public class CmdExt extends java.lang.Object implements JmolCmdExtension
Modifier and Type | Field and Description |
---|---|
private boolean |
chk |
private ScriptEval |
e |
(package private) static int |
ERROR_invalidArgument |
private java.lang.String |
fullCommand |
private java.lang.Object[] |
lastData |
private int |
slen |
private ShapeManager |
sm |
private T[] |
st |
private java.lang.String |
thisCommand |
private Viewer |
vwr |
Constructor and Description |
---|
CmdExt() |
Modifier and Type | Method and Description |
---|---|
private void |
addShapeProperty(javajs.util.List<java.lang.Object[]> propertyList,
java.lang.String key,
java.lang.Object value) |
private void |
assign() |
private void |
assignAtom(int atomIndex,
javajs.util.P3 pt,
java.lang.String type) |
private void |
assignBond(int bondIndex,
char type) |
private void |
assignConnect(int index,
int index2) |
private BS |
atomExpressionAt(int i) |
private void |
cache() |
private void |
calculate() |
private void |
capture() |
private void |
centerAt() |
private javajs.util.P3 |
centerParameter(int i) |
private boolean |
cgo() |
private void |
checkLength(int i) |
private void |
compare() |
private void |
configuration() |
private void |
connect(int index) |
private void |
console() |
private boolean |
contact() |
private java.lang.Object[] |
createFunction(java.lang.String fname,
java.lang.String xyz,
java.lang.String ret)
for the ISOSURFACE command
|
void |
data() |
private boolean |
dipole() |
boolean |
dispatch(int iTok,
boolean b,
T[] st) |
private boolean |
draw() |
private void |
ellipsoid() |
private void |
error(int err) |
boolean |
evalParallel(ScriptContext context,
ShapeManager shapeManager)
used for TRY command
|
private void |
finalizeObject(int shapeID,
int colorArgb,
float translucentLevel,
int intScale,
boolean doSet,
java.lang.Object data,
int iptDisplayProperty,
BS bs) |
private float[][] |
floatArraySet(int i,
int nX,
int nY) |
private float[][][] |
floatArraySetXYZ(int i,
int nX,
int nY,
int nZ) |
private float |
floatParameter(int i) |
private float[] |
getAtomicPotentials(BS bsSelected,
BS bsIgnore,
java.lang.String fileName) |
java.lang.Object |
getBitsetIdent(BS bs,
java.lang.String label,
java.lang.Object tokenValue,
boolean useAtomMap,
int index,
boolean isExplicitlyAll) |
private java.lang.Object |
getCapSlabObject(int i,
boolean isLcaoCartoon) |
private float |
getColorTrans(ScriptEval eval,
int i,
boolean allowNone,
int[] ret)
Checks color, translucent, opaque parameters.
|
private java.lang.String |
getContext(boolean withVariables) |
private java.lang.String |
getIsosurfaceJvxl(boolean asMesh,
int iShape) |
private java.lang.String |
getMoJvxl(int ptMO) |
private float |
getPlotMinMax(float[] data,
boolean isMax,
int tok) |
private javajs.util.P3 |
getPoint3f(int i,
boolean allowFractional) |
private javajs.util.P4 |
getPoint4f(int i) |
private java.lang.String |
getScriptID(ScriptContext context) |
private java.lang.Object |
getShapeProperty(int shapeType,
java.lang.String propertyName) |
private java.lang.Object |
getShapePropertyIndex(int shapeType,
java.lang.String propertyName,
int index) |
private T |
getToken(int i) |
private void |
getWithinDistanceVector(javajs.util.List<java.lang.Object[]> propertyList,
float distance,
javajs.util.P3 ptc,
BS bs,
boolean isShow) |
JmolCmdExtension |
init(java.lang.Object se) |
private java.lang.String |
initIsosurface(int iShape) |
private int |
intParameter(int index) |
private void |
invArg() |
private void |
invPO() |
private boolean |
isFloatParameter(int index) |
private boolean |
isosurface(int iShape) |
private boolean |
lcaoCartoon() |
private boolean |
listIsosurface(int iShape) |
private void |
mapProperty() |
private void |
measure() |
private void |
minimize() |
private boolean |
mo(boolean isInitOnly) |
private float[] |
moCombo(javajs.util.List<java.lang.Object[]> propertyList) |
private void |
modulation()
Allows for setting one or more specific t-values as well as full unit-cell
shifts (multiples of q).
|
private int |
moOffset(int index) |
void |
navigate() |
private java.lang.String |
paramAsStr(int i) |
private java.lang.Object |
parseDataArray(java.lang.String str,
boolean is3D) |
java.lang.String |
plot(T[] args) |
private boolean |
polyhedra() |
private java.lang.String |
setColorOptions(javajs.util.SB sb,
int index,
int iShape,
int nAllowed) |
private void |
setMoData(javajs.util.List<java.lang.Object[]> propertyList,
int moNumber,
float[] lc,
int offset,
boolean isNegOffset,
int modelIndex,
java.lang.String title) |
private java.lang.String |
setShapeId(int iShape,
int i,
boolean idSeen) |
private void |
setShapeProperty(int shapeType,
java.lang.String propertyName,
java.lang.Object propertyValue) |
private void |
show() |
private void |
showString(java.lang.String s) |
private void |
stereo() |
private java.lang.String |
stringParameter(int index) |
private boolean |
struts() |
private int |
tokAt(int i) |
private static int |
tokAtArray(int i,
T[] args) |
private T |
tokenAt(int i,
T[] args) |
java.lang.String |
write(T[] args) |
private Viewer vwr
private ScriptEval e
private ShapeManager sm
private boolean chk
private java.lang.String fullCommand
private java.lang.String thisCommand
private T[] st
private int slen
private java.lang.Object[] lastData
static final int ERROR_invalidArgument
public JmolCmdExtension init(java.lang.Object se)
init
in interface JmolCmdExtension
public boolean dispatch(int iTok, boolean b, T[] st) throws ScriptException
dispatch
in interface JmolCmdExtension
ScriptException
private BS atomExpressionAt(int i) throws ScriptException
ScriptException
private void checkLength(int i) throws ScriptException
ScriptException
private void error(int err) throws ScriptException
ScriptException
private void invArg() throws ScriptException
ScriptException
private void invPO() throws ScriptException
ScriptException
private java.lang.Object getShapeProperty(int shapeType, java.lang.String propertyName)
private java.lang.String paramAsStr(int i) throws ScriptException
ScriptException
private javajs.util.P3 centerParameter(int i) throws ScriptException
ScriptException
private float floatParameter(int i) throws ScriptException
ScriptException
private javajs.util.P3 getPoint3f(int i, boolean allowFractional) throws ScriptException
ScriptException
private javajs.util.P4 getPoint4f(int i) throws ScriptException
ScriptException
private int intParameter(int index) throws ScriptException
ScriptException
private boolean isFloatParameter(int index)
private void setShapeProperty(int shapeType, java.lang.String propertyName, java.lang.Object propertyValue)
private void showString(java.lang.String s)
private java.lang.String stringParameter(int index) throws ScriptException
ScriptException
private T getToken(int i) throws ScriptException
ScriptException
private int tokAt(int i)
private void cache() throws ScriptException
ScriptException
private void calculate() throws ScriptException
ScriptException
private void capture() throws ScriptException
ScriptException
private void centerAt() throws ScriptException
ScriptException
private boolean cgo() throws ScriptException
ScriptException
private void compare() throws ScriptException
ScriptException
private void configuration() throws ScriptException
ScriptException
private void measure() throws ScriptException
ScriptException
private void connect(int index) throws ScriptException
index
- 0 indicates hbond commandScriptException
private void console() throws ScriptException
ScriptException
private boolean contact() throws ScriptException
ScriptException
private boolean dipole() throws ScriptException
ScriptException
private boolean draw() throws ScriptException
ScriptException
public void data() throws ScriptException
ScriptException
private void ellipsoid() throws ScriptException
ScriptException
private boolean isosurface(int iShape) throws ScriptException
ScriptException
private boolean lcaoCartoon() throws ScriptException
ScriptException
private void mapProperty() throws ScriptException
ScriptException
private void minimize() throws ScriptException
ScriptException
private boolean mo(boolean isInitOnly) throws ScriptException
ScriptException
private void modulation() throws ScriptException
ScriptException
public void navigate() throws ScriptException
ScriptException
public java.lang.String plot(T[] args) throws ScriptException
plot
in interface JmolCmdExtension
ScriptException
private boolean polyhedra() throws ScriptException
ScriptException
public boolean evalParallel(ScriptContext context, ShapeManager shapeManager)
evalParallel
in interface JmolCmdExtension
context
- shapeManager
- public java.lang.String write(T[] args) throws ScriptException
write
in interface JmolCmdExtension
ScriptException
private void show() throws ScriptException
ScriptException
private void stereo() throws ScriptException
ScriptException
private boolean struts() throws ScriptException
ScriptException
private void addShapeProperty(javajs.util.List<java.lang.Object[]> propertyList, java.lang.String key, java.lang.Object value)
private void assign() throws ScriptException
ScriptException
private void assignAtom(int atomIndex, javajs.util.P3 pt, java.lang.String type)
private void assignBond(int bondIndex, char type)
private void assignConnect(int index, int index2)
private java.lang.String getContext(boolean withVariables)
private float[] getAtomicPotentials(BS bsSelected, BS bsIgnore, java.lang.String fileName) throws java.lang.Exception
bsSelected
- bsIgnore
- fileName
- java.lang.Exception
private float getColorTrans(ScriptEval eval, int i, boolean allowNone, int[] ret) throws ScriptException
eval
- i
- allowNone
- ret
- returned int argb colorScriptException
private java.lang.Object getCapSlabObject(int i, boolean isLcaoCartoon) throws ScriptException
ScriptException
private java.lang.String getIsosurfaceJvxl(boolean asMesh, int iShape)
private java.lang.String getMoJvxl(int ptMO) throws ScriptException
ScriptException
private java.lang.String getScriptID(ScriptContext context)
private java.lang.Object getShapePropertyIndex(int shapeType, java.lang.String propertyName, int index)
private static int tokAtArray(int i, T[] args)
private void finalizeObject(int shapeID, int colorArgb, float translucentLevel, int intScale, boolean doSet, java.lang.Object data, int iptDisplayProperty, BS bs) throws ScriptException
ScriptException
private float[] moCombo(javajs.util.List<java.lang.Object[]> propertyList)
private int moOffset(int index) throws ScriptException
ScriptException
private void setMoData(javajs.util.List<java.lang.Object[]> propertyList, int moNumber, float[] lc, int offset, boolean isNegOffset, int modelIndex, java.lang.String title) throws ScriptException
ScriptException
private float getPlotMinMax(float[] data, boolean isMax, int tok)
private java.lang.String initIsosurface(int iShape) throws ScriptException
ScriptException
private void getWithinDistanceVector(javajs.util.List<java.lang.Object[]> propertyList, float distance, javajs.util.P3 ptc, BS bs, boolean isShow)
private java.lang.String setColorOptions(javajs.util.SB sb, int index, int iShape, int nAllowed) throws ScriptException
ScriptException
private java.lang.Object[] createFunction(java.lang.String fname, java.lang.String xyz, java.lang.String ret)
fname
- xyz
- ret
- private float[][] floatArraySet(int i, int nX, int nY) throws ScriptException
ScriptException
private float[][][] floatArraySetXYZ(int i, int nX, int nY, int nZ) throws ScriptException
ScriptException
public java.lang.Object getBitsetIdent(BS bs, java.lang.String label, java.lang.Object tokenValue, boolean useAtomMap, int index, boolean isExplicitlyAll)
getBitsetIdent
in interface JmolCmdExtension
private boolean listIsosurface(int iShape) throws ScriptException
ScriptException
private java.lang.String setShapeId(int iShape, int i, boolean idSeen) throws ScriptException
ScriptException
private java.lang.Object parseDataArray(java.lang.String str, boolean is3D)