org.jmol.jvxl.readers
public class JvxlReader extends VolumeFileReader
Field Summary | |
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int | colorDataCount |
int | edgeDataCount |
int | fractionPtr |
static String | JVXL_VERSION |
int | nThisValue |
String | strFractionTemp |
int | surfaceDataCount |
boolean | thisInside |
Constructor Summary | |
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JvxlReader(SurfaceGenerator sg, BufferedReader br) |
Method Summary | |
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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).
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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