org.jmol.script

Class ScriptExpr

java.lang.Object

org.jmol.script.ScriptError

org.jmol.script.ScriptParam

org.jmol.script.ScriptExpr

All Implemented Interfaces:

JmolScriptEvaluator

Direct Known Subclasses:

ScriptEval

abstract class ScriptExpr
extends ScriptParam

The ScriptExpr class holds the main functions for processing mathematical and atom selection expressions. The two methods, parameterExpression and atomExpression are the key starting points for this processing.

Field Summary

Fields

Modifier and Type	Field and Description
private JmolCmdExtension	cmdExt
boolean	debugHigh
private javajs.util.P3	ptTemp
protected T[]	tempStatement

Fields inherited from class org.jmol.script.ScriptParam

contextVariables, coordinatesAreFractional, expressionResult, fractionalPoint, isBondSet, iToken, slen, st, theTok, theToken, 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
ScriptExpr()

Method Summary

Modifier and Type	Method and Description
BS	atomExpression(T[] code, int pcStart, int pcStop, boolean allowRefresh, boolean allowUnderflow, boolean mustBeBitSet, boolean andNotDeleted)
BS	atomExpressionAt(int index)
private BS	bitSetForModelFileNumber(int m)
abstract void	clearDefinedVariableAtomSets()
protected boolean	compareFloat(int tokOperator, float a, float b)
protected BS	compareFloatData(int tokWhat, float[] data, int tokOperator, float comparisonFloat)
private BS	compareInt(int tokWhat, int tokOperator, int ival)
private BS	compareString(int tokWhat, int tokOperator, java.lang.String comparisonString)
private boolean	compareStringValues(int tokOperator, java.lang.String propertyValue, java.lang.String comparisonValue)
protected java.util.Map<java.lang.String,java.lang.Object>	getAssocArray(int i)
protected BS	getAtomBits(int tokType, java.lang.Object specInfo)
java.lang.Object	getBitsetProperty(BS bs, int tok, javajs.util.P3 ptRef, javajs.util.P4 planeRef, java.lang.Object tokenValue, java.lang.Object opValue, boolean useAtomMap, int index, boolean asVectorIfAll)
float[]	getBitsetPropertyFloat(BS bs, int tok, float min, float max)
private SV	getBitsetPropertySelector(int i, boolean mustBeSettable, boolean isExpression)
JmolCmdExtension	getCmdExt()
private BS	getComparison(T t, int tokWhat, int tokOp, java.lang.String strOp, float[] data)
java.lang.Object	getExt(java.lang.String type)
protected static int	getSeqCode(T instruction)
private java.lang.Object	getStringObjectAsVariable(java.lang.String s, java.lang.String key)
abstract SV	getUserFunctionResult(java.lang.String name, javajs.util.Lst<SV> params, SV tokenAtom)
protected javajs.util.Lst<SV>	listBS(BS bs)
abstract BS	lookupIdentifierValue(java.lang.String identifier)
protected boolean	noCopy(int i, int dir)
private java.lang.Object	parameterExpression(int pt, int ptMax, java.lang.String key, boolean ignoreComma, boolean asVector, int ptAtom, boolean isArrayItem, java.util.Map<java.lang.String,SV> localVars, java.lang.String localVar, boolean isSpecialAssignment) This is the primary driver of the RPN (reverse Polish notation) expression processor.
protected boolean	parameterExpressionBoolean(int pt, int ptMax)
protected javajs.util.Lst<SV>	parameterExpressionList(int pt, int ptAtom, boolean isArrayItem)
protected boolean	parameterExpressionSelect(java.util.Map<java.lang.String,SV> h, T[] where)
protected java.lang.String	parameterExpressionString(int pt, int ptMax)
protected SV	parameterExpressionToken(int pt)
abstract void	refresh(boolean doDelay)
protected abstract void	setAtomProp(java.lang.String prop, java.lang.Object value, BS bs)
private void	setBitsetProperty(BS bs, int tok, int iValue, float fValue, T tokenValue)
protected boolean	setStatement(T[] st0) provides support for @x and @{....} in statements.
protected SV	setVariable(int pt, int ptMax, java.lang.String key, boolean isSet)

Methods inherited from class org.jmol.script.ScriptParam

atomCenterOrCoordinateParameter, centerParameter, centerParameterForModel, checkLast, checkLength, checkLength23, checkLength34, checkLengthErrorPt, checkToken, floatParameter, floatParameterRange, floatParameterSet, getArgbParam, getArgbParamLast, getArgbParamOrNone, getBondOrderFromString, getContextVariableAsVariable, getFloatEncodedInt, getHklPlane, getMadParameter, getObjectCenter, getParameter, getPartialBondOrderFromFloatEncodedInt, getPlaneForObject, getPoint3f, getPoint4f, getPointArray, getPointOrPlane, getPointVector, getQuaternionParameter, getStringParameter, getToken, hklParameter, intParameter, intParameterRange, isArrayParameter, isCenterParameter, isColorParam, isFloatParameter, isPoint3f, listParameter, modelNumberParameter, objectNameParameter, optParameterAsString, paramAsStr, planeParameter, restrictSelected, setBooleanProperty, setFloatProperty, setIntProperty, setStringProperty, stringParameter, stringParameterSet, tickParamAsStr, tokAt, xypParameter

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

debugHigh

public boolean debugHigh

cmdExt

private JmolCmdExtension cmdExt

tempStatement

protected T[] tempStatement

ptTemp

private javajs.util.P3 ptTemp

Constructor Detail

ScriptExpr

ScriptExpr()

Method Detail

clearDefinedVariableAtomSets

public abstract void clearDefinedVariableAtomSets()

lookupIdentifierValue

public abstract BS lookupIdentifierValue(java.lang.String identifier)
                                  throws ScriptException

Throws:

ScriptException

refresh

public abstract void refresh(boolean doDelay)
                      throws ScriptException

Throws:

ScriptException

getUserFunctionResult

public abstract SV getUserFunctionResult(java.lang.String name,
                                         javajs.util.Lst<SV> params,
                                         SV tokenAtom)
                                  throws ScriptException

Throws:

ScriptException

setAtomProp

protected abstract void setAtomProp(java.lang.String prop,
                                    java.lang.Object value,
                                    BS bs)

getCmdExt

public JmolCmdExtension getCmdExt()

getExt

public java.lang.Object getExt(java.lang.String type)

parameterExpressionList

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

Specified by:

parameterExpressionList in class ScriptParam

Throws:

ScriptException

parameterExpressionString

protected java.lang.String parameterExpressionString(int pt,
                                                     int ptMax)
                                              throws ScriptException

Throws:

ScriptException

parameterExpressionBoolean

protected boolean parameterExpressionBoolean(int pt,
                                             int ptMax)
                                      throws ScriptException

Throws:

ScriptException

parameterExpressionToken

protected SV parameterExpressionToken(int pt)
                               throws ScriptException

Throws:

ScriptException

parameterExpressionSelect

protected boolean parameterExpressionSelect(java.util.Map<java.lang.String,SV> h,
                                            T[] where)
                                     throws ScriptException

Throws:

ScriptException

parameterExpression

private java.lang.Object parameterExpression(int pt,
                                             int ptMax,
                                             java.lang.String key,
                                             boolean ignoreComma,
                                             boolean asVector,
                                             int ptAtom,
                                             boolean isArrayItem,
                                             java.util.Map<java.lang.String,SV> localVars,
                                             java.lang.String localVar,
                                             boolean isSpecialAssignment)
                                      throws ScriptException

This is the primary driver of the RPN (reverse Polish notation) expression processor. It handles all math outside of a "traditional" Jmol SELECT/RESTRICT context. [Object atomExpression() takes care of that, and also uses the RPN class.]

Parameters:

pt - token index in statement start of expression or negative for one expression only.

ptMax - token index in statement end of expression

key - variable name for debugging reference only -- null indicates return Boolean -- "" indicates return String

ignoreComma -

asVector - a flag passed on to RPN;

ptAtom - this is a for() or select() function with a specific atom selected

isArrayItem - we are storing A[x] = ... so we need to deliver "x" as well

localVars - see below -- lists all nested for(x, {exp}, select(y, {ex},...)) variables

localVar - x or y in above for(), select() examples

isSpecialAssignment - TODO

Returns:

either a vector or a value, caller's choice.

Throws:

ScriptException - errors are thrown directly to the Eval error system.

atomExpressionAt

public BS atomExpressionAt(int index)
                    throws ScriptException

Specified by:

atomExpressionAt in class ScriptParam

Throws:

ScriptException

atomExpression

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

Specified by:

atomExpression in class ScriptParam

Parameters:

code -

pcStart -

pcStop -

allowRefresh -

allowUnderflow -

mustBeBitSet -

andNotDeleted - IGNORED

Returns:

atom bitset

Throws:

ScriptException

getComparison

private BS getComparison(T t,
                         int tokWhat,
                         int tokOp,
                         java.lang.String strOp,
                         float[] data)
                  throws ScriptException

Throws:

ScriptException

noCopy

protected boolean noCopy(int i,
                         int dir)

getAssocArray

protected java.util.Map<java.lang.String,java.lang.Object> getAssocArray(int i)
                                                                  throws ScriptException

Throws:

ScriptException

listBS

protected javajs.util.Lst<SV> listBS(BS bs)

compareFloatData

protected BS compareFloatData(int tokWhat,
                              float[] data,
                              int tokOperator,
                              float comparisonFloat)

Parameters:

tokWhat -

data -

tokOperator -

comparisonFloat -

Returns:

BitSet

compareFloat

protected boolean compareFloat(int tokOperator,
                               float a,
                               float b)

compareString

private BS compareString(int tokWhat,
                         int tokOperator,
                         java.lang.String comparisonString)
                  throws ScriptException

Throws:

ScriptException

compareStringValues

private boolean compareStringValues(int tokOperator,
                                    java.lang.String propertyValue,
                                    java.lang.String comparisonValue)
                             throws ScriptException

Throws:

ScriptException

compareInt

private BS compareInt(int tokWhat,
                      int tokOperator,
                      int ival)

getBitsetPropertySelector

private SV getBitsetPropertySelector(int i,
                                     boolean mustBeSettable,
                                     boolean isExpression)
                              throws ScriptException

Throws:

ScriptException

getBitsetPropertyFloat

public float[] getBitsetPropertyFloat(BS bs,
                                      int tok,
                                      float min,
                                      float max)
                               throws ScriptException

Throws:

ScriptException

getBitsetProperty

public java.lang.Object getBitsetProperty(BS bs,
                                          int tok,
                                          javajs.util.P3 ptRef,
                                          javajs.util.P4 planeRef,
                                          java.lang.Object tokenValue,
                                          java.lang.Object opValue,
                                          boolean useAtomMap,
                                          int index,
                                          boolean asVectorIfAll)
                                   throws ScriptException

Throws:

ScriptException

bitSetForModelFileNumber

private BS bitSetForModelFileNumber(int m)

getStringObjectAsVariable

private java.lang.Object getStringObjectAsVariable(java.lang.String s,
                                                   java.lang.String key)

getAtomBits

protected BS getAtomBits(int tokType,
                         java.lang.Object specInfo)

getSeqCode

protected static int getSeqCode(T instruction)

setVariable

protected SV setVariable(int pt,
                         int ptMax,
                         java.lang.String key,
                         boolean isSet)
                  throws ScriptException

Parameters:

pt - starting point in command token sequence

ptMax - ending point in command token sequenec, possibly -1 for "all"

key - the variable name to save the result in. This must be a standard user variable, either local or global

isSet - from Set ... or Var .... or just xxx ....

Returns:

a variable or null

Throws:

ScriptException

setBitsetProperty

private void setBitsetProperty(BS bs,
                               int tok,
                               int iValue,
                               float fValue,
                               T tokenValue)
                        throws ScriptException

Throws:

ScriptException

setStatement

protected boolean setStatement(T[] st0)
                        throws ScriptException

provides support for @x and @{....} in statements. The compiler passes on these, because they must be integrated with the statement dynamically.

Parameters:

st0 - aaToken[i]

Returns:

a fixed token set -- with possible overrun of unused null tokens

Throws:

ScriptException