public class ScriptEval extends ScriptExpr
| Modifier and Type | Field and Description |
|---|---|
T[][] |
aatoken |
private boolean |
allowJSThreads |
static int |
commandHistoryLevelMax |
ScriptCompiler |
compiler |
private static int |
contextDepthMax |
private java.lang.String |
contextPath |
private java.lang.Thread |
currentThread |
private boolean |
debugScript |
private boolean |
executing |
private boolean |
executionPaused |
private boolean |
executionStepping |
private boolean |
executionStopped |
private JmolThread |
fileLoadThread |
private boolean |
forceNoAddHydrogens |
java.lang.String |
fullCommand |
java.lang.String |
functionName |
boolean |
historyDisabled |
private static int |
iProcess |
private boolean |
isCmdLine_C_Option |
private boolean |
isCmdLine_c_or_C_Option |
private boolean |
isEmbedded |
private boolean |
isFuncReturn |
boolean |
isJS |
boolean |
isStateScript |
private int |
lineEnd |
private int[][] |
lineIndices |
private short[] |
lineNumbers |
private boolean |
listCommands |
private boolean |
mustResumeEval |
javajs.util.SB |
outputBuffer |
private JmolParallelProcessor |
parallelProcessor |
int |
pc |
private int |
pcEnd |
int |
pcResume |
private static java.lang.String |
saveList |
private java.lang.String |
script |
private JmolThread |
scriptDelayThread |
private java.lang.String |
scriptExtensions |
java.lang.String |
scriptFileName |
int |
scriptLevel |
private static int |
scriptReportingLevel |
ShapeManager |
sm |
java.lang.String |
thisCommand |
private long |
timeBeginExecution |
private long |
timeEndExecution |
boolean |
tQuiet |
debugHigh, tempStatementcontextVariables, coordinatesAreFractional, fractionalPoint, isBondSet, iToken, pt1, pt2, pt3, slen, st, theTok, theToken, thisContextchk, 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 and Description |
|---|
ScriptEval() |
| Modifier and Type | Method and Description |
|---|---|
private void |
addFilterAttribute(java.util.Map<java.lang.String,java.lang.Object> htParams,
java.lang.String filter,
java.lang.String key) |
private int |
addLoadData(javajs.util.SB loadScript,
java.lang.String key,
java.util.Map<java.lang.String,java.lang.Object> htParams,
int i) |
private void |
addProcess(javajs.util.Lst<T[]> vProcess,
int pc,
int pt) |
private void |
appendBuffer(java.lang.String str,
boolean mustDo) |
private void |
breakAt(int pt) |
private boolean |
checkContinue()
checks to see if there is a pause condition, during which commands can
still be issued, but with the ! first.
|
private void |
checkExtension(int tok) |
java.lang.String |
checkFileExists(java.lang.String prefix,
boolean isAsync,
java.lang.String filename,
int i,
boolean doClear) |
ScriptContext |
checkScriptSilent(java.lang.String script)
a method for just checking a script
|
boolean |
checkSelect(java.util.Map<java.lang.String,SV> h,
T[] where)
Check a map for a WHERE phrase
|
void |
clearDefinedVariableAtomSets() |
private void |
clearState(boolean tQuiet) |
private void |
cmdAnimation() |
private void |
cmdAxes(int index) |
private void |
cmdBackground(int i) |
private void |
cmdBind() |
private void |
cmdBondorder() |
private void |
cmdBoundbox(int index) |
private void |
cmdCD() |
private void |
cmdCenter(int i) |
private void |
cmdColor() |
private void |
cmdDefine() |
private void |
cmdDelay() |
private void |
cmdDelete() |
private void |
cmdDisplay(boolean isDisplay) |
private void |
cmdDots(int iShape) |
private void |
cmdEcho(int index) |
private void |
cmdFile() |
private void |
cmdFixed() |
private boolean |
cmdFlow(int tok,
boolean isForCheck,
javajs.util.Lst<T[]> vProcess) |
private int |
cmdFlowSwitch(ContextToken c,
int tok) |
private void |
cmdFont(int shapeType,
float fontsize) |
private boolean |
cmdFor(int tok,
boolean isForCheck) |
private void |
cmdFrank(int i) |
private void |
cmdFunc() |
private void |
cmdGetProperty() |
private void |
cmdGoto(boolean isCmd) |
private void |
cmdHbond() |
private void |
cmdHelp() |
private void |
cmdHistory(int pt) |
private void |
cmdHover() |
private void |
cmdLabel(int index,
javajs.util.BS bs) |
void |
cmdLoad() |
private void |
cmdLog() |
private void |
cmdLoop() |
private void |
cmdMessage() |
private void |
cmdModel(int offset)
ONE difference between FRAME and MODEL: model 1 sets model NAMED one in the
case of PDB frame 1 always sets the first model
|
private void |
cmdMove() |
private void |
cmdMoveto() |
private boolean |
cmdPause() |
private void |
cmdPrint() |
private void |
cmdPrompt() |
private void |
cmdReset() |
private void |
cmdRestore() |
private void |
cmdRestrict() |
private void |
cmdReturn(SV tv) |
void |
cmdRotate(boolean isSpin,
boolean isSelected) |
private void |
cmdSave() |
void |
cmdScript(int tok,
java.lang.String filename,
java.lang.String theScript) |
private void |
cmdSelect(int i) |
private void |
cmdSelectionHalos(int pt) |
private void |
cmdSet() |
private void |
cmdSetEcho() |
private boolean |
cmdSetLabel(java.lang.String str) |
private void |
cmdSetPicking() |
private void |
cmdSetPickingStyle() |
private void |
cmdSlab(boolean isDepth) |
private void |
cmdSsbond() |
private void |
cmdStructure() |
private void |
cmdSubset() |
private void |
cmdSync() |
private void |
cmdThrow() |
private void |
cmdTimeout(int index) |
private void |
cmdTranslate(boolean isSelected) |
private void |
cmdUnbind() |
private void |
cmdUndoRedoMove() |
private void |
cmdUnitcell(int i) |
private void |
cmdVector() |
private void |
cmdVibration() |
private void |
cmdWireframe() |
private void |
cmdZap(boolean isZapCommand) |
private void |
cmdZoom(boolean isZoomTo) |
private void |
colorShape(int shapeType,
int index,
boolean isBackground) |
private void |
commandLoop(boolean allowJSInterrupt) |
boolean |
compileScript(java.lang.String filename,
java.lang.String strScript,
boolean debugCompiler) |
boolean |
compileScriptFile(java.lang.String filename,
boolean tQuiet) |
private boolean |
compileScriptFileInternal(java.lang.String filename,
java.lang.String localPath,
java.lang.String remotePath,
java.lang.String scriptPath) |
boolean |
compileScriptString(java.lang.String script,
boolean tQuiet) |
private void |
defineAtomSet(java.lang.String script) |
private void |
defineSets()
support for @xxx or define xxx commands
|
void |
delayScript(int millis) |
void |
deleteAtomsInVariables(javajs.util.BS bsDeleted) |
boolean |
dispatchCommands(boolean isSpt,
boolean fromFunc,
boolean isTry) |
private void |
doDelay(int millis) |
boolean |
doReport() |
RadiusData |
encodeRadiusParameter(int index,
boolean isOnly,
boolean allowAbsolute) |
float |
evalFunctionFloat(java.lang.Object func,
java.lang.Object params,
float[] values) |
boolean |
evalParallel(ScriptContext context,
ShapeManager shapeManager) |
private java.lang.Object |
evaluate(java.lang.Object expr,
boolean asVariable,
boolean compileOnly) |
void |
evaluateCompiledScript(boolean isCmdLine_c_or_C_Option,
boolean isCmdLine_C_Option,
boolean historyDisabled,
boolean listCommands,
javajs.util.SB outputBuffer,
boolean allowThreads) |
java.lang.Object |
evaluateExpression(java.lang.Object expr,
boolean asVariable,
boolean compileOnly)
a general-use method to evaluate a "SET" type expression.
|
private void |
executeCommands(boolean isTry,
boolean reportCompletion) |
int[] |
expandFloatArray(float[] a,
int min)
Accepts a float array and expands [1 -3] to [1 2 3], for example.
|
private void |
finalizeLoad(boolean isAppend,
boolean appendNew,
boolean isConcat,
boolean doOrient,
int nFiles,
int ac0,
int modelCount0) |
private java.lang.String |
fixScriptPath(java.lang.String strScript,
java.lang.String filename) |
private void |
frameControl(int i) |
boolean |
getAllowJSThreads() |
javajs.util.BS |
getAtomBitSet(java.lang.Object atomExpression)
A general method to evaluate a string representing an atom set.
|
java.lang.String |
getColorRange(int i) |
private java.lang.String |
getCommand(int pc,
boolean allThisLine,
boolean addSemi)
used for recall of commands in the application console
|
(package private) static javajs.util.SB |
getContextTrace(Viewer vwr,
ScriptContext sc,
javajs.util.SB sb,
boolean isTop) |
java.lang.String |
getErrorLineMessage2() |
java.lang.String |
getFullPathName() |
int |
getLinenumber(ScriptContext c) |
private java.lang.String |
getLoadFilesList(int i,
javajs.util.SB loadScript,
javajs.util.SB sOptions,
java.util.Map<java.lang.String,java.lang.Object> htParams,
javajs.util.Lst<java.lang.String> fNames) |
private int |
getLoadModelIndex(int i,
javajs.util.SB sOptions,
java.util.Map<java.lang.String,java.lang.Object> htParams) |
java.lang.String |
getNextStatement()
when paused, indicates what statement will be next
|
private javajs.util.P3[] |
getObjectBoundingBox(java.lang.String id) |
protected javajs.util.P3 |
getObjectCenter(java.lang.String axisID,
int index,
int modelIndex) |
void |
getPartialCharges(javajs.util.BS bs) |
protected javajs.util.P4 |
getPlaneForObject(java.lang.String id,
javajs.util.V3 vAB) |
javajs.util.Quat[] |
getQuaternionArray(java.lang.Object quaternionOrSVData,
int itype) |
java.lang.String |
getScript() |
ScriptContext |
getScriptContext(java.lang.String why) |
int |
getSetAxesTypeMad10(int index) |
private float |
getSettingFloat(int pt) |
private int |
getSettingInt(int pt) |
private java.lang.String |
getSettingStr(int pt,
boolean isJmolSet)
Accept an unquoted string if there is just one parameter regardless of its
type.
|
java.lang.Object |
getShapeProperty(int shapeType,
java.lang.String propertyName) |
boolean |
getShapePropertyData(int shapeType,
java.lang.String propertyName,
java.lang.Object[] data) |
private int |
getShapeType(int tok) |
ScriptContext |
getThisContext() |
float |
getTranslucentLevel(int i) |
SV |
getUserFunctionResult(java.lang.String name,
javajs.util.Lst<SV> params,
SV tokenAtom) |
private float |
getZoom(int ptCenter,
int i,
javajs.util.BS bs,
float currentZoom) |
void |
haltExecution() |
boolean |
isAtomExpression(int i) |
private boolean |
isCommandDisplayable(int i)
provides support for the script editor
|
boolean |
isExecuting() |
private boolean |
isLoadOption(int tok) |
boolean |
isPaused() |
boolean |
isStateScript() |
boolean |
isStepping() |
boolean |
isStopped() |
private void |
loadDssr(int modelIndex,
java.lang.String data) |
java.lang.String |
loadFileAsync(java.lang.String prefix,
java.lang.String filename,
int i,
boolean doClear)
Allows asynchronous file loading from the LOAD or SCRIPT command.
|
void |
loadFileResourceAsync(java.lang.String fileName)
load a static file asynchronously
|
private void |
loadPNGJVar(java.lang.String varName,
java.lang.Object o,
java.util.Map<java.lang.String,java.lang.Object> htParams) |
private void |
logDebugScript(T[] st,
int ifLevel) |
private void |
logLoadInfo(java.lang.String msg) |
javajs.util.BS |
lookupIdentifierValue(java.lang.String identifier) |
private javajs.util.BS |
lookupValue(java.lang.String setName,
boolean plurals) |
void |
notifyResumeStatus() |
void |
pauseExecution(boolean withDelay) |
(package private) void |
popContext(boolean isFlowCommand,
boolean statementOnly) |
private void |
processCommand(int tok) |
private void |
processShapeCommand(int tok) |
private void |
processTry(java.util.Map<java.lang.String,SV> cv) |
private void |
pushContext(ContextToken token,
java.lang.String why) |
private void |
pushContext2(ContextToken token,
java.lang.String why) |
void |
pushContextDown(java.lang.String why) |
void |
refresh(boolean doDelay)
Refresh the display NOW
|
void |
report(java.lang.String s,
boolean isError) |
private void |
resetError() |
private void |
restoreFunction(JmolScriptFunction f,
javajs.util.Lst<SV> params,
SV tokenAtom)
note that functions requiring motion cannot be run in JavaScript
|
void |
restoreScriptContext(ScriptContext context,
boolean isPopContext,
boolean isFlowCommand,
boolean statementOnly) |
void |
restrictSelected(boolean isBond,
boolean doInvert) |
void |
resumeEval(java.lang.Object sco)
From dispatchCommands and JmolThread resumeEval.
|
void |
resumePausedExecution() |
private void |
resumeViewer(java.lang.String why) |
void |
runBufferedSafely(java.lang.String script,
javajs.util.SB outputBuffer) |
private SV |
runFunctionAndRet(JmolScriptFunction function,
java.lang.String name,
javajs.util.Lst<SV> params,
SV tokenAtom,
boolean getReturn,
boolean setContextPath,
boolean allowThreads) |
void |
runScript(java.lang.String script) |
void |
runScriptBuffer(java.lang.String script,
javajs.util.SB outputBuffer,
boolean isFuncReturn)
runs a script immediately and sends selected output to a provided SB
|
static SV |
runUserAction(java.lang.String functionName,
java.lang.Object[] params,
Viewer vwr) |
private ScriptContext |
saveContext(java.lang.String saveName) |
void |
setAllowJSThreads(boolean b) |
protected void |
setAtomProp(java.lang.String prop,
java.lang.Object value,
javajs.util.BS bs) |
void |
setCompiler() |
void |
setCurrentCagePts(javajs.util.T3[] originABC,
java.lang.String name) |
void |
setDebugging() |
private boolean |
setElementColor(java.lang.String str,
int argb) |
void |
setException(ScriptException sx,
java.lang.String msg,
java.lang.String untranslated) |
private void |
setFrameSet(int i) |
boolean |
setMeshDisplayProperty(int shape,
int i,
int tok) |
private void |
setObjectArgb(java.lang.String str,
int argb) |
void |
setObjectMad10(int iShape,
java.lang.String name,
int mad10) |
private java.lang.String |
setObjectProp(java.lang.String id,
int tokCommand,
int ptColor) |
java.lang.String |
setObjectProperty() |
java.lang.String |
setObjectPropSafe(java.lang.String id,
int tokCommand)
called by Viewer in setting up a PyMOL scene.
|
private int |
setScriptExtensions() |
java.lang.String |
setShapeNameParameter(int i) |
void |
setShapeProperty(int shapeType,
java.lang.String propertyName,
java.lang.Object propertyValue) |
void |
setShapePropertyBs(int iShape,
java.lang.String propertyName,
java.lang.Object propertyValue,
javajs.util.BS bs) |
private void |
setShapeSize(int shapeType,
RadiusData rd) |
void |
setShapeSizeBs(int shapeType,
int size,
javajs.util.BS bs) |
void |
setShapeTranslucency(int shapeType,
java.lang.String prefix,
java.lang.String translucency,
float translucentLevel,
javajs.util.BS bs) |
private void |
setSize(int shape,
float scale) |
private void |
setSizeBio(int iShape) |
int |
setStatic(int tok,
int ival)
set a static variable, with checking for range
|
private boolean |
setUnits(java.lang.String units,
int tok) |
ScriptEval |
setViewer(Viewer vwr) |
void |
showString(java.lang.String str) |
void |
showStringPrint(java.lang.String s,
boolean mustDo) |
static java.lang.String |
statementAsString(Viewer vwr,
T[] statement,
int iTok,
boolean doLogMessages) |
void |
stepPausedExecution() |
void |
stopScriptThreads() |
java.lang.String |
toString() |
boolean |
useThreads() |
atomExpression, atomExpressionAt, compareFloat, compareFloatData, getAssocArray, getAtomBits, getBitsetProperty, getCmdExt, getIsoExt, getMathExt, getSeqCode, getSmilesExt, listBS, noCopy, parameterExpressionBoolean, parameterExpressionList, parameterExpressionSelect, parameterExpressionString, parameterExpressionToken, setStatement, setVariableatomCenterOrCoordinateParameter, centerParameter, centerParameterForModel, checkLast, checkLength, checkLength23, checkLength34, checkLengthErrorPt, checkToken, floatParameter, floatParameterRange, floatParameterSet, getArgbParam, getArgbParamLast, getArgbParamOrNone, getBondOrderFromString, getContextVariableAsVariable, getFloatEncodedInt, getHklPlane, getMadParameter, getParameter, getPartialBondOrderFromFloatEncodedInt, getPoint3f, getPoint4f, getPointArray, getPointOrCenterVector, getPointOrPlane, getPointVector, getQuaternionParameter, getToken, getVarParameter, hklParameter, intParameter, intParameterRange, isArrayParameter, isCenterParameter, isColorParam, isFloatParameter, isPoint3f, listParameter, listParameter4, modelNumberParameter, objectNameParameter, optParameterAsString, paramAsStr, planeParameter, setBooleanProperty, setFloatProperty, setIntProperty, setStringProperty, stringParameter, stringParameterSet, tickParamAsStr, tokAt, xypParameter, xyzpParameterbad, error, errorMore, errorStr, errorStr2, errorString, evalError, getErrorLineMessage, getErrorMessage, getErrorMessageUntranslated, integerOutOfRange, invArg, numberOutOfRange, setCursorWait, setErrorMessage, warningprivate static final java.lang.String saveList
private static int iProcess
public ShapeManager sm
public boolean isJS
private JmolThread scriptDelayThread
private JmolThread fileLoadThread
private boolean allowJSThreads
private boolean isFuncReturn
public boolean historyDisabled
private boolean debugScript
private boolean isCmdLine_C_Option
private boolean isCmdLine_c_or_C_Option
private boolean listCommands
public boolean tQuiet
private boolean executionStopped
private boolean executionPaused
private boolean executionStepping
private boolean executing
private long timeBeginExecution
private long timeEndExecution
private boolean mustResumeEval
private java.lang.Thread currentThread
public ScriptCompiler compiler
public javajs.util.SB outputBuffer
private java.lang.String contextPath
public java.lang.String scriptFileName
public java.lang.String functionName
public boolean isStateScript
public int scriptLevel
public static int commandHistoryLevelMax
private static int contextDepthMax
private static int scriptReportingLevel
public T[][] aatoken
private short[] lineNumbers
private int[][] lineIndices
private java.lang.String script
private java.lang.String scriptExtensions
public int pc
public java.lang.String thisCommand
public java.lang.String fullCommand
private int lineEnd
private int pcEnd
private boolean forceNoAddHydrogens
private JmolParallelProcessor parallelProcessor
public int pcResume
private boolean isEmbedded
public boolean getAllowJSThreads()
public void setAllowJSThreads(boolean b)
public boolean doReport()
public boolean isStateScript()
public int setStatic(int tok,
int ival)
public java.lang.String getScript()
public ScriptEval setViewer(Viewer vwr)
public void setCompiler()
public boolean compileScriptString(java.lang.String script,
boolean tQuiet)
public boolean compileScriptFile(java.lang.String filename,
boolean tQuiet)
public void evaluateCompiledScript(boolean isCmdLine_c_or_C_Option,
boolean isCmdLine_C_Option,
boolean historyDisabled,
boolean listCommands,
javajs.util.SB outputBuffer,
boolean allowThreads)
public boolean useThreads()
private void executeCommands(boolean isTry,
boolean reportCompletion)
public void resumeEval(java.lang.Object sco)
sc - private void resumeViewer(java.lang.String why)
public void runScript(java.lang.String script)
throws ScriptException
ScriptExceptionpublic void runScriptBuffer(java.lang.String script,
javajs.util.SB outputBuffer,
boolean isFuncReturn)
throws ScriptException
outputBuffer - script - ScriptExceptionpublic ScriptContext checkScriptSilent(java.lang.String script)
script - static javajs.util.SB getContextTrace(Viewer vwr, ScriptContext sc, javajs.util.SB sb, boolean isTop)
public void setDebugging()
public void haltExecution()
public void pauseExecution(boolean withDelay)
public void stepPausedExecution()
public void resumePausedExecution()
public boolean isExecuting()
public boolean isPaused()
public boolean isStepping()
public boolean isStopped()
public java.lang.String getNextStatement()
private java.lang.String getCommand(int pc,
boolean allThisLine,
boolean addSemi)
pc - allThisLine - addSemi - private void logDebugScript(T[] st, int ifLevel)
public java.lang.Object evaluateExpression(java.lang.Object expr,
boolean asVariable,
boolean compileOnly)
asVariable - expr - public void runBufferedSafely(java.lang.String script,
javajs.util.SB outputBuffer)
public static SV runUserAction(java.lang.String functionName, java.lang.Object[] params, Viewer vwr)
private java.lang.Object evaluate(java.lang.Object expr,
boolean asVariable,
boolean compileOnly)
public boolean checkSelect(java.util.Map<java.lang.String,SV> h, T[] where)
public javajs.util.BS getAtomBitSet(java.lang.Object atomExpression)
atomExpression - public boolean compileScript(java.lang.String filename,
java.lang.String strScript,
boolean debugCompiler)
private java.lang.String fixScriptPath(java.lang.String strScript,
java.lang.String filename)
private int setScriptExtensions()
private boolean compileScriptFileInternal(java.lang.String filename,
java.lang.String localPath,
java.lang.String remotePath,
java.lang.String scriptPath)
public float evalFunctionFloat(java.lang.Object func,
java.lang.Object params,
float[] values)
public SV getUserFunctionResult(java.lang.String name, javajs.util.Lst<SV> params, SV tokenAtom) throws ScriptException
ScriptExceptionprivate SV runFunctionAndRet(JmolScriptFunction function, java.lang.String name, javajs.util.Lst<SV> params, SV tokenAtom, boolean getReturn, boolean setContextPath, boolean allowThreads) throws ScriptException
ScriptExceptionprivate void processTry(java.util.Map<java.lang.String,SV> cv) throws ScriptException
ScriptExceptionprivate void breakAt(int pt)
private void restoreFunction(JmolScriptFunction f, javajs.util.Lst<SV> params, SV tokenAtom) throws ScriptException
f - params - tokenAtom - ScriptExceptionpublic void clearDefinedVariableAtomSets()
private void defineSets()
private void defineAtomSet(java.lang.String script)
public javajs.util.BS lookupIdentifierValue(java.lang.String identifier)
throws ScriptException
ScriptExceptionprivate javajs.util.BS lookupValue(java.lang.String setName,
boolean plurals)
throws ScriptException
ScriptExceptionpublic void deleteAtomsInVariables(javajs.util.BS bsDeleted)
public ScriptContext getThisContext()
private void clearState(boolean tQuiet)
public void pushContextDown(java.lang.String why)
private void pushContext(ContextToken token, java.lang.String why) throws ScriptException
ScriptExceptionprivate void pushContext2(ContextToken token, java.lang.String why)
public ScriptContext getScriptContext(java.lang.String why)
void popContext(boolean isFlowCommand,
boolean statementOnly)
public void restoreScriptContext(ScriptContext context, boolean isPopContext, boolean isFlowCommand, boolean statementOnly)
public void setException(ScriptException sx, java.lang.String msg, java.lang.String untranslated)
public static java.lang.String statementAsString(Viewer vwr, T[] statement, int iTok, boolean doLogMessages)
public java.lang.String setObjectPropSafe(java.lang.String id,
int tokCommand)
protected void setAtomProp(java.lang.String prop,
java.lang.Object value,
javajs.util.BS bs)
public void restrictSelected(boolean isBond,
boolean doInvert)
public void showString(java.lang.String str)
public void showStringPrint(java.lang.String s,
boolean mustDo)
showStringPrint in class ScriptErrorpublic void report(java.lang.String s,
boolean isError)
private void appendBuffer(java.lang.String str,
boolean mustDo)
private void addProcess(javajs.util.Lst<T[]> vProcess, int pc, int pt)
private boolean checkContinue()
throws ScriptException
ScriptExceptionpublic void delayScript(int millis)
private void doDelay(int millis)
throws ScriptException
millis - negative here bypasses max checkScriptExceptionpublic boolean evalParallel(ScriptContext context, ShapeManager shapeManager)
private boolean isCommandDisplayable(int i)
i - public void loadFileResourceAsync(java.lang.String fileName)
throws ScriptException
ScriptExceptionpublic java.lang.String loadFileAsync(java.lang.String prefix,
java.lang.String filename,
int i,
boolean doClear)
throws ScriptException
prefix - filename - or null if end of LOAD command and now just clearing out cachei - doClear - ensures only one file is in the cache for a given typeScriptExceptionprivate void logLoadInfo(java.lang.String msg)
public void notifyResumeStatus()
public void refresh(boolean doDelay)
throws ScriptException
doDelay - ScriptExceptionpublic void stopScriptThreads()
public java.lang.String getErrorLineMessage2()
public int getLinenumber(ScriptContext c)
public boolean dispatchCommands(boolean isSpt,
boolean fromFunc,
boolean isTry)
throws ScriptException
isSpt - fromFunc - isTry - ScriptExceptionprivate void commandLoop(boolean allowJSInterrupt)
throws ScriptException
ScriptExceptionprivate void processCommand(int tok)
throws ScriptException
ScriptExceptionprivate void checkExtension(int tok)
throws ScriptException
ScriptExceptionprivate void processShapeCommand(int tok)
throws ScriptException
ScriptExceptionprivate void cmdAnimation()
throws ScriptException
ScriptExceptionprivate void setFrameSet(int i)
throws ScriptException
ScriptExceptionprivate void cmdAxes(int index)
throws ScriptException
ScriptExceptionprivate void cmdBackground(int i)
throws ScriptException
ScriptExceptionprivate void cmdBind()
throws ScriptException
ScriptExceptionprivate void cmdBondorder()
throws ScriptException
ScriptExceptionprivate void cmdBoundbox(int index)
throws ScriptException
ScriptExceptionprivate void cmdCD()
throws ScriptException
ScriptExceptionprivate void cmdCenter(int i)
throws ScriptException
ScriptExceptionprivate void cmdColor()
throws ScriptException
ScriptExceptionprivate void cmdDefine()
throws ScriptException
ScriptExceptionprivate void cmdDelay()
throws ScriptException
ScriptExceptionprivate void cmdDelete()
throws ScriptException
ScriptExceptionprivate void cmdDisplay(boolean isDisplay)
throws ScriptException
ScriptExceptionprivate void cmdDots(int iShape)
throws ScriptException
ScriptExceptionprivate void cmdEcho(int index)
throws ScriptException
ScriptExceptionprivate void cmdFile()
throws ScriptException
ScriptExceptionprivate void cmdFixed()
throws ScriptException
ScriptExceptionprivate boolean cmdFor(int tok,
boolean isForCheck)
throws ScriptException
ScriptExceptionprivate boolean cmdFlow(int tok,
boolean isForCheck,
javajs.util.Lst<T[]> vProcess)
throws ScriptException
ScriptExceptionprivate int cmdFlowSwitch(ContextToken c, int tok) throws ScriptException
ScriptExceptionprivate void cmdFont(int shapeType,
float fontsize)
throws ScriptException
ScriptExceptionprivate void cmdFrank(int i)
throws ScriptException
ScriptExceptionprivate void cmdFunc()
throws ScriptException
ScriptExceptionprivate void cmdGetProperty()
throws ScriptException
ScriptExceptionprivate void cmdGoto(boolean isCmd)
throws ScriptException
ScriptExceptionprivate void cmdHbond()
throws ScriptException
ScriptExceptionprivate void cmdHelp()
throws ScriptException
ScriptExceptionprivate void cmdHistory(int pt)
throws ScriptException
ScriptExceptionprivate void cmdHover()
throws ScriptException
ScriptExceptionprivate void cmdLabel(int index,
javajs.util.BS bs)
throws ScriptException
ScriptExceptionpublic void cmdLoad()
throws ScriptException
ScriptExceptionpublic java.lang.String checkFileExists(java.lang.String prefix,
boolean isAsync,
java.lang.String filename,
int i,
boolean doClear)
throws ScriptException
ScriptExceptionprivate void addFilterAttribute(java.util.Map<java.lang.String,java.lang.Object> htParams,
java.lang.String filter,
java.lang.String key)
private int addLoadData(javajs.util.SB loadScript,
java.lang.String key,
java.util.Map<java.lang.String,java.lang.Object> htParams,
int i)
throws ScriptException
ScriptExceptionprivate void loadPNGJVar(java.lang.String varName,
java.lang.Object o,
java.util.Map<java.lang.String,java.lang.Object> htParams)
throws ScriptException
ScriptExceptionprivate java.lang.String getLoadFilesList(int i,
javajs.util.SB loadScript,
javajs.util.SB sOptions,
java.util.Map<java.lang.String,java.lang.Object> htParams,
javajs.util.Lst<java.lang.String> fNames)
throws ScriptException
ScriptExceptionprivate boolean isLoadOption(int tok)
private int getLoadModelIndex(int i,
javajs.util.SB sOptions,
java.util.Map<java.lang.String,java.lang.Object> htParams)
throws ScriptException
ScriptExceptionprivate void finalizeLoad(boolean isAppend,
boolean appendNew,
boolean isConcat,
boolean doOrient,
int nFiles,
int ac0,
int modelCount0)
throws ScriptException
ScriptExceptionprivate void cmdLog()
throws ScriptException
ScriptExceptionprivate void cmdLoop()
throws ScriptException
ScriptExceptionprivate void cmdMessage()
throws ScriptException
ScriptExceptionprivate void cmdModel(int offset)
throws ScriptException
offset - will be 2 for "anim frame ..."ScriptExceptionprivate void loadDssr(int modelIndex,
java.lang.String data)
throws ScriptException
ScriptExceptionprivate void cmdMove()
throws ScriptException
ScriptExceptionprivate void cmdMoveto()
throws ScriptException
ScriptExceptionpublic boolean isAtomExpression(int i)
private boolean cmdPause()
throws ScriptException
ScriptExceptionprivate void cmdPrint()
throws ScriptException
ScriptExceptionprivate void cmdPrompt()
throws ScriptException
ScriptExceptionprivate void cmdReset()
throws ScriptException
ScriptExceptionprivate void resetError()
private void cmdRestrict()
throws ScriptException
ScriptExceptionprivate void cmdReturn(SV tv) throws ScriptException
ScriptExceptionpublic void cmdRotate(boolean isSpin,
boolean isSelected)
throws ScriptException
ScriptExceptionprivate void cmdRestore()
throws ScriptException
ScriptExceptionprivate void cmdSave()
throws ScriptException
ScriptExceptionpublic void cmdScript(int tok,
java.lang.String filename,
java.lang.String theScript)
throws ScriptException
ScriptExceptionprivate void cmdSelect(int i)
throws ScriptException
ScriptExceptionprivate void cmdSelectionHalos(int pt)
throws ScriptException
ScriptExceptionprivate void cmdSet()
throws ScriptException
ScriptExceptionprivate void cmdSetEcho()
throws ScriptException
ScriptExceptionprivate boolean cmdSetLabel(java.lang.String str)
throws ScriptException
ScriptExceptionprivate void cmdSetPicking()
throws ScriptException
ScriptExceptionprivate void cmdSetPickingStyle()
throws ScriptException
ScriptExceptionprivate void cmdSlab(boolean isDepth)
throws ScriptException
ScriptExceptionprivate void cmdSsbond()
throws ScriptException
ScriptExceptionprivate void cmdStructure()
throws ScriptException
ScriptExceptionprivate void cmdSubset()
throws ScriptException
ScriptExceptionprivate void cmdSync()
throws ScriptException
ScriptExceptionprivate void cmdThrow()
throws ScriptException
ScriptExceptionprivate ScriptContext saveContext(java.lang.String saveName)
private void cmdTimeout(int index)
throws ScriptException
ScriptExceptionprivate void cmdTranslate(boolean isSelected)
throws ScriptException
ScriptExceptionprivate void cmdUnbind()
throws ScriptException
ScriptExceptionprivate void cmdUndoRedoMove()
throws ScriptException
ScriptExceptionpublic void setCurrentCagePts(javajs.util.T3[] originABC,
java.lang.String name)
private void cmdUnitcell(int i)
throws ScriptException
ScriptExceptionprivate void cmdVector()
throws ScriptException
ScriptExceptionprivate void cmdVibration()
throws ScriptException
ScriptExceptionprivate void cmdWireframe()
throws ScriptException
ScriptExceptionprivate void cmdZap(boolean isZapCommand)
throws ScriptException
ScriptExceptionprivate void cmdZoom(boolean isZoomTo)
throws ScriptException
ScriptExceptionprivate void colorShape(int shapeType,
int index,
boolean isBackground)
throws ScriptException
ScriptExceptionpublic void getPartialCharges(javajs.util.BS bs)
throws ScriptException
ScriptExceptionpublic RadiusData encodeRadiusParameter(int index, boolean isOnly, boolean allowAbsolute) throws ScriptException
ScriptExceptionpublic int[] expandFloatArray(float[] a,
int min)
throws ScriptException
a - min - ScriptExceptionprivate void frameControl(int i)
throws ScriptException
ScriptExceptionpublic java.lang.String getColorRange(int i)
throws ScriptException
ScriptExceptionpublic java.lang.String getFullPathName()
throws ScriptException
ScriptExceptionprivate javajs.util.P3[] getObjectBoundingBox(java.lang.String id)
protected javajs.util.P3 getObjectCenter(java.lang.String axisID,
int index,
int modelIndex)
protected javajs.util.P4 getPlaneForObject(java.lang.String id,
javajs.util.V3 vAB)
public javajs.util.Quat[] getQuaternionArray(java.lang.Object quaternionOrSVData,
int itype)
public int getSetAxesTypeMad10(int index)
throws ScriptException
ScriptExceptionprivate float getSettingFloat(int pt)
throws ScriptException
ScriptExceptionprivate int getSettingInt(int pt)
throws ScriptException
ScriptExceptionprivate java.lang.String getSettingStr(int pt,
boolean isJmolSet)
throws ScriptException
pt - isJmolSet - ScriptExceptionpublic java.lang.Object getShapeProperty(int shapeType,
java.lang.String propertyName)
public boolean getShapePropertyData(int shapeType,
java.lang.String propertyName,
java.lang.Object[] data)
private int getShapeType(int tok)
throws ScriptException
ScriptExceptionpublic float getTranslucentLevel(int i)
throws ScriptException
ScriptExceptionprivate float getZoom(int ptCenter,
int i,
javajs.util.BS bs,
float currentZoom)
throws ScriptException
ScriptExceptionprivate boolean setElementColor(java.lang.String str,
int argb)
public boolean setMeshDisplayProperty(int shape,
int i,
int tok)
throws ScriptException
shape - i - tok - ScriptExceptionprivate void setObjectArgb(java.lang.String str,
int argb)
public void setObjectMad10(int iShape,
java.lang.String name,
int mad10)
private java.lang.String setObjectProp(java.lang.String id,
int tokCommand,
int ptColor)
throws ScriptException
ScriptExceptionpublic java.lang.String setObjectProperty()
throws ScriptException
ScriptExceptionpublic java.lang.String setShapeNameParameter(int i)
throws ScriptException
ScriptExceptionpublic void setShapeProperty(int shapeType,
java.lang.String propertyName,
java.lang.Object propertyValue)
public void setShapePropertyBs(int iShape,
java.lang.String propertyName,
java.lang.Object propertyValue,
javajs.util.BS bs)
private void setShapeSize(int shapeType,
RadiusData rd)
public void setShapeSizeBs(int shapeType,
int size,
javajs.util.BS bs)
public void setShapeTranslucency(int shapeType,
java.lang.String prefix,
java.lang.String translucency,
float translucentLevel,
javajs.util.BS bs)
private void setSize(int shape,
float scale)
throws ScriptException
ScriptExceptionprivate void setSizeBio(int iShape)
throws ScriptException
ScriptExceptionprivate boolean setUnits(java.lang.String units,
int tok)
throws ScriptException
ScriptExceptionpublic java.lang.String toString()
toString in class java.lang.Object