int, int, int, int, boolean, int) 
	public abstract float getValue (int, int, int) 
}

org/jmol/jvxl/calc/MarchingCubes.class
<Unknown>
package org.jmol.jvxl.calc
public org.jmol.jvxl.calc.MarchingCubes extends org.jmol.jvxl.calc.TriangleData {
	private org.jmol.jvxl.api.VertexDataServer surfaceReader
	private org.jmol.jvxl.data.VolumeData volumeData
	private int contourType
	private boolean isContoured
	private float cutoff
	private boolean isCutoffAbsolute
	private boolean isSquared
	private boolean isXLowToHigh
	private int cubeCountX
	private int cubeCountY
	private int cubeCountZ
	private int nY
	private int nZ
	private int yzCount
	private float fractionOutside
	private boolean integrateSquared
	private java.util.BitSet bsVoxels
	private StringBuffer edgeData
	private int mode
	private static final int MODE_CUBE
	private static final int MODE_BITSET
	private static final int MODE_GETXYZ
	private final float[] vertexValues
	int edgeCount
	private final javax.vecmath.Vector3f[] voxelVertexVectors
	private final javax.vecmath.Vector3f[] edgeVectors
	private static int[] yzPlanePts
	private final int[] edgePointIndexes
	private int[][][] isoPointIndexPlanes
	private float[][] yzPlanes
	javax.vecmath.Vector3f vTemp
	private java.util.BitSet bsValues
	private final javax.vecmath.Point3f pt0
	private final javax.vecmath.Point3f pointA
	private static final int[] edgeVertexPointersLowToHigh
	private static final int[] edgeVertexPointersHighToLow
	private int[] edgeVertexPointers
	private static final int[] edgeVertexPlanesLowToHigh
	private static final int[] edgeVertexPlanesHighToLow
	private int[] edgeVertexPlanes
	private float[] fReturn
	private static final javax.vecmath.Vector3f[] cubeVertexVectors
	private static final int[] edgeTypeTable
	private final int[] linearOffsets
	private static final short[] insideMaskTable
	public java.util.BitSet getBsVoxels () 
	public void <init> () 
	public void <init> (org.jmol.jvxl.api.VertexDataServer, org.jmol.jvxl.data.VolumeData, java.util.BitSet, boolean, int, float, boolean, boolean, boolean) 
	private void calcVoxelVertexVectors () 
	private int[][] resetIndexPlane (int[][]) 
	public java.lang.String getEdgeData () 
	private void addTriangle (int, int, int, int) 
	private float getValue (int, int, int, int, int, float[]) 
	public static boolean isInside (float, float, boolean) 
	private boolean processOneCubical (int, int, int, int, int) 
	public void calcVertexPoint (int, int, int, int, javax.vecmath.Point3f) 
	private void setLinearOffsets () 
	public int getLinearOffset (int, int, int, int) 
	static void <clinit> () 
}

org/jmol/jvxl/calc/MarchingSquares$ContourVertex.class
<Unknown>
package org.jmol.jvxl.calc
 org.jmol.jvxl.calc.MarchingSquares$ContourVertex extends java.lang.Object {
	javax.vecmath.Point3f vertexXYZ
	javax.vecmath.Point3i voxelLocation
	int[] pixelLocation
	float value
	int vertexIndex
	void <init> (int, int, int, javax.vecmath.Point3f, int) 
	void setValue (float, org.jmol.jvxl.data.VolumeData) 
	void setPixelLocation (javax.vecmath.Point3i) 
}

org/jmol/jvxl/calc/MarchingSquares$PlanarSquare.class
<Unknown>
package org.jmol.jvxl.calc
 org.jmol.jvxl.calc.MarchingSquares$PlanarSquare extends java.lang.Object {
	int[] edgeMask12
	int edgeMask12All
	int nInside
	int nOutside
	int nThrough
	int contourBits
	final int[] vertexes
	float[][] fractions
	int[][] intersectionPoints
	void <init> (int) 
	void setIntersectionPoints (int, int[], float[]) 
	void setVertex (int, int) 
	void addEdgeMask (int, int, int) 
}

org/jmol/jvxl/calc/MarchingSquares.class
<Unknown>
package org.jmol.jvxl.calc
public org.jmol.jvxl.calc.MarchingSquares extends java.lang.Object {
	public static final int CONTOUR_POINT
	public static final int VERTEX_POINT
	public static final int EDGE_POINT
	private boolean logMessages
	private org.jmol.jvxl.api.VertexDataServer surfaceReader
	private org.jmol.jvxl.data.VolumeData volumeData
	private static final int nContourMax
	public static final int defaultContourCount
	private int nContourSegments
	private int nContoursSpecified
	private int contourType
	private javax.vecmath.Point4f thePlane
	private boolean is3DContour
	private int thisContour
	private float valueMin
	private float valueMax
	private int nVertices
	private final javax.vecmath.Vector3f pointVector
	private final javax.vecmath.Point3f pointA
	private final javax.vecmath.Point3f pointB
	private final javax.vecmath.Vector3f edgeVector
	private final javax.vecmath.Point3f planarOrigin
	private final javax.vecmath.Vector3f[] planarVectors
	private final javax.vecmath.Vector3f[] unitPlanarVectors
	private final float[] planarVectorLengths
	private final javax.vecmath.Matrix3f matXyzToPlane
	private boolean contourFromZero
	private static final javax.vecmath.Point3i[] squareVertexOffsets
	private static final javax.vecmath.Vector3f[] squareVertexVectors
	private static final byte[] edgeVertexes2d
	private static final byte[] insideMaskTable2d
	private int contourVertexCount
	private org.jmol.jvxl.calc.MarchingSquares$ContourVertex[] contourVertexes
	private final int[] pixelCounts
	private final javax.vecmath.Matrix3f planarMatrix
	private float[][] pixelData
	private final float[] vertexValues2d
	private final javax.vecmath.Point3f[] contourPoints
	private int squareCountX
	private int squareCountY
	private org.jmol.jvxl.calc.MarchingSquares$PlanarSquare[] planarSquares
	private int nSquares
	private float contourPlaneMinimumValue
	private float contourPlaneMaximumValue
	private int contourIndex
	private float[] squareFractions
	private final javax.vecmath.Point3f pixelOrigin
	private javax.vecmath.Vector3f[] pixelVertexVectors
	private final int[] triangleVertexList
	private final javax.vecmath.Point3i ptiTemp
	public void <init> (org.jmol.jvxl.api.VertexDataServer, org.jmol.jvxl.data.VolumeData, javax.vecmath.Point4f, int, int, boolean) 
	public int getContourType () 
	public void setMinMax (float, float) 
	private void setContourType () 
	private static int getContourType (javax.vecmath.Point4f, javax.vecmath.Vector3f[]) 
	public int generateContourData (boolean) 
	private void getPlanarVectors () 
	private void setPlanarTransform () 
	private void getPlanarOrigin () 
	public int addContourVertex (int, int, int, javax.vecmath.Point3i, javax.vecmath.Point3f, float) 
	public int getContourVertexCount () 
	public void setContourData (int, float) 
	private void loadPixelData (boolean) 
	public float getInterpolatedPixelValue (javax.vecmath.Point3f) 
	private void getPixelCounts () 
	private void createPlanarSquares () 
	public boolean createContours (float, float) 
	private int generateContourData (float) 
	private boolean isInside2d (float, float) 
	private int[] propagateNeighborPointIndexes2d (int, int, int[][], float[][]) 
	private void processOneQuadrilateral (int, float, int[], int, int) 
	private void calcVertexPoints2d (int, int, int, int) 
	private void calcVertexPoints3d (int, int, int, int) 
	private void contourLocateXYZ (int, int, javax.vecmath.Point3f) 
	private int findContourVertex (int, int) 
	private float calcContourPoint (float, float, float, javax.vecmath.Point3f) 
	private void calcPixelVertexVectors () 
	private void triangulateContours (boolean) 
	private void fillSquare (org.jmol.jvxl.calc.MarchingSquares$PlanarSquare, int, int, boolean, int) 
	private void createTriangleSet (int, int, int) 
	private static void setupMatrix (javax.vecmath.Matrix3f, javax.vecmath.Vector3f[]) 
	private void xyzToPixelVector (javax.vecmath.Vector3f) 
	private javax.vecmath.Point3f pixelPtToXYZ (int, int) 
	private javax.vecmath.Point3i locatePixel (javax.vecmath.Point3f) 
	static void <clinit> () 
}

org/jmol/jvxl/calc/TriangleData.class
<Unknown>
package org.jmol.jvxl.calc
public org.jmol.jvxl.calc.TriangleData extends java.lang.Object implements org.jmol.api.TriangleServer  {
	protected static final int[] Pwr2
	protected static final javax.vecmath.Point3i[] cubeVertexOffsets
	protected static final byte[] edgeVertexes
	protected static final byte[][] triangleTable2
	public void <init> () 
	public javax.vecmath.Point3i[] getCubeVertexOffsets () 
	public java.util.Vector intersectPlane (javax.vecmath.Point4f, javax.vecmath.Point3f[], int) 
	static void <clinit> () 
}

org/jmol/jvxl/data/JvxlData.class
<Unknown>
package org.jmol.jvxl.data
public org.jmol.jvxl.data.JvxlData extends java.lang.Object {
	public boolean wasJvxl
	public boolean wasCubic
	public String jvxlFileTitle
	public String jvxlFileMessage
	public String jvxlFileHeader
	public String jvxlExtraLine
	public String jvxlDefinitionLine
	public String jvxlSurfaceData
	public String jvxlEdgeData
	public String jvxlColorData
	public String jvxlInfoLine
	public javax.vecmath.Point4f jvxlPlane
	public int jvxlCompressionRatio
	public boolean isJvxlPrecisionColor
	public boolean jvxlDataIsColorMapped
	public boolean jvxlDataIs2dContour
	public boolean isColorReversed
	public int edgeFractionBase
	public int edgeFractionRange
	public int colorFractionBase
	public int colorFractionRange
	public boolean insideOut
	public boolean isXLowToHigh
	public boolean isContoured
	public boolean isBicolorMap
	public boolean isTruncated
	public boolean vertexDataOnly
	public float mappedDataMin
	public float mappedDataMax
	public float valueMappedToRed
	public float valueMappedToBlue
	public float cutoff
	public float pointsPerAngstrom
	public int nPointsX
	public int nPointsY
	public int nPointsZ
	public int nBytes
	public int nContours
	public int nEdges
	public int nSurfaceInts
	public int vertexCount
	public java.util.Vector[] vContours
	public int[] contourColors
	public short minColorIndex
	public short maxColorIndex
	public String[] title
	public String version
	public void <init> () 
}

org/jmol/jvxl/data/MeshData.class
<Unknown>
package org.jmol.jvxl.data
public org.jmol.jvxl.data.MeshData extends java.lang.Object {
	private static final int SEED_COUNT
	public static final int MODE_GET_VERTICES
	public static final int MODE_GET_COLOR_INDEXES
	public static final int MODE_PUT_SETS
	public static final int MODE_PUT_VERTICES
	public int polygonCount
	public javax.vecmath.Point3f[] vertices
	public short[] vertexColixes
	public int vertexCount
	public float[] vertexValues
	public int[][] polygonIndexes
	public short[] polygonColixes
	public java.util.BitSet[] surfaceSet
	public int[] vertexSets
	public int nSets
	public javax.vecmath.Point3f[] dots
	private boolean setsSuccessful
	public int vertexIncrement
	private int lastColor
	private short lastColix
	public void <init> () 
	public int addVertexCopy (javax.vecmath.Point3f, float, int) 
	private int addVertexCopy (javax.vecmath.Point3f) 
	public void addTriangleCheck (int, int, int, int, int) 
	public java.util.BitSet[] getSurfaceSet () 
	public java.util.BitSet[] getSurfaceSet (int) 
	private int findSet (int) 
	private void createSet (int, int, int) 
	private void mergeSets (int, int) 
	public void invalidateSurfaceSet (int) 
	public static boolean checkCutoff (int, int, int, float[]) 
	private boolean setABC (int) 
	public void invalidateTriangles () 
}

org/jmol/jvxl/data/VolumeData.class
<Unknown>
package org.jmol.jvxl.data
public org.jmol.jvxl.data.VolumeData extends java.lang.Object implements org.jmol.api.VolumeDataInterface  {
	public final javax.vecmath.Point3f volumetricOrigin
	public final float[] origin
	public final javax.vecmath.Vector3f[] volumetricVectors
	public final int[] voxelCounts
	public int nPoints
	public float[][][] voxelData
	public final float[] volumetricVectorLengths
	public final javax.vecmath.Vector3f[] unitVolumetricVectors
	private final javax.vecmath.Matrix3f volumetricMatrix
	private javax.vecmath.Point4f thePlane
	private float thePlaneNormalMag
	private final javax.vecmath.Point3f ptXyzTemp
	private final javax.vecmath.Vector3f pointVector
	public void <init> () 
	public void setVolumetricOrigin (float, float, float) 
	public float[] getOriginFloat () 
	public float[] getVolumetricVectorLengths () 
	public void setVolumetricVector (int, float, float, float) 
	public int[] getVoxelCounts () 
	public int setVoxelCounts (int, int, int) 
	public float[][][] getVoxelData () 
	public void setVoxelData (float[][][]) 
	public void setMatrix () 
	public void transform (javax.vecmath.Vector3f, javax.vecmath.Vector3f) 
	public void setPlaneParameters (javax.vecmath.Point4f) 
	public float calcVoxelPlaneDistance (int, int, int) 
	public float distancePointToPlane (javax.vecmath.Point3f) 
	public void voxelPtToXYZ (int, int, int, javax.vecmath.Point3f) 
	public void setUnitVectors () 
	private float scaleByVoxelVector (javax.vecmath.Vector3f, int) 
	public void xyzToVoxelPt (float, float, float, javax.vecmath.Point3i) 
	private void setVoxelPoint () 
	public float lookupInterpolatedVoxelValue (javax.vecmath.Point3f) 
	private float getInterpolatedVoxelValue (javax.vecmath.Point3f) 
	public static float getFractional2DValue (float, float, float, float, float, float) 
	private static int indexDown (float, int) 
	void offsetCenter (javax.vecmath.Point3f) 
	public void setDataDistanceToPlane (javax.vecmath.Point4f) 
	public void filterData (boolean, float) 
	public void capData (javax.vecmath.Point4f, float) 
}

org/jmol/jvxl/readers/ApbsReader.class
<Unknown>
package org.jmol.jvxl.readers
 org.jmol.jvxl.readers.ApbsReader extends org.jmol.jvxl.readers.VolumeFileReader {
	void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader) 
	protected void readTitleLines ()  throws java.lang.Exception 
	protected void readAtomCountAndOrigin ()  throws java.lang.Exception 
	protected void readVoxelVector (int)  throws java.lang.Exception 
}

org/jmol/jvxl/readers/AtomDataReader.class
<Unknown>
package org.jmol.jvxl.readers
abstract org.jmol.jvxl.readers.AtomDataReader extends org.jmol.jvxl.readers.VolumeDataReader {
	protected org.jmol.atomdata.AtomDataServer atomDataServer
	protected String fileName
	protected String fileDotModel
	protected int modelIndex
	protected org.jmol.atomdata.AtomData atomData
	protected javax.vecmath.Point3f[] atomXyz
	protected float[] atomRadius
	protected float[] atomProp
	protected int[] atomNo
	protected int[] atomIndex
	protected int[] myIndex
	protected int atomCount
	protected int myAtomCount
	protected int nearbyAtomCount
	protected int firstNearbyAtom
	protected java.util.BitSet bsMySelected
	protected java.util.BitSet bsMyIgnored
	private javax.vecmath.Point3f xyzMin
	private javax.vecmath.Point3f xyzMax
	protected boolean doAddHydrogens
	protected boolean doUsePlane
	protected boolean doUseIterator
	void <init> (org.jmol.jvxl.readers.SurfaceGenerator) 
	protected void setup () 
	protected void getAtoms (float, boolean, boolean) 
	private float getWorkingRadius (int, float) 
	protected void setHeader (java.lang.String, java.lang.String) 
	protected void setRangesAndAddAtoms (float, int, int) 
	protected boolean fixTitleLine (int) 
}

org/jmol/jvxl/readers/CubeReader.class
<Unknown>
package org.jmol.jvxl.readers
 org.jmol.jvxl.readers.CubeReader extends org.jmol.jvxl.readers.VolumeFileReader {
	void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader) 
	protected void readTitleLines ()  throws java.lang.Exception 
	protected void readAtomCountAndOrigin ()  throws java.lang.Exception 
}

org/jmol/jvxl/readers/EfvetReader.class
<Unknown>
package org.jmol.jvxl.readers
 org.jmol.jvxl.readers.EfvetReader extends org.jmol.jvxl.readers.PolygonFileReader {
	void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader) 
	void getSurfaceData ()  throws java.lang.Exception 
	private void getHeader ()  throws java.lang.Exception 
	private void getVertices ()  throws java.lang.Exception 
	private void getTriangles ()  throws java.lang.Exception 
}

org/jmol/jvxl/readers/IsoFxyReader.class
<Unknown>
package org.jmol.jvxl.readers
 org.jmol.jvxl.readers.IsoFxyReader extends org.jmol.jvxl.readers.VolumeDataReader {
	private String functionName
	private float[][] data
	private boolean isPlanarMapping
	void <init> (org.jmol.jvxl.readers.SurfaceGenerator) 
	protected void setup () 
	public float getValue (int, int, int) 
}

org/jmol/jvxl/readers/IsoFxyzReader.class
<Unknown>
package org.jmol.jvxl.readers
 org.jmol.jvxl.readers.IsoFxyzReader extends org.jmol.jvxl.readers.VolumeDataReader {
	private String functionName
	private float[][][] data
	void <init> (org.jmol.jvxl.readers.SurfaceGenerator) 
	protected void setup () 
	public float getValue (int, int, int) 
}

org/jmol/jvxl/readers/IsoMOReader.class
<Unknown>
package org.jmol.jvxl.readers
 org.jmol.jvxl.readers.IsoMOReader extends org.jmol.jvxl.readers.AtomDataReader {
	void <init> (org.jmol.jvxl.readers.SurfaceGenerator) 
	protected void setup () 
	private void fixTitleLine (int, java.util.Hashtable) 
	protected void generateCube () 
	private void getData (org.jmol.api.MOCalculationInterface, java.util.Hashtable, float[], float[]) 
}

org/jmol/jvxl/readers/IsoMepReader.class
<Unknown>
package org.jmol.jvxl.readers
 org.jmol.jvxl.readers.IsoMepReader extends org.jmol.jvxl.readers.AtomDataReader {
	void <init> (org.jmol.jvxl.readers.SurfaceGenerator) 
	protected void setup () 
	protected void generateCube () 
}

org/jmol/jvxl/readers/IsoPlaneReader.class
<Unknown>
package org.jmol.jvxl.readers
 org.jmol.jvxl.readers.IsoPlaneReader extends org.jmol.jvxl.readers.AtomDataReader {
	void <init> (org.jmol.jvxl.readers.SurfaceGenerator) 
	protected void setup () 
	public float getValue (int, int, int) 
}

org/jmol/jvxl/readers/IsoShapeReader.class
<Unknown>
package org.jmol.jvxl.readers
 org.jmol.jvxl.readers.IsoShapeReader extends org.jmol.jvxl.readers.VolumeDataReader {
	private int psi_n
	private int psi_l
	private int psi_m
	private float psi_Znuc
	private float sphere_radiusAngstroms
	private boolean allowNegative
	private double[] rfactor
	private double[] pfactor
	private static final double A0
	private static final double ROOT2
	private float radius
	private float ppa
	private int maxGrid
	private static final float[] fact
	private final javax.vecmath.Point3f ptPsi
	void <init> (org.jmol.jvxl.readers.SurfaceGenerator, float) 
	void <init> (org.jmol.jvxl.readers.SurfaceGenerator, int, int, int, float) 
	protected void setup () 
	public float getValue (int, int, int) 
	private void setHeader (java.lang.String) 
	private float autoScaleOrbital () 
	private void calcFactors (int, int, int) 
	private double hydrogenAtomPsiAt (javax.vecmath.Point3f, int, int, int) 
	protected void readSurfaceData (boolean)  throws java.lang.Exception 
	static void <clinit> () 
}

org/jmol/jvxl/readers/IsoSolventReader.class
<Unknown>
package org.jmol.jvxl.readers
 org.jmol.jvxl.readers.IsoSolventReader extends org.jmol.jvxl.readers.AtomDataReader {
	private float cavityRadius
	private float envelopeRadius
	private boolean doCalculateTroughs
	private boolean isCavity
	private boolean isPocket
	private float solventRadius
	private boolean isProperty
	private boolean doSmoothProperty
	final javax.vecmath.Point3f ptXyzTemp
	final javax.vecmath.Point3f ptS
	void <init> (org.jmol.jvxl.readers.SurfaceGenerator) 
	protected void setup () 
	public void selectPocket (boolean) 
	protected void generateCube () 
	private void generateSolventCavity () 
	void generateSolventCube (boolean) 
	void setGridLimitsForAtom (javax.vecmath.Point3f, float, javax.vecmath.Point3i, javax.vecmath.Point3i) 
	float checkSpecialVoxel (javax.vecmath.Point3f, float, javax.vecmath.Point3f, float, float, javax.vecmath.Point3f) 
	boolean voxelIsInTrough (float, float, float, float, float, float) 
	float solventDistance (javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f, float, float, float, float, float) 
}

org/jmol/jvxl/readers/JaguarReader.class
<Unknown>
package org.jmol.jvxl.readers
 org.jmol.jvxl.readers.JaguarReader extends org.jmol.jvxl.readers.VolumeFileReader {
	private float[] extents
	void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader) 
	protected void readTitleLines ()  throws java.lang.Exception 
	protected void readAtomCountAndOrigin ()  throws java.lang.Exception 
	protected void readVoxelVector (int)  throws java.lang.Exception 
	protected float nextVoxel ()  throws java.lang.Exception 
}

org/jmol/jvxl/readers/JvxlReader.class
<Unknown>
package org.jmol.jvxl.readers
public org.jmol.jvxl.readers.JvxlReader extends org.jmol.jvxl.readers.VolumeFileReader {
	private static final String JVXL_VERSION
	public static final int defaultEdgeFractionBase
	public static final int defaultEdgeFractionRange
	public static final int defaultColorFractionBase
	public static final int defaultColorFractionRange
	private int surfaceDataCount
	private int edgeDataCount
	private int colorDataCount
	private boolean haveContourData
	private int nThisValue
	private boolean thisInside
	private int fractionPtr
	private String strFractionTemp
	void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader) 
	protected static void jvxlUpdateInfo (org.jmol.jvxl.data.JvxlData, java.lang.String[], int) 
	public static void jvxlUpdateInfoLines (org.jmol.jvxl.data.JvxlData) 
	protected boolean readVolumeData (boolean) 
	protected boolean gotoAndReadVoxelData (boolean) 
	protected void initializeVoxelData () 
	protected void readSurfaceData (boolean)  throws java.lang.Exception 
	protected void readTitleLines ()  throws java.lang.Exception 
	protected static boolean jvxlCheckAtomLine (boolean, boolean, java.lang.String, java.lang.String, java.lang.StringBuffer) 
	protected void readAtomCountAndOrigin ()  throws java.lang.Exception 
	protected static void jvxlReadAtoms (java.io.BufferedReader, java.lang.StringBuffer, int, org.jmol.jvxl.data.VolumeData)  throws java.lang.Exception 
	protected int readExtraLine ()  throws java.lang.Exception 
	private void jvxlReadDefinitionLine (boolean)  throws java.lang.Exception 
	private java.lang.String jvxlReadData (java.lang.String, int) 
	public static java.lang.String jvxlCompressString (java.lang.String) 
	private static java.lang.String jvxlUncompressString (java.lang.String) 
	protected java.util.BitSet getVoxelBitSet (int)  throws java.lang.Exception 
	protected float getNextVoxelValue (java.lang.StringBuffer)  throws java.lang.Exception 
	public static void setSurfaceInfoFromBitSet (org.jmol.jvxl.data.JvxlData, java.util.BitSet, javax.vecmath.Point4f) 
	private static int jvxlEncodeBitSet (java.util.BitSet, int, java.lang.StringBuffer) 
	private static java.util.BitSet jvxlDecodeBitSet (java.lang.String) 
	protected static void setSurfaceInfo (org.jmol.jvxl.data.JvxlData, javax.vecmath.Point4f, int, java.lang.StringBuffer) 
	protected float getSurfacePointAndFraction (float, boolean, float, float, javax.vecmath.Point3f, javax.vecmath.Vector3f, float[], javax.vecmath.Point3f) 
	private float jvxlGetNextFraction (int, int, float) 
	protected java.lang.String readColorData () 
	protected void gotoData (int, int)  throws java.lang.Exception 
	private void jvxlSkipData (int, boolean)  throws java.lang.Exception 
	private void jvxlSkipDataBlock (int, boolean)  throws java.lang.Exception 
	private int countData (java.lang.String) 
	protected static void jvxlCreateHeaderWithoutTitleOrAtoms (org.jmol.jvxl.data.VolumeData, java.lang.StringBuffer) 
	protected static void jvxlCreateHeader (org.jmol.jvxl.data.VolumeData, int, javax.vecmath.Point3f[], int[], java.lang.StringBuffer) 
	private static void jvxlAddDummyAtomList (org.jmol.jvxl.data.VolumeData, java.lang.StringBuffer) 
	public static java.lang.String jvxlGetDefinitionLine (org.jmol.jvxl.data.JvxlData, boolean) 
	protected static java.lang.String jvxlExtraLine (org.jmol.jvxl.data.JvxlData, int) 
	public static java.lang.String jvxlGetFile (org.jmol.jvxl.api.MeshDataServer, org.jmol.jvxl.data.JvxlData, org.jmol.jvxl.data.MeshData, java.lang.String[], java.lang.String, boolean, int, java.lang.String, java.lang.String) 
	private static void jvxlEncodeContourData (java.util.Vector[], java.lang.StringBuffer) 
	protected static float jvxlFractionFromCharacter (int, int, int, float) 
	protected static float jvxlValueFromCharacter2 (int, int, float, float, int, int) 
	protected static float jvxlFractionFromCharacter2 (int, int, int, int) 
	protected static char jvxlValueAsCharacter (float, float, float, int, int) 
	public static char jvxlFractionAsCharacter (float) 
	protected static char jvxlFractionAsCharacter (float, int, int) 
	private static void jvxlAppendCharacter2 (float, float, float, int, int, java.lang.StringBuffer, java.lang.StringBuffer) 
	public static void jvxlUpdateSurfaceData (org.jmol.jvxl.data.JvxlData, float[], int, int, char) 
	public static void jvxlCreateColorData (org.jmol.jvxl.data.JvxlData, float[]) 
	public static java.lang.String jvxlEncodeTriangleData (int[][], int, int[]) 
	public static java.lang.String jvxlEncodeVertexData (org.jmol.jvxl.api.MeshDataServer, org.jmol.jvxl.data.JvxlData, int[], javax.vecmath.Point3f[], float[], int, short[], int, boolean) 
	private void getEncodedVertexData ()  throws java.lang.Exception 
	private void jvxlDecodeContourData (java.lang.String)  throws java.lang.Exception 
	public static void set3dContourVector (java.util.Vector, int[][], javax.vecmath.Point3f[]) 
	private java.lang.String getXmlData (java.lang.String, java.lang.String, boolean)  throws java.lang.Exception 
	public javax.vecmath.Point3f[] jvxlDecodeVertexData (java.lang.String, boolean) 
	int[][] jvxlDecodeTriangleData (java.lang.String, java.lang.String, boolean) 
	private static java.lang.String getXmlAttrib (java.lang.String, java.lang.String) 
	private static int setNext (java.lang.String, java.lang.String, int[], int) 
}

org/jmol/jvxl/readers/LimitedLineReader.class
<Unknown>
package org.jmol.jvxl.readers
 org.jmol.jvxl.readers.LimitedLineReader extends java.lang.Object {
	private char[] buf
	private int cchBuf
	private int ichCurrent
	private int iLine
	void <init> (java.io.BufferedReader, int) 
	java.lang.String info () 
	int iLine () 
	java.lang.String readNonCommentLine () 
}

org/jmol/jvxl/readers/MapFileReader.class
<Unknown>
package org.jmol.jvxl.readers
abstract org.jmol.jvxl.readers.MapFileReader extends org.jmol.jvxl.readers.VolumeFileReader {
	protected int mapc
	protected int mapr
	protected int maps
	protected int nx
	protected int ny
	protected int nz
	protected int mode
	protected int[] nxyzStart
	protected int na
	protected int nb
	protected int nc
	protected float a
	protected float b
	protected float c
	protected float alpha
	protected float beta
	protected float gamma
	protected javax.vecmath.Point3f origin
	protected javax.vecmath.Point3f adjustment
	protected javax.vecmath.Point3f[] vectors
	void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader) 
	protected abstract void readParameters ()  throws java.lang.Exception 
	protected int readVolumetricHeader () 
	protected void getVectorsAndOrigin () 
}

org/jmol/jvxl/readers/MrcBinaryReader.class
<Unknown>
package org.jmol.jvxl.readers
 org.jmol.jvxl.readers.MrcBinaryReader extends org.jmol.jvxl.readers.MapFileReader {
	protected String[] labels
	private static byte[] b8
	void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.lang.String, boolean) 
	protected void readParameters ()  throws java.lang.Exception 
	protected float nextVoxel ()  throws java.lang.Exception 
	protected void skipData (int)  throws java.lang.Exception 
	static void <clinit> () 
}

org/jmol/jvxl/readers/ObjReader.class
<Unknown>
package org.jmol.jvxl.readers
 org.jmol.jvxl.readers.ObjReader extends org.jmol.jvxl.readers.PolygonFileReader {
	private int nPolygons
	String pmeshError
	javax.vecmath.Point3f pt
	void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.lang.String, java.io.BufferedReader) 
	void getSurfaceData ()  throws java.lang.Exception 
	private boolean readPmesh () 
	private boolean readVertices ()  throws java.lang.Exception 
	private boolean readPolygons () 
}

org/jmol/jvxl/readers/Parameters.class
<Unknown>
package org.jmol.jvxl.readers
public org.jmol.jvxl.readers.Parameters extends java.lang.Object {
	public static final int STATE_UNINITIALIZED
	public static final int STATE_INITIALIZED
	public static final int STATE_DATA_READ
	public static final int STATE_DATA_COLORED
	int state
	boolean logMessages
	boolean logCompression
	boolean logCube
	boolean isSilent
	float assocCutoff
	static final int NO_ANISOTROPY
	static final int IS_SILENT
	public static final int IS_SOLVENTTYPE
	static final int HAS_MAXGRID
	static final int CAN_CONTOUR
	public int dataType
	int surfaceType
	static final int SURFACE_NONE
	static final int SURFACE_SPHERE
	static final int SURFACE_ELLIPSOID2
	static final int SURFACE_ELLIPSOID3
	static final int SURFACE_LOBE
	static final int SURFACE_LCAOCARTOON
	public static final int SURFACE_LONEPAIR
	public static final int SURFACE_RADICAL
	static final int SURFACE_FUNCTIONXY
	static final int SURFACE_FUNCTIONXYZ
	static final int SURFACE_SOLVENT
	static final int SURFACE_SASURFACE
	static final int SURFACE_MOLECULARORBITAL
	static final int SURFACE_ATOMICORBITAL
	static final int SURFACE_MEP
	static final int SURFACE_FILE
	static final int SURFACE_INFO
	static final int SURFACE_MOLECULAR
	static final int SURFACE_NOMAP
	static final int SURFACE_PROPERTY
	String calculationType
	boolean addHydrogens
	float solventRadius
	float solventExtendedAtomRadius
	float solventAtomRadiusFactor
	float solventAtomRadiusAbsolute
	float solventAtomRadiusOffset
	boolean propertySmoothing
	boolean useIonic
	float envelopeRadius
	float cavityRadius
	boolean isCavity
	Boolean pocket
	int minSet
	javax.vecmath.Point4f cappingPlane
	boolean doCapIsosurface
	float[] theProperty
	float solvent_ptsPerAngstrom
	int solvent_gridMax
	static final float ANGSTROMS_PER_BOHR
	static final int defaultEdgeFractionBase
	static final int defaultEdgeFractionRange
	static final int defaultColorFractionBase
	static final int defaultColorFractionRange
	static final float defaultMappedDataMin
	static final float defaultMappedDataMax
	static final float defaultCutoff
	static final float defaultOrbitalCutoff
	public static final float defaultQMOrbitalCutoff
	static final float defaultQMElectronDensityCutoff
	static final int defaultContourCount
	static final int nContourMax
	static final int defaultColorNegative
	static final int defaultColorPositive
	static final int defaultColorNegativeLCAO
	static final int defaultColorPositiveLCAO
	static final float defaultSolventRadius
	static final float defaultMepCutoff
	static final float defaultMepMin
	static final float defaultMepMax
	boolean colorBySign
	boolean colorByPhase
	boolean colorBySets
	int colorNeg
	int colorPos
	int colorPosLCAO
	int colorNegLCAO
	int colorPhase
	boolean iAddGridPoints
	boolean remappable
	int atomIndex
	boolean isAngstroms
	float scale
	float[] anisotropy
	boolean isAnisotropic
	javax.vecmath.Matrix3f eccentricityMatrix
	javax.vecmath.Matrix3f eccentricityMatrixInverse
	boolean isEccentric
	float eccentricityScale
	float eccentricityRatio
	float[] aniosU
	float[] anisoB
	String lcaoType
	public java.util.Vector functionXYinfo
	int psi_n
	int psi_l
	int psi_m
	float psi_Znuc
	float psi_ptsPerAngstrom
	public static final int MEP_MAX_GRID
	int mep_gridMax
	float mep_ptsPerAngstrom
	float mep_marginAngstroms
	int qmOrbitalType
	int qmOrbitalCount
	static final int QM_TYPE_UNKNOWN
	static final int QM_TYPE_GAUSSIAN
	static final int QM_TYPE_SLATER
	java.util.Hashtable moData
	java.util.Hashtable mo
	float[] moCoefficients
	public static final int MO_MAX_GRID
	int qm_gridMax
	float qm_ptsPerAngstrom
	float qm_marginAngstroms
	int qm_nAtoms
	int qm_moNumber
	javax.vecmath.Point3f center
	javax.vecmath.Point3f point
	float distance
	String script
	java.util.BitSet bsSelected
	java.util.BitSet bsIgnore
	java.util.BitSet bsSolvent
	boolean iUseBitSets
	String[] title
	boolean blockCubeData
	boolean readAllData
	int fileIndex
	String fileName
	int modelIndex
	boolean isXLowToHigh
	boolean insideOut
	float cutoff
	boolean isCutoffAbsolute
	boolean isPositiveOnly
	boolean rangeAll
	public boolean rangeDefined
	float valueMappedToRed
	float valueMappedToBlue
	float mappedDataMin
	float mappedDataMax
	boolean isColorReversed
	boolean isBicolorMap
	boolean isSquared
	javax.vecmath.Point4f thePlane
	boolean isContoured
	int nContours
	int thisContour
	boolean contourFromZero
	float resolution
	int downsampleFactor
	int maxSet
	public void <init> () 
	void initialize () 
	void setAnisotropy (javax.vecmath.Point3f) 
	void setEccentricity (javax.vecmath.Point4f) 
	void setPlane (javax.vecmath.Point4f) 
	void setSphere (float) 
	void setEllipsoid (javax.vecmath.Point4f) 
	public void setEllipsoid (float[]) 
	void setLobe (javax.vecmath.Point4f) 
	void setLp (javax.vecmath.Point4f) 
	void setRadical (javax.vecmath.Point4f) 
	void setLcao (java.lang.String, int) 
	void setRadius (boolean, float) 
	void setSolvent (java.lang.String, float) 
	void setFunctionXY (java.util.Vector) 
	void setFunctionXYZ (java.util.Vector) 
	boolean setAtomicOrbital (float[]) 
	void setMep (float[], boolean) 
	void setMO (int, boolean) 
	void setMapRanges (org.jmol.jvxl.readers.SurfaceReader) 
}

org/jmol/jvxl/readers/PltFormattedReader.class
<Unknown>
package org.jmol.jvxl.readers
 org.jmol.jvxl.readers.PltFormattedReader extends org.jmol.jvxl.readers.VolumeFileReader {
	void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader) 
	protected int readVolumetricHeader () 
	protected void readTitleLines ()  throws java.lang.Exception 
	protected void readAtomCountAndOrigin ()  throws java.lang.Exception 
	protected void readVoxelVectors ()  throws java.lang.Exception 
	private java.lang.String getLine ()  throws java.io.IOException 
}

org/jmol/jvxl/readers/PmeshReader.class
<Unknown>
package org.jmol.jvxl.readers
 org.jmol.jvxl.readers.PmeshReader extends org.jmol.jvxl.readers.PolygonFileReader {
	private int nPolygons
	private boolean isBinary
	static final String PMESH_BINARY_MAGIC_NUMBER
	String pmeshError
	private String[] tokens
	private int iToken
	void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.lang.String, java.io.BufferedReader) 
	private boolean checkBinary (java.lang.String) 
	void getSurfaceData ()  throws java.lang.Exception 
	private boolean readPmesh () 
	boolean readBinaryHeader () 
	private boolean readVertices ()  throws java.lang.Exception 
	private boolean readPolygons ()  throws java.lang.Exception 
	private java.lang.String nextToken ()  throws java.lang.Exception 
	private int getInt ()  throws java.lang.Exception 
	private float getFloat ()  throws java.lang.Exception 
}

org/jmol/jvxl/readers/PolygonFileReader.class
<Unknown>
package org.jmol.jvxl.readers
abstract org.jmol.jvxl.readers.PolygonFileReader extends org.jmol.jvxl.readers.SurfaceFileReader {
	protected int nVertices
	protected int nTriangles
	void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader) 
	void discardTempData (boolean) 
	boolean readVolumeParameters () 
	boolean readVolumeData (boolean) 
	protected void readSurfaceData (boolean)  throws java.lang.Exception 
	abstract void getSurfaceData ()  throws java.lang.Exception 
}

org/jmol/jvxl/readers/SurfaceFileReader.class
<Unknown>
package org.jmol.jvxl.readers
abstract org.jmol.jvxl.readers.SurfaceFileReader extends org.jmol.jvxl.readers.SurfaceReader {
	protected java.io.BufferedReader br
	protected org.jmol.util.BinaryDocument binarydoc
	String line
	int[] next
	void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader) 
	static java.lang.String determineFileType (java.io.BufferedReader) 
	void discardTempData (boolean) 
	java.lang.String[] getTokens () 
	float parseFloat () 
	float parseFloat (java.lang.String) 
	int parseInt () 
	int parseInt (java.lang.String) 
	int parseIntNext (java.lang.String) 
	protected void skipTo (java.lang.String, java.lang.String)  throws java.lang.Exception 
}

org/jmol/jvxl/readers/SurfaceGenerator.class
<Unknown>
package org.jmol.jvxl.readers
public org.jmol.jvxl.readers.SurfaceGenerator extends java.lang.Object {
	private org.jmol.util.ColorEncoder colorEncoder
	private org.jmol.jvxl.data.JvxlData jvxlData
	private org.jmol.jvxl.data.MeshData meshData
	private org.jmol.jvxl.readers.Parameters params
	private org.jmol.jvxl.data.VolumeData volumeData
	private org.jmol.jvxl.api.MeshDataServer meshDataServer
	private org.jmol.atomdata.AtomDataServer atomDataServer
	private org.jmol.jvxl.calc.MarchingSquares marchingSquares
	private String version
	private String fileType
	org.jmol.jvxl.readers.SurfaceReader surfaceReader
	int colorPtr
	private boolean rangeDefined
	final javax.vecmath.Vector3f vAC
	final javax.vecmath.Vector3f vAB
	final javax.vecmath.Vector3f vNorm
	final javax.vecmath.Point3f ptRef
	public void setVersion (java.lang.String) 
	public void <init> () 
	public void <init> (org.jmol.atomdata.AtomDataServer, org.jmol.jvxl.api.MeshDataServer, org.jmol.util.ColorEncoder, org.jmol.jvxl.data.MeshData, org.jmol.jvxl.data.JvxlData) 
	private void setup (org.jmol.atomdata.AtomDataServer, org.jmol.jvxl.api.MeshDataServer, org.jmol.util.ColorEncoder, org.jmol.jvxl.data.MeshData, org.jmol.jvxl.data.JvxlData) 
	public boolean isStateDataRead () 
	public int getDataType () 
	org.jmol.jvxl.api.MeshDataServer getMeshDataServer () 
	org.jmol.atomdata.AtomDataServer getAtomDataServer () 
	org.jmol.util.ColorEncoder getColorEncoder () 
	public void setJvxlData (org.jmol.jvxl.data.JvxlData) 
	public org.jmol.jvxl.data.JvxlData getJvxlData () 
	org.jmol.jvxl.data.MeshData getMeshData () 
	void setMarchingSquares (org.jmol.jvxl.calc.MarchingSquares) 
	org.jmol.jvxl.calc.MarchingSquares getMarchingSquares () 
	public org.jmol.jvxl.readers.Parameters getParams () 
	public java.lang.String getScript () 
	public java.lang.String[] getTitle () 
	public java.util.BitSet getBsSelected () 
	public java.util.BitSet getBsIgnore () 
	public java.util.Vector getFunctionXYinfo () 
	org.jmol.jvxl.data.VolumeData getVolumeData () 
	public javax.vecmath.Point4f getPlane () 
	public int getColor (int) 
	public void setModelIndex (int) 
	public boolean getIUseBitSets () 
	public boolean getIAddGridPoints () 
	public boolean getIsPositiveOnly () 
	public boolean isInsideOut () 
	public float getCutoff () 
	public java.util.Hashtable getMoData () 
	public boolean isCubeData () 
	public boolean setParameter (java.lang.String, java.lang.Object) 
	public boolean setParameter (java.lang.String, java.lang.Object, java.util.BitSet) 
	private void getSurfaceSets () 
	private void processState () 
	private boolean setReader () 
	private void generateSurface () 
	private void mapSurface (java.lang.Object) 
	void colorIsosurface () 
	public java.lang.Object getProperty (java.lang.String, int) 
	private org.jmol.jvxl.readers.SurfaceReader setFileData (java.lang.Object) 
	void initializeIsosurface () 
	public void initState () 
	public java.lang.String setLcao () 
	private void getFunctionZfromXY () 
	private float distanceVerticalToPlane (float, float, javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f) 
	private static float findNearestThreePoints (float, float, float[][], int[]) 
}

org/jmol/jvxl/readers/SurfaceReader.class
<Unknown>
package org.jmol.jvxl.readers
public abstract org.jmol.jvxl.readers.SurfaceReader extends java.lang.Object implements org.jmol.jvxl.api.VertexDataServer  {
	protected org.jmol.jvxl.readers.SurfaceGenerator sg
	protected org.jmol.jvxl.api.MeshDataServer meshDataServer
	protected org.jmol.util.ColorEncoder colorEncoder
	protected org.jmol.jvxl.readers.Parameters params
	protected org.jmol.jvxl.data.MeshData meshData
	protected org.jmol.jvxl.data.JvxlData jvxlData
	protected org.jmol.jvxl.data.VolumeData volumeData
	private String edgeData
	protected boolean isProgressive
	protected boolean isXLowToHigh
	private float assocCutoff
	boolean vertexDataOnly
	boolean hasColorData
	static final float ANGSTROMS_PER_BOHR
	static final float defaultMappedDataMin
	static final float defaultMappedDataMax
	static final float defaultCutoff
	private int edgeCount
	protected javax.vecmath.Point3f volumetricOrigin
	protected javax.vecmath.Vector3f[] volumetricVectors
	protected int[] voxelCounts
	protected float[][][] voxelData
	protected long nBytes
	protected int nDataPoints
	protected int nPointsX
	protected int nPointsY
	protected int nPointsZ
	protected boolean isJvxl
	protected boolean isApbsDx
	protected int edgeFractionBase
	protected int edgeFractionRange
	protected int colorFractionBase
	protected int colorFractionRange
	protected StringBuffer jvxlFileHeaderBuffer
	protected StringBuffer fractionData
	protected String jvxlEdgeDataRead
	protected String jvxlColorDataRead
	protected java.util.BitSet jvxlVoxelBitSet
	protected java.util.Vector[] vContours
	protected boolean jvxlDataIsColorMapped
	protected boolean jvxlDataIsPrecisionColor
	protected boolean jvxlDataIs2dContour
	protected float jvxlCutoff
	protected int jvxlNSurfaceInts
	protected char cJvxlEdgeNaN
	protected int contourVertexCount
	protected org.jmol.jvxl.calc.MarchingSquares marchingSquares
	private org.jmol.jvxl.calc.MarchingCubes marchingCubes
	protected final javax.vecmath.Point3f ptTemp
	private static final String[] colorPhases
	void <init> (org.jmol.jvxl.readers.SurfaceGenerator) 
	void setVolumeData (org.jmol.jvxl.data.VolumeData) 
	abstract boolean readVolumeParameters () 
	abstract boolean readVolumeData (boolean) 
	void jvxlUpdateInfo () 
	boolean createIsosurface (boolean) 
	void resetIsosurface () 
	void discardTempData (boolean) 
	protected void initializeVolumetricData () 
	protected abstract void readSurfaceData (boolean)  throws java.lang.Exception 
	protected boolean gotoAndReadVoxelData (boolean) 
	protected void gotoData (int, int)  throws java.lang.Exception 
	protected java.lang.String readColorData () 
	public float getValue (int, int, int) 
	private void generateSurfaceData () 
	public int getSurfacePointIndexAndFraction (float, boolean, int, int, int, javax.vecmath.Point3i, int, int, float, float, javax.vecmath.Point3f, javax.vecmath.Vector3f, boolean, float[]) 
	protected float getSurfacePointAndFraction (float, boolean, float, float, javax.vecmath.Point3f, javax.vecmath.Vector3f, float[], javax.vecmath.Point3f) 
	public int addVertexCopy (javax.vecmath.Point3f, float, int) 
	public void addTriangleCheck (int, int, int, int, boolean, int) 
	void colorIsosurface () 
	void applyColorScale () 
	private void colorData () 
	static int getColorPhaseIndex (java.lang.String) 
	private float getPhase (javax.vecmath.Point3f) 
	float getMinMappedValue () 
	float getMaxMappedValue () 
	protected short getColorIndexFromPalette (float) 
	protected int getArgbFromPalette (float) 
	void updateTriangles () 
	void updateSurfaceData () 
	public void selectPocket (boolean) 
	void excludeMinimumSet () 
	void excludeMaximumSet () 
	static void <clinit> () 
}

org/jmol/jvxl/readers/VolumeDataReader.class
<Unknown>
package org.jmol.jvxl.readers
 org.jmol.jvxl.readers.VolumeDataReader extends org.jmol.jvxl.readers.SurfaceReader {
	protected int dataType
	protected boolean precalculateVoxelData
	protected boolean allowMapData
	protected javax.vecmath.Point3f center
	protected javax.vecmath.Point3f point
	protected float[] anisotropy
	protected boolean isAnisotropic
	protected javax.vecmath.Matrix3f eccentricityMatrix
	protected javax.vecmath.Matrix3f eccentricityMatrixInverse
	protected boolean isEccentric
	protected float eccentricityScale
	protected float eccentricityRatio
	void <init> (org.jmol.jvxl.readers.SurfaceGenerator) 
	void setup () 
	boolean readVolumeParameters () 
	boolean readVolumeData (boolean) 
	protected void readVoxelDataIndividually (boolean)  throws java.lang.Exception 
	protected int setVoxelRange (int, float, float, float, int) 
	protected void readSurfaceData (boolean)  throws java.lang.Exception 
	protected void generateCube () 
}

org/jmol/jvxl/readers/VolumeFileReader.class
<Unknown>
package org.jmol.jvxl.readers
abstract org.jmol.jvxl.readers.VolumeFileReader extends org.jmol.jvxl.readers.SurfaceFileReader {
	protected boolean endOfData
	protected boolean negativeAtomCount
	protected int atomCount
	private int nSurfaces
	protected boolean isAngstroms
	protected boolean canDownsample
	protected int[] downsampleRemainders
	void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader) 
	boolean readVolumeParameters () 
	boolean readVolumeData (boolean) 
	protected int readVolumetricHeader () 
	protected void readTitleLines ()  throws java.lang.Exception 
	protected java.lang.String skipComments (boolean)  throws java.lang.Exception 
	protected void readAtomCountAndOrigin ()  throws java.lang.Exception 
	protected void readVoxelVector (int)  throws java.lang.Exception 
	protected int readExtraLine ()  throws java.lang.Exception 
	protected void readSurfaceData (boolean)  throws java.lang.Exception 
	private void skipVoxels (int)  throws java.lang.Exception 
	protected java.util.BitSet getVoxelBitSet (int)  throws java.lang.Exception 
	protected float getNextVoxelValue ()  throws java.lang.Exception 
	protected float nextVoxel ()  throws java.lang.Exception 
	protected void gotoData (int, int)  throws java.lang.Exception 
	protected void skipData (int)  throws java.lang.Exception 
	private int countData (java.lang.String) 
}

org/jmol/jvxl/readers/XplorReader.class
<Unknown>
package org.jmol.jvxl.readers
 org.jmol.jvxl.readers.XplorReader extends org.jmol.jvxl.readers.MapFileReader {
	private int nBlock
	private int linePt
	private int nRead
	void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader) 
	protected void readParameters ()  throws java.lang.Exception 
	private java.lang.String getLine ()  throws java.io.IOException 
	protected float nextVoxel ()  throws java.lang.Exception 
}

org/jmol/shapesurface/Isosurface.class
<Unknown>
package org.jmol.shapesurface
public org.jmol.shapesurface.Isosurface extends org.jmol.shape.MeshCollection implements org.jmol.jvxl.api.MeshDataServer  {
	private org.jmol.shapesurface.IsosurfaceMesh[] isomeshes
	private org.jmol.shapesurface.IsosurfaceMesh thisMesh
	private int lighting
	private boolean iHaveBitSets
	private boolean explicitContours
	private int atomIndex
	private int moNumber
	private short defaultColix
	private javax.vecmath.Point3f center
	private boolean isPhaseColored
	private boolean isColorExplicit
	protected org.jmol.jvxl.readers.SurfaceGenerator sg
	private org.jmol.jvxl.data.JvxlData jvxlData
	private org.jmol.util.ColorEncoder colorEncoder
	private int indexColorPositive
	private int indexColorNegative
	private int nLCAO
	private javax.vecmath.Point4f lcaoDir
	private boolean associateNormals
	private static final int MAX_OBJECT_CLICK_DISTANCE_SQUARED
	private final javax.vecmath.Point3i ptXY
	public void <init> () 
	public void allocMesh (java.lang.String) 
	public void initShape () 
	private void newSg () 
	protected void clearSg () 
	public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet) 
	private void setPropertySuper (java.lang.String, java.lang.Object, java.util.BitSet) 
	public java.lang.Object getProperty (java.lang.String, int) 
	protected void getColorState (java.lang.StringBuffer, org.jmol.shape.Mesh) 
	private boolean getScriptBitSets (java.lang.String, java.util.BitSet[]) 
	private void initializeIsosurface () 
	private void initState () 
	private void discardTempData (boolean) 
	private short getDefaultColix () 
	private void drawLcaoCartoon (javax.vecmath.Vector3f, javax.vecmath.Vector3f, javax.vecmath.Vector3f, int) 
	private void createLcaoLobe (javax.vecmath.Vector3f, float, int) 
	public void invalidateTriangles () 
	public void fillMeshData (org.jmol.jvxl.data.MeshData, int) 
	public void notifySurfaceGenerationCompleted () 
	public void notifySurfaceMappingCompleted () 
	public javax.vecmath.Point3f[] calculateGeodesicSurface (java.util.BitSet, float) 
	public int getSurfacePointIndexAndFraction (float, boolean, int, int, int, javax.vecmath.Point3i, int, int, float, float, javax.vecmath.Point3f, javax.vecmath.Vector3f, boolean, float[]) 
	public int addVertexCopy (javax.vecmath.Point3f, float, int) 
	public void addTriangleCheck (int, int, int, int, boolean, int) 
	private void setModelIndex () 
	protected void setScriptInfo () 
	private void setJvxlInfo () 
	public java.util.Vector getShapeDetail () 
	protected void remapColors () 
	private java.lang.String getUserColorScheme (java.lang.String) 
	public float getValue (int, int, int) 
	public boolean checkObjectHovered (int, int, java.util.BitSet) 
	public org.jmol.util.Point3fi checkObjectClicked (int, int, int, java.util.BitSet) 
	private void navigate (int) 
	private void setHeading (javax.vecmath.Point3f, javax.vecmath.Vector3f, int) 
	private boolean getClosestNormal (org.jmol.shapesurface.IsosurfaceMesh, javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Vector3f) 
	private void getClosestPoint (org.jmol.shapesurface.IsosurfaceMesh, int, javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Vector3f) 
	private java.lang.String findValue (int, int, boolean, java.util.BitSet) 
	public int getColixArgb (short) 
}

org/jmol/shapesurface/IsosurfaceMesh.class
<Unknown>
package org.jmol.shapesurface
public org.jmol.shapesurface.IsosurfaceMesh extends org.jmol.shape.Mesh {
	org.jmol.jvxl.data.JvxlData jvxlData
	int vertexIncrement
	int firstRealVertex
	int dataType
	boolean hasGridPoints
	Object calculatedArea
	Object calculatedVolume
	public boolean isSolvent
	public float[] vertexValues
	public short[] vertexColixes
	java.util.Hashtable assocGridPointMap
	java.util.Hashtable assocGridPointNormals
	public short[] polygonColixes
	private int lastColor
	private short lastColix
	private int iA
	private int iB
	private int iC
	java.util.BitSet[] surfaceSet
	int[] vertexSets
	int nSets
	int thisSet
	javax.vecmath.Point3f[] centers
	public static final int CONTOUR_NPOLYGONS
	public static final int CONTOUR_BITSET
	public static final int CONTOUR_VALUE
	public static final int CONTOUR_COLOR
	public static final int CONTOUR_FDATA
	public static final int CONTOUR_POINTS
	void <init> (java.lang.String, org.jmol.g3d.Graphics3D, short, int) 
	void clear (java.lang.String, boolean) 
	void allocVertexColixes () 
	int addVertexCopy (javax.vecmath.Point3f, float, int, boolean) 
	int addVertexCopy (javax.vecmath.Point3f, float) 
	public void setTranslucent (boolean, float) 
	void addTriangleCheck (int, int, int, int, int) 
	void invalidateTriangles () 
	private boolean setABC (int) 
	java.lang.Object calculateArea () 
	java.lang.Object calculateVolume () 
	public void sumVertexNormals (javax.vecmath.Vector3f[]) 
	javax.vecmath.Point3f[] getCenters () 
	javax.vecmath.Point4f getFacePlane (int, javax.vecmath.Vector3f) 
	java.util.Vector[] getContours () 
	public static void setContourVector (java.util.Vector, int, java.util.BitSet, float, int, java.lang.StringBuffer) 
	private void get3dContour (java.util.Vector, float, int) 
	private float checkPt (int, int, float) 
	public static javax.vecmath.Point3f getContourPoint (javax.vecmath.Point3f[], int, int, float) 
	private void dumpData () 
}

org/jmol/shapesurface/IsosurfaceRenderer.class
<Unknown>
package org.jmol.shapesurface
public org.jmol.shapesurface.IsosurfaceRenderer extends org.jmol.shape.MeshRenderer {
	private boolean iShowNormals
	protected boolean iHideBackground
	protected boolean isBicolorMap
	protected short backgroundColix
	protected int nError
	protected float[] vertexValues
	protected org.jmol.shapesurface.IsosurfaceMesh imesh
	private final javax.vecmath.Point3f ptTemp
	private final javax.vecmath.Point3i ptTempi
	public void <init> () 
	protected void render () 
	protected void transform () 
	protected void render2 (boolean) 
	private void renderLonePair (boolean) 
	private void renderContourLines () 
	protected void renderPoints () 
	protected void renderTriangles (boolean, boolean, boolean) 
	private void renderNormals () 
}

org/jmol/shapesurface/LcaoCartoon.class
<Unknown>
package org.jmol.shapesurface
public org.jmol.shapesurface.LcaoCartoon extends org.jmol.shapesurface.Isosurface {
	private String thisType
	private int myColorPt
	private String lcaoID
	private java.util.BitSet thisSet
	private boolean isMolecular
	private javax.vecmath.Vector3f rotationAxis
	private Float lcaoScale
	private boolean isTranslucent
	private float translucentLevel
	private Integer lcaoColorPos
	private Integer lcaoColorNeg
	boolean isLonePair
	boolean isRadical
	public void <init> () 
	public void initShape () 
	public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet) 
	private void setLcaoOn (boolean) 
	private void setLcaoOn (int, boolean) 
	private void deleteLcaoCartoon () 
	private void deleteLcaoCartoon (int) 
	private void createLcaoCartoon () 
	private void createLcaoCartoon (int) 
	private java.lang.String getID (java.lang.String, int) 
	public java.lang.String getShapeState () 
}

org/jmol/shapesurface/LcaoCartoonRenderer.class
<Unknown>
package org.jmol.shapesurface
public org.jmol.shapesurface.LcaoCartoonRenderer extends org.jmol.shapesurface.IsosurfaceRenderer {
	public void <init> () 
}

org/jmol/shapesurface/MolecularOrbital.class
<Unknown>
package org.jmol.shapesurface
public org.jmol.shapesurface.MolecularOrbital extends org.jmol.shapesurface.Isosurface {
	private String moTranslucency
	private Float moTranslucentLevel
	private javax.vecmath.Point4f moPlane
	private Float moCutoff
	private Float moResolution
	private Float moScale
	private Integer moColorPos
	private Integer moColorNeg
	private boolean moIsPositiveOnly
	private int moFill
	private int moMesh
	private int moDots
	private int moFrontOnly
	private String moTitleFormat
	private boolean moDebug
	private int myColorPt
	private String strID
	private int moNumber
	private java.util.Hashtable htModels
	private java.util.Hashtable thisModel
	public void <init> () 
	public void initShape () 
	public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet) 
	private java.lang.String getId (int) 
	public java.lang.Object getProperty (java.lang.String, int) 
	protected void clearSg () 
	private boolean getSettings (java.lang.String) 
	private void setOrbital (int) 
	public java.lang.String getShapeState () 
	private java.lang.String getMoState (int) 
}

org/jmol/shapesurface/MolecularOrbitalRenderer.class
<Unknown>
package org.jmol.shapesurface
public org.jmol.shapesurface.MolecularOrbitalRenderer extends org.jmol.shapesurface.IsosurfaceRenderer {
	private java.text.NumberFormat nf
	public void <init> () 
	protected void render () 
	private void renderInfo () 
}

org/jmol/shapesurface/Pmesh.class
<Unknown>
package org.jmol.shapesurface
public org.jmol.shapesurface.Pmesh extends org.jmol.shapesurface.Isosurface {
	public void <init> () 
	public void initShape () 
}

org/jmol/shapesurface/PmeshRenderer.class
<Unknown>
package org.jmol.shapesurface
public org.jmol.shapesurface.PmeshRenderer extends org.jmol.shapesurface.IsosurfaceRenderer {
	public void <init> () 
}