org.jmol.script

Class ScriptParam

java.lang.Object

org.jmol.script.ScriptError

org.jmol.script.ScriptParam

All Implemented Interfaces:

JmolScriptEvaluator

Direct Known Subclasses:

ScriptExpr

public abstract class ScriptParam
extends ScriptError

The ScriptParam class holds methods used to parse parameters in Jmol scripts.

Field Summary

Fields

Modifier and Type	Field and Description
java.util.Map<java.lang.String,SV>	contextVariables
protected boolean	coordinatesAreFractional
java.lang.Object	expressionResult
protected javajs.util.P3	fractionalPoint
boolean	isBondSet
int	iToken
int	slen
T[]	st
int	theTok
T	theToken
ScriptContext	thisContext

Fields inherited from class org.jmol.script.ScriptError

chk, error, ERROR_axisExpected, ERROR_backgroundModelError, ERROR_badArgumentCount, ERROR_badMillerIndices, ERROR_badRGBColor, ERROR_booleanExpected, ERROR_booleanOrNumberExpected, ERROR_booleanOrWhateverExpected, ERROR_cannotSet, ERROR_colorExpected, ERROR_colorOrPaletteRequired, ERROR_commandExpected, ERROR_coordinateOrNameOrExpressionRequired, ERROR_drawObjectNotDefined, ERROR_endOfStatementUnexpected, ERROR_expressionExpected, ERROR_expressionOrIntegerExpected, ERROR_filenameExpected, ERROR_fileNotFoundException, ERROR_incompatibleArguments, ERROR_insufficientArguments, ERROR_integerExpected, ERROR_integerOutOfRange, ERROR_invalidArgument, ERROR_invalidParameterOrder, ERROR_keywordExpected, ERROR_moCoefficients, ERROR_moIndex, ERROR_moModelError, ERROR_moOccupancy, ERROR_moOnlyOne, ERROR_multipleModelsDisplayedNotOK, ERROR_multipleModelsNotOK, ERROR_noData, ERROR_noPartialCharges, ERROR_noUnitCell, ERROR_numberExpected, ERROR_numberMustBe, ERROR_numberOutOfRange, ERROR_objectNameExpected, ERROR_planeExpected, ERROR_propertyNameExpected, ERROR_spaceGroupNotFound, ERROR_stringExpected, ERROR_stringOrIdentifierExpected, ERROR_tooManyPoints, ERROR_tooManyScriptLevels, ERROR_unrecognizedAtomProperty, ERROR_unrecognizedBondProperty, ERROR_unrecognizedCommand, ERROR_unrecognizedExpression, ERROR_unrecognizedObject, ERROR_unrecognizedParameter, ERROR_unrecognizedParameterWarning, ERROR_unrecognizedShowParameter, ERROR_what, ERROR_writeWhat, errorMessage, errorMessageUntranslated, errorType, iCommandError, ignoreError, vwr

Constructor Summary

Constructors

Constructor and Description
ScriptParam()

Method Summary

Modifier and Type	Method and Description
protected javajs.util.P3	atomCenterOrCoordinateParameter(int i)
abstract BS	atomExpression(T[] code, int pcStart, int pcStop, boolean allowRefresh, boolean allowUnderflow, boolean mustBeBitSet, boolean andNotDeleted)
abstract BS	atomExpressionAt(int i)
javajs.util.P3	centerParameter(int i)
protected javajs.util.P3	centerParameterForModel(int i, int modelIndex)
int	checkLast(int i)
int	checkLength(int length)
int	checkLength23()
protected int	checkLength34()
protected int	checkLengthErrorPt(int length, int errorPt)
protected boolean	checkToken(int i)
float	floatParameter(int index)
protected float	floatParameterRange(int i, float min, float max)
float[]	floatParameterSet(int i, int nMin, int nMax) process a general string or set of parameters as an array of floats, allowing for relatively free form input
int	getArgbParam(int index)
protected int	getArgbParamLast(int index, boolean allowNone)
protected int	getArgbParamOrNone(int index, boolean allowNone)
static int	getBondOrderFromString(java.lang.String s)
private int	getColorTriad(int i)
SV	getContextVariableAsVariable(java.lang.String var)
(package private) static int	getFloatEncodedInt(java.lang.String strDecimal) Encodes a string such as "2.10" as an integer instead of a float so as to distinguish "2.1" from "2.10" used for model numbers and partial bond orders.
javajs.util.P4	getHklPlane(javajs.util.P3 pt)
int	getMadParameter()
protected abstract javajs.util.P3	getObjectCenter(java.lang.String id, int index, int modelIndex)
java.lang.Object	getParameter(java.lang.String key, int tokType, boolean nullAsString)
static int	getPartialBondOrderFromFloatEncodedInt(int bondOrderInteger) reads standard n.m float-as-integer n*1000000 + m and returns (n % 6) << 5 + (m % 0x1F)
private static int	getPartialBondOrderFromString(java.lang.String s)
protected abstract javajs.util.P4	getPlaneForObject(java.lang.String id, javajs.util.V3 vAB)
javajs.util.P3	getPoint3f(int i, boolean allowFractional)
javajs.util.P4	getPoint4f(int i)
javajs.util.P3[]	getPointArray(int i, int nPoints, boolean allowNull) may return null values in some cases
protected java.lang.Object	getPointOrPlane(int index, boolean integerOnly, boolean allowFractional, boolean doConvert, boolean implicitFractional, int minDim, int maxDim)
javajs.util.Lst<javajs.util.P3>	getPointVector(T t, int i)
javajs.util.Quat	getQuaternionParameter(int i)
protected java.lang.String	getStringParameter(java.lang.String var, boolean orReturnName)
T	getToken(int i)
javajs.util.P4	hklParameter(int i)
int	intParameter(int index)
int	intParameterRange(int i, int min, int max)
boolean	isArrayParameter(int i)
boolean	isCenterParameter(int i)
boolean	isColorParam(int i)
boolean	isFloatParameter(int index)
boolean	isPoint3f(int i)
javajs.util.Lst<java.lang.Object>	listParameter(int i, int nMin, int nMax)
int	modelNumberParameter(int index)
java.lang.String	objectNameParameter(int index)
java.lang.String	optParameterAsString(int i)
java.lang.String	paramAsStr(int i)
protected abstract javajs.util.Lst<SV>	parameterExpressionList(int pt, int ptAtom, boolean isArrayItem)
javajs.util.P4	planeParameter(int i)
protected abstract void	restrictSelected(boolean isBond, boolean doInvert)
void	setBooleanProperty(java.lang.String key, boolean value)
protected boolean	setFloatProperty(java.lang.String key, float value)
protected boolean	setIntProperty(java.lang.String key, int value)
protected void	setStringProperty(java.lang.String key, java.lang.String value)
java.lang.String	stringParameter(int index)
java.lang.String[]	stringParameterSet(int i)
TickInfo	tickParamAsStr(int index, boolean allowUnitCell, boolean allowScale, boolean allowFirst)
int	tokAt(int i)
javajs.util.P3	xypParameter(int index)

Methods inherited from class org.jmol.script.ScriptError

bad, error, errorMore, errorStr, errorStr2, errorString, evalError, getErrorLineMessage, getErrorMessage, getErrorMessageUntranslated, integerOutOfRange, invArg, numberOutOfRange, setCursorWait, setErrorMessage, showString, warning

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.jmol.api.JmolScriptEvaluator

checkScriptSilent, checkSelect, compileScriptFile, compileScriptString, deleteAtomsInVariables, evalFunctionFloat, evalParallel, evaluateCompiledScript, evaluateExpression, getAllowJSThreads, getAtomBitSet, getAtomBitSetVector, getContextVariables, getDefinedAtomSets, getNextStatement, getScript, getScriptContext, getThisContext, haltExecution, isExecuting, isPaused, isStateScript, isStepping, isStopped, loadFileResourceAsync, notifyResumeStatus, pauseExecution, pushContextDown, resumeEval, resumePausedExecution, runScript, runScriptBuffer, setCompiler, setDebugging, setObjectPropSafe, setViewer, stepPausedExecution, stopScriptThreads

Field Detail

contextVariables

public java.util.Map<java.lang.String,SV> contextVariables

thisContext

public ScriptContext thisContext

iToken

public int iToken

theTok

public int theTok

theToken

public T theToken

st

public T[] st

slen

public int slen

fractionalPoint

protected javajs.util.P3 fractionalPoint

coordinatesAreFractional

protected boolean coordinatesAreFractional

isBondSet

public boolean isBondSet

expressionResult

public java.lang.Object expressionResult

Constructor Detail

ScriptParam

public ScriptParam()

Method Detail

atomExpressionAt

public abstract BS atomExpressionAt(int i)
                             throws ScriptException

Throws:

ScriptException

atomExpression

public abstract BS atomExpression(T[] code,
                                  int pcStart,
                                  int pcStop,
                                  boolean allowRefresh,
                                  boolean allowUnderflow,
                                  boolean mustBeBitSet,
                                  boolean andNotDeleted)
                           throws ScriptException

Throws:

ScriptException

getObjectCenter

protected abstract javajs.util.P3 getObjectCenter(java.lang.String id,
                                                  int index,
                                                  int modelIndex)

getPlaneForObject

protected abstract javajs.util.P4 getPlaneForObject(java.lang.String id,
                                                    javajs.util.V3 vAB)

parameterExpressionList

protected abstract javajs.util.Lst<SV> parameterExpressionList(int pt,
                                                               int ptAtom,
                                                               boolean isArrayItem)
                                                        throws ScriptException

Throws:

ScriptException

restrictSelected

protected abstract void restrictSelected(boolean isBond,
                                         boolean doInvert)

getToken

public T getToken(int i)
           throws ScriptException

Throws:

ScriptException

tokAt

public int tokAt(int i)

checkToken

protected boolean checkToken(int i)

getParameter

public java.lang.Object getParameter(java.lang.String key,
                                     int tokType,
                                     boolean nullAsString)

getStringParameter

protected java.lang.String getStringParameter(java.lang.String var,
                                              boolean orReturnName)

getContextVariableAsVariable

public SV getContextVariableAsVariable(java.lang.String var)

paramAsStr

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

Throws:

ScriptException

stringParameter

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

Throws:

ScriptException

stringParameterSet

public java.lang.String[] stringParameterSet(int i)
                                      throws ScriptException

Throws:

ScriptException

objectNameParameter

public java.lang.String objectNameParameter(int index)
                                     throws ScriptException

Throws:

ScriptException

atomCenterOrCoordinateParameter

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

Parameters:

i -

Returns:

point -- ORIGINAL, non-copied atom, if a single atom

Throws:

ScriptException

isCenterParameter

public boolean isCenterParameter(int i)

centerParameter

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

Throws:

ScriptException

centerParameterForModel

protected javajs.util.P3 centerParameterForModel(int i,
                                                 int modelIndex)
                                          throws ScriptException

Throws:

ScriptException

planeParameter

public javajs.util.P4 planeParameter(int i)
                              throws ScriptException

Throws:

ScriptException

hklParameter

public javajs.util.P4 hklParameter(int i)
                            throws ScriptException

Throws:

ScriptException

getHklPlane

public javajs.util.P4 getHklPlane(javajs.util.P3 pt)

getPointOrPlane

protected java.lang.Object getPointOrPlane(int index,
                                           boolean integerOnly,
                                           boolean allowFractional,
                                           boolean doConvert,
                                           boolean implicitFractional,
                                           int minDim,
                                           int maxDim)
                                    throws ScriptException

Throws:

ScriptException

isPoint3f

public boolean isPoint3f(int i)

getPoint3f

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

Throws:

ScriptException

getPoint4f

public javajs.util.P4 getPoint4f(int i)
                          throws ScriptException

Throws:

ScriptException

xypParameter

public javajs.util.P3 xypParameter(int index)
                            throws ScriptException

Throws:

ScriptException

optParameterAsString

public java.lang.String optParameterAsString(int i)
                                      throws ScriptException

Throws:

ScriptException

intParameter

public int intParameter(int index)
                 throws ScriptException

Throws:

ScriptException

isFloatParameter

public boolean isFloatParameter(int index)

floatParameter

public float floatParameter(int index)
                     throws ScriptException

Throws:

ScriptException

getPointArray

public javajs.util.P3[] getPointArray(int i,
                                      int nPoints,
                                      boolean allowNull)
                               throws ScriptException

may return null values in some cases

Parameters:

i -

nPoints -

allowNull - if allowing null values (as in setting atom properties such as vxyz or xyz)

Returns:

array of P3, with possible null values

Throws:

ScriptException

listParameter

public javajs.util.Lst<java.lang.Object> listParameter(int i,
                                                       int nMin,
                                                       int nMax)
                                                throws ScriptException

Throws:

ScriptException

floatParameterSet

public float[] floatParameterSet(int i,
                                 int nMin,
                                 int nMax)
                          throws ScriptException

process a general string or set of parameters as an array of floats, allowing for relatively free form input

Parameters:

i -

nMin -

nMax -

Returns:

array of floats

Throws:

ScriptException

isArrayParameter

public boolean isArrayParameter(int i)

getQuaternionParameter

public javajs.util.Quat getQuaternionParameter(int i)
                                        throws ScriptException

Throws:

ScriptException

checkLast

public int checkLast(int i)
              throws ScriptException

Throws:

ScriptException

checkLength

public int checkLength(int length)
                throws ScriptException

Throws:

ScriptException

checkLengthErrorPt

protected int checkLengthErrorPt(int length,
                                 int errorPt)
                          throws ScriptException

Throws:

ScriptException

checkLength23

public int checkLength23()
                  throws ScriptException

Throws:

ScriptException

checkLength34

protected int checkLength34()
                     throws ScriptException

Throws:

ScriptException

modelNumberParameter

public int modelNumberParameter(int index)
                         throws ScriptException

Throws:

ScriptException

getMadParameter

public int getMadParameter()
                    throws ScriptException

Throws:

ScriptException

intParameterRange

public int intParameterRange(int i,
                             int min,
                             int max)
                      throws ScriptException

Throws:

ScriptException

floatParameterRange

protected float floatParameterRange(int i,
                                    float min,
                                    float max)
                             throws ScriptException

Throws:

ScriptException

getPointVector

public javajs.util.Lst<javajs.util.P3> getPointVector(T t,
                                                      int i)
                                               throws ScriptException

Throws:

ScriptException

getFloatEncodedInt

static int getFloatEncodedInt(java.lang.String strDecimal)

Encodes a string such as "2.10" as an integer instead of a float so as to distinguish "2.1" from "2.10" used for model numbers and partial bond orders. 2147483647 is maxvalue, so this allows loading simultaneously up to 2147 files, each with 999999 models (or trajectories)

Parameters:

strDecimal -

Returns:

float encoded as an integer

getPartialBondOrderFromFloatEncodedInt

public static int getPartialBondOrderFromFloatEncodedInt(int bondOrderInteger)

reads standard n.m float-as-integer n*1000000 + m and returns (n % 6) << 5 + (m % 0x1F)

Parameters:

bondOrderInteger -

Returns:

Bond order partial mask

getBondOrderFromString

public static int getBondOrderFromString(java.lang.String s)

getPartialBondOrderFromString

private static int getPartialBondOrderFromString(java.lang.String s)

isColorParam

public boolean isColorParam(int i)

getArgbParam

public int getArgbParam(int index)
                 throws ScriptException

Throws:

ScriptException

getArgbParamLast

protected int getArgbParamLast(int index,
                               boolean allowNone)
                        throws ScriptException

Throws:

ScriptException

getArgbParamOrNone

protected int getArgbParamOrNone(int index,
                                 boolean allowNone)
                          throws ScriptException

Throws:

ScriptException

getColorTriad

private int getColorTriad(int i)
                   throws ScriptException

Throws:

ScriptException

tickParamAsStr

public TickInfo tickParamAsStr(int index,
                               boolean allowUnitCell,
                               boolean allowScale,
                               boolean allowFirst)
                        throws ScriptException

Parameters:

index -

allowUnitCell - IGNORED

allowScale -

allowFirst -

Returns:

TickInfo

Throws:

ScriptException

setBooleanProperty

public void setBooleanProperty(java.lang.String key,
                               boolean value)

setIntProperty

protected boolean setIntProperty(java.lang.String key,
                                 int value)

setFloatProperty

protected boolean setFloatProperty(java.lang.String key,
                                   float value)

setStringProperty

protected void setStringProperty(java.lang.String key,
                                 java.lang.String value)