org.jmol.scriptext

Class CmdExt

java.lang.Object

org.jmol.scriptext.CmdExt

All Implemented Interfaces:

JmolCmdExtension

Direct Known Subclasses:

IsoExt

public class CmdExt
extends java.lang.Object
implements JmolCmdExtension

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	chk
protected ScriptEval	e
(package private) static int	ERROR_invalidArgument
protected int	slen
protected T[]	st
protected Viewer	vwr

Constructor Summary

Constructors

Constructor and Description
CmdExt()

Method Summary

Modifier and Type	Method and Description
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)
protected BS	atomExpressionAt(int i)
private void	cache()
private void	calculate()
private void	capture()
private void	centerAt()
protected javajs.util.P3	centerParameter(int i)
protected void	checkLength(int i)
private void	compare()
private void	configuration()
private void	connect(int index)
private void	console()
void	data()
java.lang.String	dispatch(int iTok, boolean b, T[] st)
private void	ellipsoid()
protected void	error(int err)
boolean	evalParallel(ScriptContext context, ShapeManager shapeManager) used for TRY command
protected void	finalizeObject(int shapeID, int colorArgb, float translucentLevel, int intScale, boolean doSet, java.lang.Object data, int iptDisplayProperty, BS bs)
protected float	floatParameter(int i)
java.lang.Object	getBitsetIdent(BS bs, java.lang.String label, java.lang.Object tokenValue, boolean useAtomMap, int index, boolean isExplicitlyAll)
protected 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, boolean isNBO)
private float	getPlotMinMax(float[] data, boolean isMax, int tok)
protected javajs.util.P3	getPoint3f(int i, boolean allowFractional)
private java.lang.String	getScriptID(ScriptContext context)
protected java.lang.Object	getShapeProperty(int shapeType, java.lang.String propertyName)
private java.lang.Object	getShapePropertyIndex(int shapeType, java.lang.String propertyName, int index)
protected T	getToken(int i)
JmolCmdExtension	init(java.lang.Object se)
protected int	intParameter(int index)
protected void	invArg()
protected void	invPO()
protected boolean	isFloatParameter(int index)
(package private) boolean	listIsosurface(int iShape)
private void	mapProperty()
private void	measure()
private void	minimize()
private void	modulation() Allows for setting one or more specific t-values as well as full unit-cell shifts (multiples of q).
void	navigate()
protected java.lang.String	paramAsStr(int i)
private java.lang.Object	parseDataArray(java.lang.String str, boolean is3D)
protected java.lang.String	plot(T[] args)
private int	plotProp()
private boolean	polyhedra()
protected java.lang.String	setShapeId(int iShape, int i, boolean idSeen)
protected void	setShapeProperty(int shapeType, java.lang.String propertyName, java.lang.Object propertyValue)
private void	show()
protected void	showString(java.lang.String s)
private void	stereo()
protected java.lang.String	stringParameter(int index)
private boolean	struts()
protected int	tokAt(int i)
private static int	tokAtArray(int i, T[] args)
private T	tokenAt(int i, T[] args)
private java.lang.String	write(T[] args)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

vwr

protected Viewer vwr

e

protected ScriptEval e

chk

protected boolean chk

st

protected T[] st

slen

protected int slen

ERROR_invalidArgument

static final int ERROR_invalidArgument

See Also:

Constant Field Values

Constructor Detail

CmdExt

public CmdExt()

Method Detail

init

public JmolCmdExtension init(java.lang.Object se)

Specified by:

init in interface JmolCmdExtension

dispatch

public java.lang.String dispatch(int iTok,
                                 boolean b,
                                 T[] st)
                          throws ScriptException

Specified by:

dispatch in interface JmolCmdExtension

Throws:

ScriptException

atomExpressionAt

protected BS atomExpressionAt(int i)
                       throws ScriptException

Throws:

ScriptException

checkLength

protected void checkLength(int i)
                    throws ScriptException

Throws:

ScriptException

error

protected void error(int err)
              throws ScriptException

Throws:

ScriptException

invArg

protected void invArg()
               throws ScriptException

Throws:

ScriptException

invPO

protected void invPO()
              throws ScriptException

Throws:

ScriptException

getShapeProperty

protected java.lang.Object getShapeProperty(int shapeType,
                                            java.lang.String propertyName)

paramAsStr

protected java.lang.String paramAsStr(int i)
                               throws ScriptException

Throws:

ScriptException

centerParameter

protected javajs.util.P3 centerParameter(int i)
                                  throws ScriptException

Throws:

ScriptException

floatParameter

protected float floatParameter(int i)
                        throws ScriptException

Throws:

ScriptException

getPoint3f

protected javajs.util.P3 getPoint3f(int i,
                                    boolean allowFractional)
                             throws ScriptException

Throws:

ScriptException

intParameter

protected int intParameter(int index)
                    throws ScriptException

Throws:

ScriptException

isFloatParameter

protected boolean isFloatParameter(int index)

setShapeProperty

protected void setShapeProperty(int shapeType,
                                java.lang.String propertyName,
                                java.lang.Object propertyValue)

showString

protected void showString(java.lang.String s)

stringParameter

protected java.lang.String stringParameter(int index)
                                    throws ScriptException

Throws:

ScriptException

getToken

protected T getToken(int i)
              throws ScriptException

Throws:

ScriptException

tokAt

protected int tokAt(int i)

cache

private void cache()
            throws ScriptException

Throws:

ScriptException

calculate

private void calculate()
                throws ScriptException

Throws:

ScriptException

capture

private void capture()
              throws ScriptException

Throws:

ScriptException

centerAt

private void centerAt()
               throws ScriptException

Throws:

ScriptException

compare

private void compare()
              throws ScriptException

Throws:

ScriptException

configuration

private void configuration()
                    throws ScriptException

Throws:

ScriptException

measure

private void measure()
              throws ScriptException

Throws:

ScriptException

connect

private void connect(int index)
              throws ScriptException

Parameters:

index - 0 indicates hbond command

Throws:

ScriptException

console

private void console()
              throws ScriptException

Throws:

ScriptException

data

public void data()
          throws ScriptException

Throws:

ScriptException

ellipsoid

private void ellipsoid()
                throws ScriptException

Throws:

ScriptException

mapProperty

private void mapProperty()
                  throws ScriptException

Throws:

ScriptException

minimize

private void minimize()
               throws ScriptException

Throws:

ScriptException

modulation

private void modulation()
                 throws ScriptException

Allows for setting one or more specific t-values as well as full unit-cell shifts (multiples of q).

Throws:

ScriptException

navigate

public void navigate()
              throws ScriptException

Throws:

ScriptException

plot

protected java.lang.String plot(T[] args)
                         throws ScriptException

Throws:

ScriptException

plotProp

private int plotProp()

polyhedra

private boolean polyhedra()
                   throws ScriptException

Throws:

ScriptException

evalParallel

public boolean evalParallel(ScriptContext context,
                            ShapeManager shapeManager)

used for TRY command

Specified by:

evalParallel in interface JmolCmdExtension

Parameters:

context -

shapeManager -

Returns:

true if successful; false if not

write

private java.lang.String write(T[] args)
                        throws ScriptException

Throws:

ScriptException

show

private void show()
           throws ScriptException

Throws:

ScriptException

stereo

private void stereo()
             throws ScriptException

Throws:

ScriptException

struts

private boolean struts()
                throws ScriptException

Throws:

ScriptException

assign

private void assign()
             throws ScriptException

Throws:

ScriptException

assignAtom

private void assignAtom(int atomIndex,
                        javajs.util.P3 pt,
                        java.lang.String type)

assignBond

private void assignBond(int bondIndex,
                        char type)

assignConnect

private void assignConnect(int index,
                           int index2)

getContext

private java.lang.String getContext(boolean withVariables)

getColorTrans

protected float getColorTrans(ScriptEval eval,
                              int i,
                              boolean allowNone,
                              int[] ret)
                       throws ScriptException

Checks color, translucent, opaque parameters.

Parameters:

eval -

i -

allowNone -

ret - returned int argb color

Returns:

translucentLevel and sets iToken and ret[0]

Throws:

ScriptException

getIsosurfaceJvxl

private java.lang.String getIsosurfaceJvxl(boolean asMesh,
                                           int iShape)

getMoJvxl

private java.lang.String getMoJvxl(int ptMO,
                                   boolean isNBO)
                            throws ScriptException

Throws:

ScriptException

getScriptID

private java.lang.String getScriptID(ScriptContext context)

getShapePropertyIndex

private java.lang.Object getShapePropertyIndex(int shapeType,
                                               java.lang.String propertyName,
                                               int index)

tokenAt

private T tokenAt(int i,
                  T[] args)

tokAtArray

private static int tokAtArray(int i,
                              T[] args)

finalizeObject

protected void finalizeObject(int shapeID,
                              int colorArgb,
                              float translucentLevel,
                              int intScale,
                              boolean doSet,
                              java.lang.Object data,
                              int iptDisplayProperty,
                              BS bs)
                       throws ScriptException

Throws:

ScriptException

getPlotMinMax

private float getPlotMinMax(float[] data,
                            boolean isMax,
                            int tok)

getBitsetIdent

public java.lang.Object getBitsetIdent(BS bs,
                                       java.lang.String label,
                                       java.lang.Object tokenValue,
                                       boolean useAtomMap,
                                       int index,
                                       boolean isExplicitlyAll)

Specified by:

getBitsetIdent in interface JmolCmdExtension

listIsosurface

boolean listIsosurface(int iShape)
                throws ScriptException

Throws:

ScriptException

setShapeId

protected java.lang.String setShapeId(int iShape,
                                      int i,
                                      boolean idSeen)
                               throws ScriptException

Throws:

ScriptException

parseDataArray

private java.lang.Object parseDataArray(java.lang.String str,
                                        boolean is3D)