org.jmol.viewer
Class Eval
class
Eval
extends Object
Method Summary |
void | animation() |
void | animationDirection() |
void | animationMode() |
void | assignBitsetVariable(String variable, BitSet bs) |
Point3f | atomCenterOrCoordinateParameter(int i) |
float | atomProperty(Atom atom, int tokWhat, boolean asInt) |
void | axes(int index) |
void | background(int i) |
Object | bitsetTokenVector(Object v) |
BitSet | bitSetForModelFileNumber(int m) |
void | bondorder() |
boolean | booleanParameter(int i) |
void | boundbox(int index) |
void | calculate() |
void | center(int i) |
void | centerAt() |
Point3f | centerParameter(int i) |
boolean | changeElementColor(String str, int argb) |
boolean | checkContinue() |
void | checkLength(int length) |
void | checkLength(int length, int errorPt) |
int | checkLength23() |
void | checkLength34() |
Object | checkScriptSilent(String script) |
boolean | checkToken(int i) |
void | clearDefinitionsAndLoadPredefined() |
void | clearPredefined(String[] list) |
void | clearState(boolean tQuiet) |
void | color() |
void | colorObject(int tokObject, int index) |
static int | colorPtToInt(Point3f pt) |
void | colorShape(int shapeType, int index, boolean isBackground) |
BitSet | comparatorInstruction(int tokWhat, float[] data, int tokOperator, int comparisonValue, float comparisonFloat) |
void | configuration() |
void | connect() |
void | console() |
String | contextTrace() |
void | data() |
void | dataFrame(int datatype) |
void | define() |
void | delay() |
void | delay(long millis) |
void | delete() |
void | deleteAtomsInVariables(BitSet bsDeleted) |
void | dipole() |
void | display(boolean isDisplay) |
void | dots(int iShape) |
void | draw() |
void | echo(int index, boolean isImage) |
void | ellipsoid() |
void | error(int error) |
void | error(int error, String value) |
void | error(int error, String value, String more) |
boolean | error(int error, String value, String more, boolean warningOnly) |
void | evalError(String message) |
static Object | evaluateExpression(Viewer viewer, Object expr)
a general-use method to evaluate a "SET" type expression. |
BitSet | expression(int index) |
BitSet | expression(Token[] code, int pcStart, int pcStop, boolean allowRefresh, boolean allowUnderflow, boolean mustBeBitSet, boolean andNotDeleted) |
String | extractCommandOption(String name) |
void | file() |
float | floatParameter(int i, float min, float max) |
float | floatParameter(int index) |
int | floatParameterSet(int i, float[] fparams) |
float | floatSetting(int pt, float min, float max) |
float | floatSetting(int pt) |
void | flowControl(int tok) |
void | font(int shapeType, float fontsize) |
void | frame(int offset) |
void | frameControl(int i, boolean isSubCmd) |
void | frank(int index) |
void | function() |
int | getArgbParam(int index) |
int | getArgbParam(int index, boolean allowNone) |
int | getArgbParamLast(int index, boolean allowNone) |
BitSet | getAtomBits(int tokType, Object specInfo) |
static BitSet | getAtomBitSet(Eval e, Viewer viewer, Object atomExpression) |
static Vector | getAtomBitSetVector(Eval e, Viewer viewer, Object atomExpression) |
String | getBitsetIdent(BitSet bs, String label, Object tokenValue, boolean useAtomMap) |
protected Object | getBitsetProperty(BitSet bs, int tok, Point3f ptRef, Point4f planeRef, Object tokenValue, Object opValue, boolean useAtomMap, int ptAtom) |
Token | getBitsetPropertySelector(int i, boolean mustBeSettable) |
int | getColorTriad(int i) |
String | getCommand(int pc) |
Token | getContextVariableAsToken(String var) |
Vector3f | getDrawObjectAxis(String axisID) |
Point3f | getDrawObjectCenter(String axisID) |
String | getErrorMessage() |
int | getExecutionWalltime() |
String | getFullPathName() |
Function | getFunction(String name) |
String | getFunctionCalls(String selectedFunction) |
Token | getFunctionReturn(String name, Vector params) |
String | getIsosurfaceJvxl() |
int | getLinenumber() |
int | getMadParameter() |
MinimizerInterface | getMinimizer() |
String | getMoJvxl(int ptMO) |
String | getNextComment() |
Object | getNumericParameter(String var) |
Object | getParameter(String var, boolean asToken) |
String | getParameterEscaped(String var) |
Point3f | getPoint3f(int i, boolean allowFractional) |
Point4f | getPoint4f(int i) |
Object | getPointOrPlane(int index, boolean integerOnly, boolean allowFractional, boolean doConvert, boolean implicitFractional, int minDim, int maxDim) |
void | getProperty() |
String | getScript() |
static int | getSeqCode(Token instruction) |
int | getSetAxesTypeMad(int index) |
String | getShapeNameParameter(int i) |
int | getShapeType(int tok) |
String | getState() |
Object | getStringObjectAsToken(String s, String key) |
SymmetryInterface | getSymmetry() |
Token | getToken(int i) |
float | getTranslucentLevel(int i) |
float | getZoomFactor(int i, int ptCenter, float radius, float factor0) |
void | gotocmd() |
void | haltExecution() |
void | hbond(boolean isCommand) |
void | help() |
void | history(int pt) |
Point4f | hklParameter(int i) |
void | hover() |
boolean | ifCmd() |
void | initIsosurface(int iShape) |
boolean | insertArrayValue(String key, Token result) |
void | instructionDispatchLoop(boolean doList) |
void | integerOutOfRange(int min, int max) |
int | intParameter(int index) |
int | intParameter(int i, int min, int max) |
int | intSetting(int pt, int val, int min, int max) |
int | intSetting(int pt) |
void | invertSelected() |
boolean | isCenterParameter(int i) |
boolean | isColorParam(int i) |
boolean | isExecutionPaused() |
boolean | isFloatParameter(int index) |
void | isosurface(int iShape) |
boolean | isPoint3f(int i) |
boolean | isScriptExecuting() |
void | label(int index) |
void | lcaoCartoon() |
boolean | listIsosurface(int iShape) |
void | load() |
boolean | loadError(String msg) |
boolean | loadFunction(String name, Vector params) |
boolean | loadScript(String filename, String script, boolean debugCompiler) |
boolean | loadScriptFile(String filename, boolean tQuiet) |
boolean | loadScriptFileInternal(String filename) |
boolean | loadScriptString(String script, boolean tQuiet) |
void | logDebugScript(int ifLevel) |
BitSet | lookupIdentifierValue(String identifier) |
BitSet | lookupValue(String variable, boolean plurals) |
void | message() |
void | minimize() |
boolean | mo(boolean isInitOnly) |
int | modelNumberParameter(int index) |
void | monitor() |
int | moOffset(int index) |
void | move() |
void | moveto() |
void | navigate() |
void | numberOutOfRange(float min, float max) |
String | objectNameParameter(int index) |
String | optParameterAsString(int i) |
String | parameterAsString(int i) |
Object | parameterExpression(int pt, int ptMax, String key, boolean asVector) |
Object | parameterExpression(int pt, int ptMax, String key, boolean asVector, int ptAtom, Hashtable localVars, String localVar) |
void | pause() |
void | pauseExecution() |
void | planeExpected() |
Point4f | planeParameter(int i) |
void | pmesh() |
void | pointGroup() |
void | polyhedra() |
void | popContext() |
void | predefine(String script) |
void | print() |
void | proteinShape(int shapeType) |
void | pushContext(Function function) |
float | radiusParameter(int index, float defaultValue)
Based on the form of the parameters, returns and encoded radius
as follows:
script meaning range encoded
+1.2 offset [0 - 10] x
-1.2 offset 0) x
1.2 absolute (0 - 10] x + 10
-30% 70% (-100 - 0) x + 200
+30% 130% (0 x + 200
80% percent (0 x + 100
in each case, numbers can be integer or float
|
void | refresh() |
void | reset() |
void | restore() |
void | restrict() |
void | restrictSelected(boolean doInvert) |
void | resumePausedExecution() |
void | returnCmd() |
void | rotate(boolean isSpin, boolean isSelected) |
void | runEval(boolean checkScriptOnly, boolean openFiles, boolean historyDisabled, boolean listCommands) |
void | runScript(String script) |
void | runScript(String script, StringBuffer outputBuffer) |
void | save() |
void | script(int tok) |
void | scriptStatus(String s) |
void | select() |
void | selectionHalo(int pt) |
void | set() |
void | setAtomShapeSize(int shape, int defOn) |
void | setBitsetProperty(BitSet bs, int tok, int iValue, float fValue, Token tokenValue) |
void | setBondmode() |
void | setBooleanProperty(String key, boolean value) |
String | setColorOptions(int index, int iShape, int nAllowed) |
void | setEcho() |
static String | setErrorLineMessage(String filename, int lineCurrent, int pcCurrent, String lineInfo) |
void | setErrorMessage(String err) |
boolean | setFloatProperty(String key, float value) |
void | setHbond() |
boolean | setIntProperty(String key, int value) |
boolean | setLabel(String str) |
boolean | setMeasurementUnits(String units) |
boolean | setMeshDisplayProperty(int shape, int i, int tok) |
void | setMoData(int shape, int moNumber, int offset, int modelIndex, String title) |
void | setMonitor() |
String | setObjectProperty() |
boolean | setParameter(String key, int intVal, boolean isJmolSet, boolean showing) |
void | setPicking() |
void | setPickingStyle() |
void | setProperty() |
int | setShapeId(int iShape, int i, boolean idSeen) |
void | setShapeProperty(int shapeType, String propertyName, Object propertyValue) |
void | setShapeSize(int shapeType, int size) |
void | setShapeTranslucency(int shapeType, String prefix, String translucency, float translucentLevel, BitSet bs) |
void | setSpin(String key, int value) |
void | setSsbond() |
boolean | setStatement(int pc) |
void | setStringProperty(String key, String value) |
void | setUserColors() |
void | setVariable(int pt, int ptMax, String key, boolean showing) |
void | show() |
void | showString(String str) |
void | slab(boolean isDepth) |
void | ssbond() |
String | statementAsString() |
void | stereo() |
String | stringParameter(int index) |
String | stringSetting(int pt, boolean isJmolSet) |
void | structure() |
void | subset() |
void | sync() |
int | tokAt(int i) |
int | tokAt(int i, Token[] args) |
Token | tokenAt(int i, Token[] args) |
Token | tokenSetting(int pt) |
String | toString() |
void | translate() |
void | translateSelected() |
void | unitcell(int index) |
void | vector() |
void | vibration() |
boolean | warning(int error, String value, String more) |
void | wireframe() |
String | write(Token[] args) |
Point3f | xypParameter(int index) |
void | zap(boolean isZapCommand) |
void | zoom(boolean isZoomTo) |
private
Token[][] aatoken
private int commandHistoryLevelMax
private Hashtable contextVariables
private boolean coordinatesAreFractional
private Thread currentThread
private Object[] data
private boolean debugScript
private boolean error
private String errorMessage
static final String[] errors
private Boolean executionPaused
private Object expressionResult
static final int ERROR_axisExpected
static final int ERROR_badArgumentCount
static final int ERROR_badMillerIndices
static final int ERROR_badRGBColor
static final int ERROR_booleanExpected
static final int ERROR_booleanOrNumberExpected
static final int ERROR_booleanOrWhateverExpected
static final int ERROR_colorExpected
static final int ERROR_colorOrPaletteRequired
static final int ERROR_coordinateOrNameOrExpressionRequired
static final int ERROR_drawObjectNotDefined
static final int ERROR_endOfStatementUnexpected
static final int ERROR_expressionExpected
static final int ERROR_expressionOrIntegerExpected
static final int ERROR_filenameExpected
static final int ERROR_fileNotFoundException
static final int ERROR_incompatibleArguments
static final int ERROR_insufficientArguments
static final int ERROR_integerExpected
static final int ERROR_integerOutOfRange
static final int ERROR_invalidArgument
static final int ERROR_invalidParameterOrder
static final int ERROR_keywordExpected
static final int ERROR_multipleModelsNotOK
static final int ERROR_noUnitCell
static final int ERROR_numberExpected
static final int ERROR_numberMustBe
static final int ERROR_numberOutOfRange
static final int ERROR_objectNameExpected
static final int ERROR_propertyNameExpected
static final int ERROR_spaceGroupNotFound
static final int ERROR_stringExpected
static final int ERROR_stringOrIdentifierExpected
static final int ERROR_tooManyScriptLevels
static final int ERROR_unrecognizedAtomProperty
static final int ERROR_unrecognizedBondProperty
static final int ERROR_unrecognizedCommand
static final int ERROR_unrecognizedExpression
static final int ERROR_unrecognizedObject
static final int ERROR_unrecognizedParameter
static final int ERROR_unrecognizedParameterWarning
static final int ERROR_unrecognizedShowParameter
static final int ERROR_what
private static final String EXPRESSION_KEY
private String filename
private boolean fileOpenCheck
private String fullCommand
private String functionName
private boolean historyDisabled
private boolean ignoreError
private Boolean interruptExecution
private boolean isBondSet
private boolean isExecuting
boolean isForCheck
boolean isScriptCheck
private boolean isStateScript
boolean isSyntaxCheck
int iToken
private int lastMoNumber
private int lineEnd
private int[] lineIndices
private short[] lineNumbers
boolean logMessages
private StringBuffer outputBuffer
private int pc
private int pcEnd
private String script
private int scriptLevel
private static final int scriptLevelMax
private int scriptReportingLevel
private
Token[] statement
private int statementLength
private final StringBuffer strbufLog
static final String SCRIPT_COMPLETED
private
Token[] tempStatement
private int theTok
private String thisCommand
private long timeBeginExecution
private long timeEndExecution
private boolean tQuiet
private Hashtable variables
private void animation()
private void animationDirection()
private void animationMode()
private void assignBitsetVariable(String variable, BitSet bs)
private Point3f atomCenterOrCoordinateParameter(int i)
private float atomProperty(
Atom atom, int tokWhat, boolean asInt)
private void axes(int index)
private void background(int i)
Object bitsetTokenVector(Object v)
BitSet bitSetForModelFileNumber(int m)
private void bondorder()
private boolean booleanParameter(int i)
private void boundbox(int index)
private void calculate()
private void center(int i)
private void centerAt()
private Point3f centerParameter(int i)
private boolean changeElementColor(String str, int argb)
private boolean checkContinue()
private void checkLength(int length)
private void checkLength(int length, int errorPt)
private int checkLength23()
private void checkLength34()
Object checkScriptSilent(String script)
private boolean checkToken(int i)
void clearDefinitionsAndLoadPredefined()
private void clearPredefined(String[] list)
private void clearState(boolean tQuiet)
private void color()
private void colorObject(int tokObject, int index)
static int colorPtToInt(Point3f pt)
private void colorShape(int shapeType, int index, boolean isBackground)
private BitSet comparatorInstruction(int tokWhat, float[] data, int tokOperator, int comparisonValue, float comparisonFloat)
private void configuration()
private void connect()
private void console()
String contextTrace()
private void data()
private void dataFrame(int datatype)
private void define()
private void delay()
private void delay(long millis)
private void delete()
void deleteAtomsInVariables(BitSet bsDeleted)
private void dipole()
private void display(boolean isDisplay)
private void dots(int iShape)
private void draw()
private void echo(int index, boolean isImage)
private void ellipsoid()
void error(int error)
void error(int error, String value)
void error(int error, String value, String more)
boolean error(int error, String value, String more, boolean warningOnly)
void evalError(String message)
static Object evaluateExpression(
Viewer viewer, Object expr)
a general-use method to evaluate a "SET" type expression.
Parameters: viewer expr
Returns: an object of one of the following types:
Boolean, Integer, Float, String, Point3f, BitSet
private BitSet expression(int index)
private BitSet expression(
Token[] code, int pcStart, int pcStop, boolean allowRefresh, boolean allowUnderflow, boolean mustBeBitSet, boolean andNotDeleted)
private String extractCommandOption(String name)
private void file()
private float floatParameter(int i, float min, float max)
private float floatParameter(int index)
private int floatParameterSet(int i, float[] fparams)
private float floatSetting(int pt, float min, float max)
private float floatSetting(int pt)
private void flowControl(int tok)
private void font(int shapeType, float fontsize)
private void frame(int offset)
private void frameControl(int i, boolean isSubCmd)
private void frank(int index)
private void function()
private int getArgbParam(int index)
private int getArgbParam(int index, boolean allowNone)
private int getArgbParamLast(int index, boolean allowNone)
private BitSet getAtomBits(int tokType, Object specInfo)
static BitSet getAtomBitSet(
Eval e,
Viewer viewer, Object atomExpression)
static Vector getAtomBitSetVector(
Eval e,
Viewer viewer, Object atomExpression)
String getBitsetIdent(BitSet bs, String label, Object tokenValue, boolean useAtomMap)
protected Object getBitsetProperty(BitSet bs, int tok, Point3f ptRef, Point4f planeRef, Object tokenValue, Object opValue, boolean useAtomMap, int ptAtom)
private
Token getBitsetPropertySelector(int i, boolean mustBeSettable)
private int getColorTriad(int i)
private String getCommand(int pc)
private
Token getContextVariableAsToken(String var)
private Vector3f getDrawObjectAxis(String axisID)
private Point3f getDrawObjectCenter(String axisID)
String getErrorMessage()
int getExecutionWalltime()
private String getFullPathName()
private
Function getFunction(String name)
private String getFunctionCalls(String selectedFunction)
Token getFunctionReturn(String name, Vector params)
private String getIsosurfaceJvxl()
private int getLinenumber()
private int getMadParameter()
private String getMoJvxl(int ptMO)
private String getNextComment()
private Object getNumericParameter(String var)
private Object getParameter(String var, boolean asToken)
private String getParameterEscaped(String var)
private Point3f getPoint3f(int i, boolean allowFractional)
private Point4f getPoint4f(int i)
private Object getPointOrPlane(int index, boolean integerOnly, boolean allowFractional, boolean doConvert, boolean implicitFractional, int minDim, int maxDim)
private void getProperty()
String getScript()
private static int getSeqCode(
Token instruction)
private int getSetAxesTypeMad(int index)
private String getShapeNameParameter(int i)
private int getShapeType(int tok)
String getState()
private Object getStringObjectAsToken(String s, String key)
private
Token getToken(int i)
private float getTranslucentLevel(int i)
private float getZoomFactor(int i, int ptCenter, float radius, float factor0)
private void gotocmd()
void haltExecution()
private void hbond(boolean isCommand)
private void help()
private void history(int pt)
private Point4f hklParameter(int i)
private void hover()
private boolean ifCmd()
private void initIsosurface(int iShape)
private boolean insertArrayValue(String key,
Token result)
private void instructionDispatchLoop(boolean doList)
private void integerOutOfRange(int min, int max)
private int intParameter(int index)
private int intParameter(int i, int min, int max)
private int intSetting(int pt, int val, int min, int max)
private int intSetting(int pt)
private void invertSelected()
private boolean isCenterParameter(int i)
private boolean isColorParam(int i)
boolean isExecutionPaused()
private boolean isFloatParameter(int index)
private void isosurface(int iShape)
private boolean isPoint3f(int i)
boolean isScriptExecuting()
private void label(int index)
private void lcaoCartoon()
private boolean listIsosurface(int iShape)
private void load()
private boolean loadError(String msg)
private boolean loadFunction(String name, Vector params)
private boolean loadScript(String filename, String script, boolean debugCompiler)
boolean loadScriptFile(String filename, boolean tQuiet)
private boolean loadScriptFileInternal(String filename)
boolean loadScriptString(String script, boolean tQuiet)
private void logDebugScript(int ifLevel)
private BitSet lookupIdentifierValue(String identifier)
private BitSet lookupValue(String variable, boolean plurals)
private void message()
private void minimize()
private boolean mo(boolean isInitOnly)
private int modelNumberParameter(int index)
private void monitor()
private int moOffset(int index)
private void move()
private void moveto()
private void navigate()
private void numberOutOfRange(float min, float max)
private String objectNameParameter(int index)
private String optParameterAsString(int i)
private String parameterAsString(int i)
private Object parameterExpression(int pt, int ptMax, String key, boolean asVector)
private Object parameterExpression(int pt, int ptMax, String key, boolean asVector, int ptAtom, Hashtable localVars, String localVar)
private void pause()
void pauseExecution()
private void planeExpected()
private Point4f planeParameter(int i)
private void pmesh()
private void pointGroup()
private void polyhedra()
private void popContext()
private void predefine(String script)
private void print()
private void proteinShape(int shapeType)
private void pushContext(
Function function)
private float radiusParameter(int index, float defaultValue)
Based on the form of the parameters, returns and encoded radius
as follows:
script meaning range encoded
+1.2 offset [0 - 10] x
-1.2 offset 0) x
1.2 absolute (0 - 10] x + 10
-30% 70% (-100 - 0) x + 200
+30% 130% (0 x + 200
80% percent (0 x + 100
in each case, numbers can be integer or float
Parameters: index defaultValue a default value or Float.NaN
Returns: one of the above possibilities
Throws: ScriptException
private void refresh()
private void reset()
private void restore()
private void restrict()
private void restrictSelected(boolean doInvert)
void resumePausedExecution()
private void returnCmd()
private void rotate(boolean isSpin, boolean isSelected)
void runEval(boolean checkScriptOnly, boolean openFiles, boolean historyDisabled, boolean listCommands)
private void runScript(String script)
void runScript(String script, StringBuffer outputBuffer)
private void save()
private void script(int tok)
private void scriptStatus(String s)
private void select()
private void selectionHalo(int pt)
private void set()
private void setAtomShapeSize(int shape, int defOn)
private void setBitsetProperty(BitSet bs, int tok, int iValue, float fValue,
Token tokenValue)
private void setBondmode()
private void setBooleanProperty(String key, boolean value)
private String setColorOptions(int index, int iShape, int nAllowed)
private void setEcho()
static String setErrorLineMessage(String filename, int lineCurrent, int pcCurrent, String lineInfo)
private void setErrorMessage(String err)
private boolean setFloatProperty(String key, float value)
private void setHbond()
private boolean setIntProperty(String key, int value)
private boolean setLabel(String str)
private boolean setMeasurementUnits(String units)
private boolean setMeshDisplayProperty(int shape, int i, int tok)
private void setMoData(int shape, int moNumber, int offset, int modelIndex, String title)
private void setMonitor()
private String setObjectProperty()
private boolean setParameter(String key, int intVal, boolean isJmolSet, boolean showing)
private void setPicking()
private void setPickingStyle()
private void setProperty()
private int setShapeId(int iShape, int i, boolean idSeen)
private void setShapeProperty(int shapeType, String propertyName, Object propertyValue)
private void setShapeSize(int shapeType, int size)
private void setShapeTranslucency(int shapeType, String prefix, String translucency, float translucentLevel, BitSet bs)
private void setSpin(String key, int value)
private void setSsbond()
private boolean setStatement(int pc)
private void setStringProperty(String key, String value)
private void setUserColors()
private void setVariable(int pt, int ptMax, String key, boolean showing)
private void show()
private void showString(String str)
private void slab(boolean isDepth)
private void ssbond()
private String statementAsString()
private void stereo()
private String stringParameter(int index)
private String stringSetting(int pt, boolean isJmolSet)
private void structure()
private void subset()
private void sync()
private int tokAt(int i)
private int tokAt(int i,
Token[] args)
private
Token tokenSetting(int pt)
public String toString()
private void translate()
private void translateSelected()
private void unitcell(int index)
private void vector()
private void vibration()
private boolean warning(int error, String value, String more)
private void wireframe()
String write(
Token[] args)
private Point3f xypParameter(int index)
private void zap(boolean isZapCommand)
private void zoom(boolean isZoomTo)