org.jmol.jvxl.readers
Class JvxlReader
java.lang.Object
org.jmol.jvxl.readers.VoxelReader
org.jmol.jvxl.readers.VolumeFileReader
org.jmol.jvxl.readers.JvxlReader
- All Implemented Interfaces:
- VertexDataServer
public class JvxlReader
- extends VolumeFileReader
Fields inherited from class org.jmol.jvxl.readers.VoxelReader |
ANGSTROMS_PER_BOHR, cJvxlEdgeNaN, colorEncoder, colorFractionBase, colorFractionRange, contourVertexCount, defaultColorFractionBase, defaultColorFractionRange, defaultCutoff, defaultEdgeFractionBase, defaultEdgeFractionRange, defaultMappedDataMax, defaultMappedDataMin, edgeFractionBase, edgeFractionRange, fractionData, fReturn, isApbsDx, isJvxl, isProgressive, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, marchingSquares, meshData, meshDataServer, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, sg, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData |
Method Summary |
private int |
countData(java.lang.String str)
|
protected float |
getNextVoxelValue(java.lang.StringBuffer sb)
|
protected void |
gotoAndReadVoxelData(boolean isMapData)
|
protected void |
gotoData(int n,
int nPoints)
|
protected void |
initializeVoxelData()
|
private static void |
jvxlAddDummyAtomList(VolumeData v,
java.lang.StringBuffer bs)
|
protected static boolean |
jvxlCheckAtomLine(boolean isXLowToHigh,
boolean isAngstroms,
java.lang.String strAtomCount,
java.lang.String atomLine,
java.lang.StringBuffer bs)
checks an atom line for "ANGSTROMS", possibly overriding the data's
natural units, BOHR (similar to Gaussian CUBE files). |
(package private) static java.lang.String |
jvxlCompressString(java.lang.String data)
|
static void |
jvxlCreateColorData(JvxlData jvxlData,
float[] vertexValues)
|
protected static void |
jvxlCreateHeader(VolumeData v,
int nAtoms,
javax.vecmath.Point3f[] atomXyz,
int[] atomNo,
java.lang.StringBuffer sb)
|
protected static void |
jvxlCreateHeaderWithoutTitleOrAtoms(VolumeData v,
java.lang.StringBuffer bs)
|
static int |
jvxlCreateSurfaceData(JvxlData jvxlData,
float[][][] voxelData,
float cutoff,
boolean isCutoffAbsolute,
int nX,
int nY,
int nZ)
|
protected static java.lang.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 java.lang.String |
jvxlGetDefinitionLine(JvxlData jvxlData,
boolean isInfo)
|
static java.lang.String |
jvxlGetFile(JvxlData jvxlData,
java.lang.String[] title,
java.lang.String msg,
boolean includeHeader,
int nSurfaces,
java.lang.String state,
java.lang.String comment)
|
private float |
jvxlGetNextFraction(int base,
int range,
float fracOffset)
|
protected static void |
jvxlReadAtoms(java.io.BufferedReader br,
java.lang.StringBuffer bs,
int atomCount,
VolumeData v)
|
private java.lang.String |
jvxlReadData(java.lang.String type,
int nPoints)
|
private void |
jvxlReadDefinitionLine(boolean showMsg)
|
private void |
jvxlSkipData(int nPoints,
boolean doSkipColorData)
|
private void |
jvxlSkipDataBlock(int nPoints,
boolean isInt)
|
private static java.lang.String |
jvxlUncompressString(java.lang.String data)
|
protected static void |
jvxlUpdateInfo(JvxlData jvxlData,
java.lang.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 java.lang.String |
readColorData()
|
protected int |
readExtraLine()
|
protected float |
readSurfacePoint(float cutoff,
boolean isCutoffAbsolute,
float valueA,
float valueB,
javax.vecmath.Point3f pointA,
javax.vecmath.Vector3f edgeVector,
float[] fReturn,
javax.vecmath.Point3f ptReturn)
|
protected void |
readTitleLines()
|
protected void |
readVolumeData(boolean isMapData)
|
protected void |
readVoxelData(boolean isMapDataIgnored)
|
protected static void |
setSurfaceInfo(JvxlData jvxlData,
javax.vecmath.Point4f thePlane,
int nSurfaceInts,
java.lang.StringBuffer surfaceData)
|
Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader |
determineFileType, discardTempData, getTokens, nextVoxel, parseFloat, parseFloat, parseFloatNext, parseInt, parseInt, parseInt, parseIntNext, readVolumeParameters, readVolumetricHeader, readVoxelVector, skipComments |
Methods inherited from class org.jmol.jvxl.readers.VoxelReader |
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, excludeMaximumSet, excludeMinimumSet, getCalcPoint, getColorIndexFromPalette, getColorPhaseIndex, getMaxMappedValue, getMinMappedValue, getSurfacePointIndex, initializeVolumetricData, isInside, jvxlUpdateInfo, resetIsosurface, selectPocket, setVolumeData, updateSurfaceData, updateTriangles |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
JVXL_VERSION
private static final java.lang.String JVXL_VERSION
- See Also:
- Constant Field Values
surfaceDataCount
private int surfaceDataCount
edgeDataCount
private int edgeDataCount
colorDataCount
private int colorDataCount
nThisValue
private int nThisValue
thisInside
private boolean thisInside
fractionPtr
private int fractionPtr
strFractionTemp
private java.lang.String strFractionTemp
JvxlReader
JvxlReader(SurfaceGenerator sg,
java.io.BufferedReader br)
jvxlUpdateInfo
protected static void jvxlUpdateInfo(JvxlData jvxlData,
java.lang.String[] title,
int nBytes)
jvxlUpdateInfoLines
public static void jvxlUpdateInfoLines(JvxlData jvxlData)
readVolumeData
protected void readVolumeData(boolean isMapData)
- Overrides:
readVolumeData
in class VolumeFileReader
gotoAndReadVoxelData
protected void gotoAndReadVoxelData(boolean isMapData)
- Overrides:
gotoAndReadVoxelData
in class VoxelReader
initializeVoxelData
protected void initializeVoxelData()
readVoxelData
protected void readVoxelData(boolean isMapDataIgnored)
throws java.lang.Exception
- Overrides:
readVoxelData
in class VolumeFileReader
- Throws:
java.lang.Exception
readTitleLines
protected void readTitleLines()
throws java.lang.Exception
- Overrides:
readTitleLines
in class VolumeFileReader
- Throws:
java.lang.Exception
jvxlCheckAtomLine
protected static boolean jvxlCheckAtomLine(boolean isXLowToHigh,
boolean isAngstroms,
java.lang.String strAtomCount,
java.lang.String atomLine,
java.lang.StringBuffer bs)
- checks an atom line for "ANGSTROMS", possibly overriding the data's
natural units, BOHR (similar to Gaussian CUBE files).
- Parameters:
isXLowToHigh
- isAngstroms
- strAtomCount
- atomLine
- bs
-
- Returns:
- isAngstroms
readAtomCountAndOrigin
protected void readAtomCountAndOrigin()
throws java.lang.Exception
- Overrides:
readAtomCountAndOrigin
in class VolumeFileReader
- Throws:
java.lang.Exception
jvxlReadAtoms
protected static void jvxlReadAtoms(java.io.BufferedReader br,
java.lang.StringBuffer bs,
int atomCount,
VolumeData v)
throws java.lang.Exception
- Throws:
java.lang.Exception
readExtraLine
protected int readExtraLine()
throws java.lang.Exception
- Overrides:
readExtraLine
in class VolumeFileReader
- Throws:
java.lang.Exception
jvxlReadDefinitionLine
private void jvxlReadDefinitionLine(boolean showMsg)
throws java.lang.Exception
- Throws:
java.lang.Exception
jvxlReadData
private java.lang.String jvxlReadData(java.lang.String type,
int nPoints)
jvxlCompressString
static java.lang.String jvxlCompressString(java.lang.String data)
jvxlUncompressString
private static java.lang.String jvxlUncompressString(java.lang.String data)
getNextVoxelValue
protected float getNextVoxelValue(java.lang.StringBuffer sb)
throws java.lang.Exception
- Overrides:
getNextVoxelValue
in class VolumeFileReader
- Throws:
java.lang.Exception
setSurfaceInfo
protected static void setSurfaceInfo(JvxlData jvxlData,
javax.vecmath.Point4f thePlane,
int nSurfaceInts,
java.lang.StringBuffer surfaceData)
readSurfacePoint
protected float readSurfacePoint(float cutoff,
boolean isCutoffAbsolute,
float valueA,
float valueB,
javax.vecmath.Point3f pointA,
javax.vecmath.Vector3f edgeVector,
float[] fReturn,
javax.vecmath.Point3f ptReturn)
- Overrides:
readSurfacePoint
in class VoxelReader
jvxlGetNextFraction
private float jvxlGetNextFraction(int base,
int range,
float fracOffset)
readColorData
protected java.lang.String readColorData()
- Overrides:
readColorData
in class VoxelReader
gotoData
protected void gotoData(int n,
int nPoints)
throws java.lang.Exception
- Overrides:
gotoData
in class VolumeFileReader
- Throws:
java.lang.Exception
jvxlSkipData
private void jvxlSkipData(int nPoints,
boolean doSkipColorData)
throws java.lang.Exception
- Throws:
java.lang.Exception
jvxlSkipDataBlock
private void jvxlSkipDataBlock(int nPoints,
boolean isInt)
throws java.lang.Exception
- Throws:
java.lang.Exception
countData
private int countData(java.lang.String str)
jvxlCreateHeaderWithoutTitleOrAtoms
protected static void jvxlCreateHeaderWithoutTitleOrAtoms(VolumeData v,
java.lang.StringBuffer bs)
jvxlCreateHeader
protected static void jvxlCreateHeader(VolumeData v,
int nAtoms,
javax.vecmath.Point3f[] atomXyz,
int[] atomNo,
java.lang.StringBuffer sb)
jvxlAddDummyAtomList
private static void jvxlAddDummyAtomList(VolumeData v,
java.lang.StringBuffer bs)
jvxlCreateSurfaceData
public static int jvxlCreateSurfaceData(JvxlData jvxlData,
float[][][] voxelData,
float cutoff,
boolean isCutoffAbsolute,
int nX,
int nY,
int nZ)
jvxlGetDefinitionLine
public static java.lang.String jvxlGetDefinitionLine(JvxlData jvxlData,
boolean isInfo)
jvxlExtraLine
protected static java.lang.String jvxlExtraLine(JvxlData jvxlData,
int n)
jvxlGetFile
public static java.lang.String jvxlGetFile(JvxlData jvxlData,
java.lang.String[] title,
java.lang.String msg,
boolean includeHeader,
int nSurfaces,
java.lang.String state,
java.lang.String comment)
jvxlFractionFromCharacter
protected static float jvxlFractionFromCharacter(int ich,
int base,
int range,
float fracOffset)
jvxlValueFromCharacter2
protected static float jvxlValueFromCharacter2(int ich,
int ich2,
float min,
float max,
int base,
int range)
jvxlFractionFromCharacter2
protected static float jvxlFractionFromCharacter2(int ich1,
int ich2,
int base,
int range)
jvxlValueAsCharacter
protected static char jvxlValueAsCharacter(float value,
float min,
float max,
int base,
int range)
jvxlFractionAsCharacter
protected static char jvxlFractionAsCharacter(float fraction,
int base,
int range)
jvxlValueAsCharacter2
protected static char jvxlValueAsCharacter2(float value,
float min,
float max,
int base,
int range,
char[] remainder)
jvxlUpdateSurfaceData
public static void jvxlUpdateSurfaceData(JvxlData jvxlData,
float[] vertexValues,
int vertexCount,
int vertexIncrement,
char isNaN)
jvxlCreateColorData
public static void jvxlCreateColorData(JvxlData jvxlData,
float[] vertexValues)