org.jmol.jvxl.readers
public class JvxlReader extends VolumeFileReader
| Field Summary | |
|---|---|
| int | colorDataCount |
| int | edgeDataCount |
| int | fractionPtr |
| static String | JVXL_VERSION |
| int | nThisValue |
| String | strFractionTemp |
| int | surfaceDataCount |
| boolean | thisInside |
| Constructor Summary | |
|---|---|
| JvxlReader(SurfaceGenerator sg, BufferedReader br) | |
| Method Summary | |
|---|---|
| int | countData(String str) |
| protected float | getNextVoxelValue(StringBuffer sb) |
| protected void | gotoAndReadVoxelData(boolean isMapData) |
| protected void | gotoData(int n, int nPoints) |
| protected void | initializeVoxelData() |
| static void | jvxlAddDummyAtomList(VolumeData v, StringBuffer bs) |
| protected static boolean | jvxlCheckAtomLine(boolean isXLowToHigh, boolean isAngstroms, String strAtomCount, String atomLine, StringBuffer bs)
checks an atom line for "ANGSTROMS", possibly overriding the data's
natural units, BOHR (similar to Gaussian CUBE files).
|
| static String | jvxlCompressString(String data) |
| static void | jvxlCreateColorData(JvxlData jvxlData, float[] vertexValues) |
| protected static void | jvxlCreateHeader(VolumeData v, int nAtoms, Point3f[] atomXyz, int[] atomNo, StringBuffer sb) |
| protected static void | jvxlCreateHeaderWithoutTitleOrAtoms(VolumeData v, StringBuffer bs) |
| static int | jvxlCreateSurfaceData(JvxlData jvxlData, float[][][] voxelData, float cutoff, boolean isCutoffAbsolute, int nX, int nY, int nZ) |
| protected static String | jvxlExtraLine(JvxlData jvxlData, int n) |
| protected static char | jvxlFractionAsCharacter(float fraction, int base, int range) |
| protected static float | jvxlFractionFromCharacter(int ich, int base, int range, float fracOffset) |
| protected static float | jvxlFractionFromCharacter2(int ich1, int ich2, int base, int range) |
| static String | jvxlGetDefinitionLine(JvxlData jvxlData, boolean isInfo) |
| static String | jvxlGetFile(JvxlData jvxlData, String[] title, String msg, boolean includeHeader, int nSurfaces, String state, String comment) |
| float | jvxlGetNextFraction(int base, int range, float fracOffset) |
| protected static void | jvxlReadAtoms(BufferedReader br, StringBuffer bs, int atomCount, VolumeData v) |
| String | jvxlReadData(String type, int nPoints) |
| void | jvxlReadDefinitionLine(boolean showMsg) |
| void | jvxlSkipData(int nPoints, boolean doSkipColorData) |
| void | jvxlSkipDataBlock(int nPoints, boolean isInt) |
| static String | jvxlUncompressString(String data) |
| protected static void | jvxlUpdateInfo(JvxlData jvxlData, String[] title, int nBytes) |
| static void | jvxlUpdateInfoLines(JvxlData jvxlData) |
| static void | jvxlUpdateSurfaceData(JvxlData jvxlData, float[] vertexValues, int vertexCount, int vertexIncrement, char isNaN) |
| protected static char | jvxlValueAsCharacter(float value, float min, float max, int base, int range) |
| protected static char | jvxlValueAsCharacter2(float value, float min, float max, int base, int range, char[] remainder) |
| protected static float | jvxlValueFromCharacter2(int ich, int ich2, float min, float max, int base, int range) |
| protected void | readAtomCountAndOrigin() |
| protected String | readColorData() |
| protected int | readExtraLine() |
| protected float | readSurfacePoint(float cutoff, boolean isCutoffAbsolute, float valueA, float valueB, Point3f pointA, Vector3f edgeVector, float[] fReturn, Point3f ptReturn) |
| protected void | readTitleLines() |
| protected void | readVolumeData(boolean isMapData) |
| protected void | readVoxelData(boolean isMapDataIgnored) |
| protected static void | setSurfaceInfo(JvxlData jvxlData, Point4f thePlane, int nSurfaceInts, StringBuffer surfaceData) |
Parameters: isXLowToHigh isAngstroms strAtomCount atomLine bs
Returns: isAngstroms