Class ScriptEval

Method Details

• getAllowJSThreads

  public boolean getAllowJSThreads()

• setAllowJSThreads

  public void setAllowJSThreads(boolean b)

• doReport

  public boolean doReport()

• isStateScript

  public boolean isStateScript()

• setStatic

  public int setStatic(int tok, int ival)

  set a static variable, with checking for range

• getScript

  public String getScript()

• setViewer

  public ScriptEval setViewer(Viewer vwr)

• setCompiler

  public void setCompiler()

• compileScriptString

  public boolean compileScriptString(String script, boolean tQuiet)

• compileScriptFile

  public boolean compileScriptFile(String filename, boolean tQuiet)

• evaluateCompiledScript

  public void evaluateCompiledScript(boolean isCmdLine_c_or_C_Option, boolean isCmdLine_C_Option, boolean historyDisabled, boolean listCommands, javajs.util.SB outputBuffer, boolean allowThreads)

• useThreads

  public boolean useThreads()

• executeCommands

  private int executeCommands(boolean isTry, boolean reportCompletion)

• resumeEval

  public void resumeEval(Object sco)

  From dispatchCommands and JmolThread resumeEval. After throwing a ScriptInterruption, all statements following the current one are lost. When a JavaScript timeout returns from a DELAY, MOVE, MOVETO, or other sleep-requiring command, it is the ScriptContext that contains all have to worry about this, because the current thread is just put to sleep, not stopped, but in JavaScript, where we only have one thread, we need to manage this more carefully. We re-enter the halted script here, using a saved script context. The program counter is incremented to skip the initiating statement, and all parent contexts up the line are set with mustResumeEval = true.

  Parameters:

  sco -

• resumeViewer

  private void resumeViewer(String why)

• runScript

  public void runScript(String script) throws ScriptException

  Throws:

  ScriptException

• runScriptBuffer

  public void runScriptBuffer(String script, javajs.util.SB outputBuffer, boolean isFuncReturn) throws ScriptException

  runs a script immediately and sends selected output to a provided SB

  Parameters:

  outputBuffer -

  script -

  Throws:

  ScriptException

• checkScriptSilent

  public ScriptContext checkScriptSilent(String script)

  a method for just checking a script

  Parameters:

  script -

  Returns:

  a ScriptContext that indicates errors and provides a tokenized version of the script that has passed all syntax checking, both in the compiler and the evaluator

• getContextTrace

  static javajs.util.SB getContextTrace(Viewer vwr, ScriptContext sc, javajs.util.SB sb, boolean isTop)

• setDebugging

  public void setDebugging()

• haltExecution

  public void haltExecution()

• pauseExecution

  public void pauseExecution(boolean withDelay)

• stepPausedExecution

  public void stepPausedExecution()

• resumePausedExecution

  public void resumePausedExecution()

• isExecuting

  public boolean isExecuting()

• isPaused

  public boolean isPaused()

• isStepping

  public boolean isStepping()

• isStopped

  public boolean isStopped()

• getNextStatement

  public String getNextStatement()

  when paused, indicates what statement will be next

  Returns:

  a string indicating the statement

• getCommand

  private String getCommand(int pc, boolean allThisLine, boolean addSemi)

  used for recall of commands in the application console

  Parameters:

  pc -

  allThisLine -

  addSemi -

  Returns:

  a string representation of the command

• logDebugScript

  private void logDebugScript(T[] st, int ifLevel)

• evaluateExpression

  public Object evaluateExpression(Object expr, boolean asVariable, boolean compileOnly)

  a general-use method to evaluate a "SET" type expression.

  Parameters:

  asVariable -

  expr -

  Returns:

  an object of one of the following types: Boolean, Integer, Float, String, Point3f, BitSet

• runBufferedSafely

  public void runBufferedSafely(String script, javajs.util.SB outputBuffer)

• runUserAction

  public static SV runUserAction(String functionName, Object[] params, Viewer vwr)

• evaluate

  private Object evaluate(Object expr, boolean asVariable, boolean compileOnly)

• checkSelect

  public boolean checkSelect(Map<String,SV> h, T[] where)

  Check a map for a WHERE phrase

• getAtomBitSet

  public javajs.util.BS getAtomBitSet(Object atomExpression)

  A general method to evaluate a string representing an atom set. Excepts one atom expression or one per line as "OR". Excepts "()" as "none".

  Parameters:

  atomExpression -

  Returns:

  is a bitset indicating the selected atoms

• compileScript

  public boolean compileScript(String filename, String strScript, boolean debugCompiler)

• fixScriptPath

  private String fixScriptPath(String strScript, String filename)

• setScriptExtensions

  private int setScriptExtensions()

• getScriptFileInternal

  private String getScriptFileInternal(String filename, String localPath, String remotePath, String scriptPath)

  Retrieve the uncompiled script or null if failed

  Parameters:

  filename -

  localPath -

  remotePath -

  scriptPath -

  Returns:

  Jmol script or null

• evalFunctionFloat

  public float evalFunctionFloat(Object func, Object params, float[] values)

• getUserFunctionResult

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

  Throws:

  ScriptException

• runFunctionAndRet

  private SV runFunctionAndRet(JmolScriptFunction function, String name, javajs.util.Lst<SV> params, SV tokenAtom, boolean getReturn, boolean setContextPath, boolean allowThreads) throws ScriptException

  Throws:

  ScriptException

• postProcessTry

  private void postProcessTry(Map<String,SV> cv)

• breakAt

  private void breakAt(int pt)

• restoreFunction

  private void restoreFunction(JmolScriptFunction f, javajs.util.Lst<SV> params, SV tokenAtom) throws ScriptException

  note that functions requiring motion cannot be run in JavaScript

  Parameters:

  f -

  params -

  tokenAtom -

  Throws:

  ScriptException

• clearDefinedVariableAtomSets

  public void clearDefinedVariableAtomSets()

• defineSets

  private void defineSets()

  support for @xxx or define xxx commands

• defineAtomSet

  private void defineAtomSet(String script)

• lookupIdentifierValue

  public javajs.util.BS lookupIdentifierValue(String identifier) throws ScriptException

  Throws:

  ScriptException

• lookupValue

  private javajs.util.BS lookupValue(String setName, boolean plurals) throws ScriptException

  Throws:

  ScriptException

• deleteAtomsInVariables

  public void deleteAtomsInVariables(javajs.util.BS bsDeleted)

• getThisContext

  public ScriptContext getThisContext()

• clearState

  private void clearState(boolean tQuiet)

• pushContextDown

  public void pushContextDown(String why)

• pushContext

  private void pushContext(ContextToken token, String why) throws ScriptException

  Throws:

  ScriptException

• pushContext2

  private void pushContext2(ContextToken token, String why)

• getScriptContext

  public ScriptContext getScriptContext(String why)

• popContext

  void popContext(boolean isFlowCommand, boolean statementOnly)

• restoreScriptContext

  public void restoreScriptContext(ScriptContext context, boolean isPopContext, boolean isFlowCommand, boolean statementOnly)

• setException

  public void setException(ScriptException sx, String msg, String untranslated)

• statementAsString

  public static String statementAsString(Viewer vwr, T[] statement, int iTok, boolean doLogMessages)

• setObjectPropSafe

  public String setObjectPropSafe(String id, int tokCommand)

  called by Viewer in setting up a PyMOL scene.

• setAtomProp

  protected void setAtomProp(String prop, Object value, javajs.util.BS bs)

• restrictSelected

  public void restrictSelected(boolean isBond, boolean doInvert)

• showString

  public void showString(String str)

• showStringPrint

  public void showStringPrint(String s, boolean mustDo)

  Specified by:

  showStringPrint in class ScriptError

• report

  public void report(String s, boolean isError)

• appendBuffer

  private void appendBuffer(String str, boolean mustDo)

• addProcess

  private void addProcess(javajs.util.Lst<T[]> vProcess, int pc, int pt)

• checkContinue

  private boolean checkContinue() throws ScriptException

  checks to see if there is a pause condition, during which commands can still be issued, but with the ! first.

  Returns:

  false if there was a problem

  Throws:

  ScriptException

• delayScript

  public void delayScript(int millis)

• doDelay

  private void doDelay(int millis) throws ScriptException

  Parameters:

  millis - negative here bypasses max check

  Throws:

  ScriptException

• evalParallel

  public boolean evalParallel(ScriptContext context, ShapeManager shapeManager)

• isCommandDisplayable

  private boolean isCommandDisplayable(int i)

  provides support for the script editor

  Parameters:

  i -

  Returns:

  true if displayable (not a } )

• loadFileResourceAsync

  public void loadFileResourceAsync(String fileName) throws ScriptException

  load a static file asynchronously

  Throws:

  ScriptException

• loadFileAsync

  public String loadFileAsync(String prefix, String filename, int i, boolean doClear) throws ScriptException

  Allows asynchronous file loading from the LOAD or SCRIPT command. Saves the context, initiates a FileLoadThread instance. When the file loading completes, the file data (sans filename) is saved in the FileManager cache under cache://localLoad_xxxxx. Context is resumed at this command in the script, and the file is then retrieved from the cache. Only run from JSmol/HTML5 when vwr.isJS; Incompatibilities: LOAD and SCRIPT commands, load() function only; only one "?" per LOAD command

  Parameters:

  prefix -

  filename - or null if end of LOAD command and now just clearing out cache

  i -

  doClear - ensures only one file is in the cache for a given type

  Returns:

  cached file name if it exists

  Throws:

  ScriptException

• cancelFileThread

  private void cancelFileThread()

• logLoadInfo

  private void logLoadInfo(String msg, boolean isData)

• notifyResumeStatus

  public void notifyResumeStatus()

• refresh

  public void refresh(boolean doDelay) throws ScriptException

  Refresh the display NOW

  Parameters:

  doDelay -

  Throws:

  ScriptException

• stopScriptThreads

  public void stopScriptThreads()

• getErrorLineMessage2

  public String getErrorLineMessage2()

• getLinenumber

  public int getLinenumber(ScriptContext c)

• dispatchCommands

  public boolean dispatchCommands(boolean isSpt, boolean fromFunc, boolean isTry) throws ScriptException

  Parameters:

  isSpt -

  fromFunc -

  isTry -

  Returns:

  false only when still working through resumeEval

  Throws:

  ScriptException

• commandLoop

  private void commandLoop(boolean allowJSInterrupt) throws ScriptException

  Throws:

  ScriptException

• notifyScriptEditor

  private void notifyScriptEditor(int pc)

• processCommand

  private void processCommand(int tok) throws ScriptException

  Throws:

  ScriptException

• checkExtension

  private void checkExtension(int tok) throws ScriptException

  Throws:

  ScriptException

• processShapeCommand

  private void processShapeCommand(int tok) throws ScriptException

  Throws:

  ScriptException

• cmdAnimation

  private void cmdAnimation() throws ScriptException

  Throws:

  ScriptException

• setFrameSet

  private void setFrameSet(int i) throws ScriptException

  Throws:

  ScriptException

• cmdAxes

  private void cmdAxes(int index) throws ScriptException

  Throws:

  ScriptException

• cmdBackground

  private void cmdBackground(int i) throws ScriptException

  Throws:

  ScriptException

• cmdBind

  private void cmdBind() throws ScriptException

  Throws:

  ScriptException

• cmdBondorder

  private void cmdBondorder() throws ScriptException

  Throws:

  ScriptException

• cmdBoundbox

  private void cmdBoundbox(int index) throws ScriptException

  Throws:

  ScriptException

• cmdCD

  private void cmdCD() throws ScriptException

  Throws:

  ScriptException

• cmdCenter

  private void cmdCenter(int i) throws ScriptException

  Throws:

  ScriptException

• cmdColor

  private void cmdColor() throws ScriptException

  Throws:

  ScriptException

• cmdDefine

  private void cmdDefine() throws ScriptException

  Throws:

  ScriptException

• cmdDelay

  private void cmdDelay() throws ScriptException

  Throws:

  ScriptException

• cmdDelete

  private void cmdDelete() throws ScriptException

  Throws:

  ScriptException

• cmdDisplay

  private void cmdDisplay(boolean isDisplay) throws ScriptException

  Throws:

  ScriptException

• cmdDots

  private void cmdDots(int iShape) throws ScriptException

  Throws:

  ScriptException

• cmdEcho

  private void cmdEcho(int index) throws ScriptException

  Throws:

  ScriptException

• cmdFile

  private void cmdFile() throws ScriptException

  Throws:

  ScriptException

• cmdFixed

  private void cmdFixed() throws ScriptException

  Throws:

  ScriptException

• cmdFor

  private boolean cmdFor(int tok, boolean isForCheck) throws ScriptException

  Throws:

  ScriptException

• cmdFlow

  private boolean cmdFlow(int tok, boolean isForCheck, javajs.util.Lst<T[]> vProcess) throws ScriptException

  Throws:

  ScriptException

• cmdFlowSwitch

  private int cmdFlowSwitch(ContextToken c, int tok) throws ScriptException

  Throws:

  ScriptException

• cmdFont

  private void cmdFont(int shapeType, float fontsize) throws ScriptException

  Throws:

  ScriptException

• cmdFrank

  private void cmdFrank(int i) throws ScriptException

  Throws:

  ScriptException

• cmdFunc

  private void cmdFunc() throws ScriptException

  Throws:

  ScriptException

• cmdGetProperty

  private void cmdGetProperty() throws ScriptException

  Throws:

  ScriptException

• cmdGoto

  private void cmdGoto(boolean isCmd) throws ScriptException

  Throws:

  ScriptException

• cmdHbond

  private void cmdHbond() throws ScriptException

  Throws:

  ScriptException

• cmdHelp

  private void cmdHelp() throws ScriptException

  Throws:

  ScriptException

• cmdHistory

  private void cmdHistory(int pt) throws ScriptException

  Throws:

  ScriptException

• cmdHover

  private void cmdHover() throws ScriptException

  Throws:

  ScriptException

• cmdLabel

  private void cmdLabel(int index, javajs.util.BS bs) throws ScriptException

  Throws:

  ScriptException

• cmdLoad

  public void cmdLoad() throws ScriptException

  Throws:

  ScriptException

• checkFileExists

  public String checkFileExists(String prefix, boolean isAsync, String filename, int i, boolean doClear) throws ScriptException

  Throws:

  ScriptException

• addFilterAttribute

  private void addFilterAttribute(Map<String,Object> htParams, String filter, String key)

• addLoadData

  private int addLoadData(javajs.util.SB loadScript, String key, Map<String,Object> htParams, int i) throws ScriptException

  Throws:

  ScriptException

• loadPNGJVar

  private void loadPNGJVar(String varName, Object o, Map<String,Object> htParams) throws ScriptException

  Throws:

  ScriptException

• getLoadFilesList

  private String getLoadFilesList(int i, javajs.util.SB loadScript, javajs.util.SB sOptions, Map<String,Object> htParams, javajs.util.Lst<String> fNames) throws ScriptException

  Throws:

  ScriptException

• isLoadOption

  private boolean isLoadOption(int tok)

• getLoadModelIndex

  private int getLoadModelIndex(int i, javajs.util.SB sOptions, Map<String,Object> htParams) throws ScriptException

  Throws:

  ScriptException

• finalizeLoad

  private void finalizeLoad(boolean isAppend, boolean appendNew, boolean isConcat, boolean doOrient, int nFiles, int ac0, int modelCount0, boolean isData) throws ScriptException

  Throws:

  ScriptException

• cmdLog

  private void cmdLog() throws ScriptException

  Throws:

  ScriptException

• cmdLoop

  private void cmdLoop() throws ScriptException

  Throws:

  ScriptException

• cmdMessage

  private void cmdMessage() throws ScriptException

  Throws:

  ScriptException

• cmdModel

  private void cmdModel(int offset) throws ScriptException

  ONE difference between FRAME and MODEL: model 1 sets model NAMED one in the case of PDB frame 1 always sets the first model

  Parameters:

  offset - will be 2 for "anim frame ..."

  Throws:

  ScriptException

• loadDssr

  private void loadDssr(int modelIndex, String data) throws ScriptException

  Throws:

  ScriptException

• cmdMove

  private void cmdMove() throws ScriptException

  Throws:

  ScriptException

• cmdMoveto

  private void cmdMoveto() throws ScriptException

  Throws:

  ScriptException

• isAtomExpression

  public boolean isAtomExpression(int i)

• cmdPause

  private boolean cmdPause() throws ScriptException

  Throws:

  ScriptException

• cmdPrint

  private void cmdPrint() throws ScriptException

  Throws:

  ScriptException

• cmdPrompt

  private void cmdPrompt() throws ScriptException

  Throws:

  ScriptException

• cmdReset

  private void cmdReset() throws ScriptException

  Throws:

  ScriptException

• resetError

  private void resetError()

• cmdRestrict

  private void cmdRestrict() throws ScriptException

  Throws:

  ScriptException

• cmdReturn

  private void cmdReturn(SV tv) throws ScriptException

  Throws:

  ScriptException

• cmdRotate

  public void cmdRotate(boolean isSpin, boolean isSelected) throws ScriptException

  Throws:

  ScriptException

• cmdRestore

  private void cmdRestore() throws ScriptException

  Throws:

  ScriptException

• cmdSave

  private void cmdSave() throws ScriptException

  Throws:

  ScriptException

• cmdScript

  public void cmdScript(int tok, String filename, String theScript) throws ScriptException

  Throws:

  ScriptException

• isMenu

  private boolean isMenu(String s)

• cmdSelect

  private void cmdSelect(int i) throws ScriptException

  Parameters:

  i - 2 from RESTRICT BONDS, otherwise 1

  Throws:

  ScriptException

• cmdSelectionHalos

  private void cmdSelectionHalos(int pt) throws ScriptException

  Throws:

  ScriptException

• cmdSet

  private void cmdSet() throws ScriptException

  Throws:

  ScriptException

• cmdScale

  private void cmdScale(int pt) throws ScriptException

  Throws:

  ScriptException

• cmdSetEcho

  private void cmdSetEcho(int i) throws ScriptException

  Throws:

  ScriptException

• cmdSetLabel

  private boolean cmdSetLabel(String str) throws ScriptException

  Throws:

  ScriptException

• cmdSetPicking

  private void cmdSetPicking() throws ScriptException

  Throws:

  ScriptException

• cmdSetPickingStyle

  private void cmdSetPickingStyle() throws ScriptException

  Throws:

  ScriptException

• cmdSlab

  private void cmdSlab(boolean isDepth) throws ScriptException

  Throws:

  ScriptException

• cmdSsbond

  private void cmdSsbond() throws ScriptException

  Throws:

  ScriptException

• cmdStructure

  private void cmdStructure() throws ScriptException

  Throws:

  ScriptException

• cmdSubset

  private void cmdSubset() throws ScriptException

  Throws:

  ScriptException

• cmdSync

  private void cmdSync() throws ScriptException

  Throws:

  ScriptException

• cmdThrow

  private void cmdThrow() throws ScriptException

  Throws:

  ScriptException

• saveContext

  private ScriptContext saveContext(String saveName)

• cmdTimeout

  private void cmdTimeout(int index) throws ScriptException

  Throws:

  ScriptException

• cmdTranslate

  private void cmdTranslate(boolean isSelected) throws ScriptException

  Throws:

  ScriptException

• cmdUnbind

  private void cmdUnbind() throws ScriptException

  Throws:

  ScriptException

• cmdUndoRedo

  public void cmdUndoRedo(int tok) throws ScriptException

  Throws:

  ScriptException

• setModelCagePts

  public void setModelCagePts(int iModel, javajs.util.T3[] originABC, String name)

• cmdUnitcell

  private void cmdUnitcell(int i) throws ScriptException

  Throws:

  ScriptException

• cmdVector

  private void cmdVector() throws ScriptException

  Throws:

  ScriptException

• cmdVibration

  private void cmdVibration() throws ScriptException

  Throws:

  ScriptException

• cmdWireframe

  private void cmdWireframe() throws ScriptException

  Throws:

  ScriptException

• cmdZap

  private void cmdZap(boolean isZapCommand) throws ScriptException

  Throws:

  ScriptException

• cmdZoom

  private void cmdZoom(boolean isZoomTo) throws ScriptException

  Throws:

  ScriptException

• colorShape

  private void colorShape(int shapeType, int index, boolean isBackground) throws ScriptException

  Throws:

  ScriptException

• getPartialCharges

  public void getPartialCharges(javajs.util.BS bs) throws ScriptException

  Throws:

  ScriptException

• encodeRadiusParameter

  public RadiusData encodeRadiusParameter(int index, boolean isOnly, boolean allowAbsolute) throws ScriptException

  Throws:

  ScriptException

• expandFloatArray

  public Object expandFloatArray(float[] a, int min, boolean asBS) throws ScriptException

  Accepts a float array and expands [1 -3] to [1 2 3], for example.

  Parameters:

  a -

  min -

  asBS -

  Returns:

  float[] or BS

  Throws:

  ScriptException

• frameControl

  private void frameControl(int i) throws ScriptException

  Throws:

  ScriptException

• getColorRange

  public String getColorRange(int i) throws ScriptException

  Throws:

  ScriptException

• getFullPathName

  public String getFullPathName(boolean withType) throws ScriptException

  Throws:

  ScriptException

• getObjectBoundingBox

  private javajs.util.P3[] getObjectBoundingBox(String id)

• getObjectCenter

  protected javajs.util.P3 getObjectCenter(String axisID, int index, int modelIndex)

• getPlaneForObject

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

• getQuaternionArray

  public javajs.util.Quat[] getQuaternionArray(Object quaternionOrSVData, int itype)

• getSetAxesTypeMad10

  public int getSetAxesTypeMad10(int index) throws ScriptException

  Throws:

  ScriptException

• getSettingFloat

  private float getSettingFloat(int pt) throws ScriptException

  Throws:

  ScriptException

• getSettingInt

  private int getSettingInt(int pt) throws ScriptException

  Throws:

  ScriptException

• getSettingStr

  private String getSettingStr(int pt, boolean isJmolSet) throws ScriptException

  Accept an unquoted string if there is just one parameter regardless of its type. In other words, these commands cannot accept a variable name by itself.

  Parameters:

  pt -

  isJmolSet -

  Returns:

  string parameter

  Throws:

  ScriptException

• getShapeProperty

  public Object getShapeProperty(int shapeType, String propertyName)

• getShapePropertyData

  public boolean getShapePropertyData(int shapeType, String propertyName, Object[] data)

• getShapeType

  private int getShapeType(int tok) throws ScriptException

  Throws:

  ScriptException

• getTranslucentLevel

  public float getTranslucentLevel(int i) throws ScriptException

  Throws:

  ScriptException

• getZoom

  private float getZoom(int ptCenter, int i, javajs.util.BS bs, float currentZoom) throws ScriptException

  Throws:

  ScriptException

• setElementColor

  private boolean setElementColor(String str, int argb)

• setMeshDisplayProperty

  public boolean setMeshDisplayProperty(int shape, int i, int tok) throws ScriptException

  Parameters:

  shape -

  i -

  tok -

  Returns:

  true if successful

  Throws:

  ScriptException

• setObjectArgb

  private void setObjectArgb(String str, int argb)

• setObjectMad10

  public void setObjectMad10(int iShape, String name, int mad10)

• setObjectProp

  private String setObjectProp(String id, int tokCommand, int ptColor) throws ScriptException

  Throws:

  ScriptException

• setObjectProperty

  public String setObjectProperty() throws ScriptException

  Throws:

  ScriptException

• setShapeNameParameter

  public String setShapeNameParameter(int i) throws ScriptException

  Throws:

  ScriptException

• setShapeProperty

  public void setShapeProperty(int shapeType, String propertyName, Object propertyValue)

• setShapePropertyBs

  public void setShapePropertyBs(int iShape, String propertyName, Object propertyValue, javajs.util.BS bs)

• setShapeSize

  private void setShapeSize(int shapeType, RadiusData rd)

• setShapeSizeBs

  public void setShapeSizeBs(int shapeType, int size, javajs.util.BS bs)

• setShapeTranslucency

  public void setShapeTranslucency(int shapeType, String prefix, String translucency, float translucentLevel, javajs.util.BS bs)

• setSize

  private void setSize(int shape, float scale) throws ScriptException

  Throws:

  ScriptException

• setSizeBio

  private void setSizeBio(int iShape) throws ScriptException

  Throws:

  ScriptException

• setUnits

  private boolean setUnits(String units, int tok) throws ScriptException

  Throws:

  ScriptException

• toString

  public String toString()

  Overrides:

  toString in class Object