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)

• evaluateCompiledScript

  public void evaluateCompiledScript(Object[] params, boolean isCmdLine_c_or_C_Option, boolean isCmdLine_C_Option, boolean historyDisabled, boolean listCommands, SB outputBuffer, boolean allowThreads)

• useThreads

  public boolean useThreads(boolean allowWaitFor)

• 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 -

• runScript

  public void runScript(String script) throws ScriptException

  Throws:

  ScriptException

• runScriptBuffer

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

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

  Parameters:

  script -

  outputBuffer -

  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

• 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

• evaluateExpression

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

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

  Parameters:

  expr -

  asVariable -

  Returns:

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

• runBufferedSafely

  public void runBufferedSafely(String script, SB outputBuffer)

• runUserAction

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

• checkSelect

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

  Check a map for a WHERE phrase

• getAtomBitSet

  public 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)

• evalFunctionFloat

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

• getUserFunctionResult

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

  Throws:

  ScriptException

• clearDefinedVariableAtomSets

  public void clearDefinedVariableAtomSets()

• lookupIdentifierValue

  public BS lookupIdentifierValue(String identifier) throws ScriptException

  Throws:

  ScriptException

• deleteAtomsInVariables

  public void deleteAtomsInVariables(BS bsDeleted)

• getThisContext

  public ScriptContext getThisContext()

• pushContextDown

  public void pushContextDown(String why)

• getScriptContext

  public ScriptContext getScriptContext(String why)

• 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, 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)

• delayScript

  public void delayScript(int millis)

• evalParallel

  public boolean evalParallel(ScriptContext context, ShapeManager shapeManager)

• 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

• 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

• 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

• isAtomExpression

  public boolean isAtomExpression(int i)

• cmdRotate

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

  Throws:

  ScriptException

• cmdScript

  public void cmdScript(int tok, String filename, String theScript, Lst<SV> params) throws ScriptException

  Throws:

  ScriptException

• cmdUndoRedo

  public void cmdUndoRedo(int tok) throws ScriptException

  Throws:

  ScriptException

• getPartialCharges

  public void getPartialCharges(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

• getColorRange

  public String getColorRange(int i) throws ScriptException

  Throws:

  ScriptException

• getFullPathName

  public String getFullPathName(boolean withType) throws ScriptException

  Throws:

  ScriptException

• getObjectBoundingBox

  public P3[] getObjectBoundingBox(String id)

• getObjectCenter

  protected P3 getObjectCenter(String axisID, int index, int modelIndex)

• getPlaneForObject

  protected P4 getPlaneForObject(String id, V3 vAB)

• getQuaternionArray

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

• getSetAxesTypeMad10

  public int getSetAxesTypeMad10(int index) throws ScriptException

  Throws:

  ScriptException

• getShapeProperty

  public Object getShapeProperty(int shapeType, String propertyName)

• getShapePropertyData

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

• getTranslucentLevel

  public float getTranslucentLevel(int i) throws ScriptException

  Throws:

  ScriptException

• setMeshDisplayProperty

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

  Parameters:

  shape -

  i -

  tok -

  Returns:

  true if successful

  Throws:

  ScriptException

• setObjectMad10

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

• 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, BS bs)

• setShapeSizeBs

  public void setShapeSizeBs(int shapeType, int size, BS bs)

• setShapeTranslucency

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

• toString

  public String toString()

  Overrides:

  toString in class Object

• getCurrentModelFileAsString

  public String getCurrentModelFileAsString(String fname)

• getCmdExt

  public CmdExt getCmdExt()

• getIsoExt

  public IsoExt getIsoExt()

• getMathExt

  public MathExt getMathExt()

• getSmilesExt

  public SmilesExt getSmilesExt()

• parameterExpressionList

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

  Throws:

  ScriptException

• parameterExpressionString

  protected 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(Map<String,SV> h, T[] where) throws ScriptException

  Throws:

  ScriptException

• atomExpressionAt

  public BS atomExpressionAt(int index) throws ScriptException

  Throws:

  ScriptException

• atomExpression

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

  Parameters:

  code -

  pcStart -

  pcStop -

  allowRefresh -

  allowUnderflow -

  ret - -- true return value; may not be a BS

  andNotDeleted - IGNORED

  Returns:

  atom bitset

  Throws:

  ScriptException

• noCopy

  protected boolean noCopy(int i, int dir)

• getAssocArray

  protected Map<String,Object> getAssocArray(int i) throws ScriptException

  Throws:

  ScriptException

• listBS

  protected 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)

• getBitsetPropertyFloat

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

  Throws:

  ScriptException

• getBitsetProperty

  public Object getBitsetProperty(BS bs, Lst<SV> pts, int tok, P3 ptRef, P4 planeRef, Object tokenValue, Object opValue, boolean useAtomMap, int index, boolean asVectorIfAll) throws ScriptException

  Throws:

  ScriptException

• getAtomBits

  protected BS getAtomBits(int tokType, Object specInfo)

• getSeqCode

  protected static int getSeqCode(T instruction)

• setVariable

  public SV setVariable(int pt, int ptMax, 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

• setStatement

  protected boolean setStatement(T[] st0, int pt0) 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]

  pt0 -

  Returns:

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

  Throws:

  ScriptException

• isFunction

  protected boolean isFunction(String sf)

• addFunction

  protected void addFunction(ScriptFunction f)

• getFunction

  protected ScriptFunction getFunction(String sf)