Package org.jmol.script
Class ScriptParam
- java.lang.Object
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- org.jmol.script.ScriptError
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- org.jmol.script.ScriptParam
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- All Implemented Interfaces:
JmolScriptEvaluator
- Direct Known Subclasses:
ScriptExpr
public abstract class ScriptParam extends ScriptError
The ScriptParam class holds methods used to parse parameters in Jmol scripts.
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Field Summary
Fields Modifier and Type Field Description Map<String,SV>
contextVariables
boolean
coordinatesAreFractional
javajs.util.P3
fractionalPoint
boolean
isBondSet
int
iToken
javajs.util.P3
pt1
javajs.util.P3
pt2
javajs.util.P3
pt3
int
slen
T[]
st
int
theTok
T
theToken
ScriptContext
thisContext
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Fields inherited from class org.jmol.script.ScriptError
chk, error, ERROR_axisExpected, ERROR_backgroundModelError, ERROR_badArgumentCount, ERROR_badMillerIndices, ERROR_badRGBColor, ERROR_booleanExpected, ERROR_booleanOrNumberExpected, ERROR_booleanOrWhateverExpected, ERROR_cannotSet, ERROR_colorExpected, ERROR_colorOrPaletteRequired, ERROR_commandExpected, ERROR_coordinateOrNameOrExpressionRequired, ERROR_drawObjectNotDefined, ERROR_endOfStatementUnexpected, ERROR_expressionExpected, ERROR_expressionOrIntegerExpected, ERROR_filenameExpected, ERROR_fileNotFoundException, ERROR_incompatibleArguments, ERROR_insufficientArguments, ERROR_integerExpected, ERROR_integerOutOfRange, ERROR_invalidArgument, ERROR_invalidParameterOrder, ERROR_keywordExpected, ERROR_moCoefficients, ERROR_moIndex, ERROR_moModelError, ERROR_moOccupancy, ERROR_moOnlyOne, ERROR_multipleModelsDisplayedNotOK, ERROR_multipleModelsNotOK, ERROR_noData, ERROR_noPartialCharges, ERROR_noUnitCell, ERROR_numberExpected, ERROR_numberMustBe, ERROR_numberOutOfRange, ERROR_objectNameExpected, ERROR_planeExpected, ERROR_propertyNameExpected, ERROR_spaceGroupNotFound, ERROR_stringExpected, ERROR_stringOrIdentifierExpected, ERROR_tooManyPoints, ERROR_tooManyScriptLevels, ERROR_unrecognizedAtomProperty, ERROR_unrecognizedBondProperty, ERROR_unrecognizedCommand, ERROR_unrecognizedExpression, ERROR_unrecognizedObject, ERROR_unrecognizedParameter, ERROR_unrecognizedParameterWarning, ERROR_unrecognizedShowParameter, ERROR_what, ERROR_writeWhat, errorMessage, errorMessageUntranslated, errorType, iCommandError, ignoreError, vwr
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Constructor Summary
Constructors Constructor Description ScriptParam()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description javajs.util.P3
atomCenterOrCoordinateParameter(int i, Object[] ret)
javajs.util.P3
centerParameter(int i, Object[] ret)
protected javajs.util.P3
centerParameterForModel(int i, int modelIndex, Object[] ret)
int
checkLast(int i)
int
checkLength(int length)
int
checkLength23()
protected int
checkLength34()
int
checkLengthErrorPt(int length, int errorPt)
protected boolean
checkToken(int i)
float
floatParameter(int index)
protected float
floatParameterRange(int i, float min, float max)
float[]
floatParameterSet(int i, int nMin, int nMax)
process a general string or set of parameters as an array of floats, allowing for relatively free form inputint
getArgbParam(int index)
protected int
getArgbParamLast(int index, boolean allowNone)
protected int
getArgbParamOrNone(int index, boolean allowNone)
static int
getBondOrderFromString(String s)
private int
getColorTriad(int i)
SV
getContextVariableAsVariable(String var, boolean isLocal)
(package private) static int
getFloatEncodedInt(String strDecimal)
Encodes a string such as "2.10" as an integer instead of a float so as to distinguish "2.1" from "2.10" used for model numbers and partial bond orders.javajs.util.P4
getHklPlane(javajs.util.P3 pt)
int
getMadParameter()
Object
getParameter(String key, int tokType, boolean nullAsString)
static int
getPartialBondOrderFromFloatEncodedInt(int bondOrderInteger)
reads standard n.m float-as-integer n*1000000 + m and returns (n % 7) << 5 + (m % 0x1F)private static int
getPartialBondOrderFromString(String s)
javajs.util.P3
getPoint3f(int i, boolean allowFractional, boolean throwE)
javajs.util.P4
getPoint4f(int i)
javajs.util.P3[]
getPointArray(int i, int nPoints, boolean allowNull)
may return null values in some casesjavajs.util.Lst<javajs.util.P3>
getPointOrCenterVector(T t)
Object
getPointOrPlane(int index, boolean integerOnly, boolean allowFractional, boolean doConvert, boolean implicitFractional, int minDim, int maxDim, boolean throwE)
javajs.util.Lst<javajs.util.P3>
getPointVector(T t, int i)
javajs.util.Quat
getQuaternionParameter(int i, javajs.util.BS bsAtoms, boolean divideByCurrent)
T
getToken(int i)
protected Object
getVarParameter(String var, boolean orReturnName)
javajs.util.P4
hklParameter(int i)
int
intParameter(int index)
int
intParameterRange(int i, int min, int max)
boolean
isArrayParameter(int i)
boolean
isCenterParameter(int i)
boolean
isColorParam(int i)
boolean
isFloatParameter(int index)
boolean
isPoint3f(int i)
javajs.util.Lst<Object>
listParameter(int i, int nMin, int nMax)
javajs.util.Lst<Object>
listParameter4(int i, int nMin, int nMax, boolean allowString)
int
modelNumberParameter(int index)
String
objectNameParameter(int index)
String
optParameterAsString(int i)
String
paramAsStr(int i)
javajs.util.P4
planeParameter(int i)
void
setBooleanProperty(String key, boolean value)
protected boolean
setFloatProperty(String key, float value)
protected boolean
setIntProperty(String key, int value)
protected void
setStringProperty(String key, String value)
String
stringParameter(int index)
String[]
stringParameterSet(int i)
TickInfo
tickParamAsStr(int index, boolean allowUnitCell, boolean allowScale, boolean allowFirst)
int
tokAt(int i)
javajs.util.P3
xypParameter(int index)
javajs.util.P4
xyzpParameter(int index)
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Methods inherited from class org.jmol.script.ScriptError
bad, error, errorMore, errorStr, errorStr2, errorString, evalError, getErrorLineMessage, getErrorMessage, getErrorMessageUntranslated, integerOutOfRange, invArg, numberOutOfRange, setCursorWait, setErrorMessage, showStringPrint, warning
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface org.jmol.api.JmolScriptEvaluator
checkScriptSilent, checkSelect, compileScriptFile, compileScriptString, deleteAtomsInVariables, evalFunctionFloat, evalParallel, evaluateCompiledScript, evaluateExpression, getAllowJSThreads, getAtomBitSet, getNextStatement, getScript, getScriptContext, getThisContext, haltExecution, isExecuting, isPaused, isStateScript, isStepping, isStopped, loadFileResourceAsync, notifyResumeStatus, pauseExecution, pushContextDown, resumeEval, resumePausedExecution, runScript, runScriptBuffer, setCompiler, setDebugging, setObjectPropSafe, setStatic, setViewer, stepPausedExecution, stopScriptThreads
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Field Detail
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thisContext
public ScriptContext thisContext
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iToken
public int iToken
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theTok
public int theTok
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theToken
public T theToken
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st
public T[] st
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slen
public int slen
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fractionalPoint
public javajs.util.P3 fractionalPoint
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coordinatesAreFractional
public boolean coordinatesAreFractional
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isBondSet
public boolean isBondSet
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pt1
public javajs.util.P3 pt1
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pt2
public javajs.util.P3 pt2
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pt3
public javajs.util.P3 pt3
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Method Detail
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getToken
public T getToken(int i) throws ScriptException
- Throws:
ScriptException
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tokAt
public int tokAt(int i)
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checkToken
protected boolean checkToken(int i)
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paramAsStr
public String paramAsStr(int i) throws ScriptException
- Throws:
ScriptException
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stringParameter
public String stringParameter(int index) throws ScriptException
- Throws:
ScriptException
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stringParameterSet
public String[] stringParameterSet(int i) throws ScriptException
- Throws:
ScriptException
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objectNameParameter
public String objectNameParameter(int index) throws ScriptException
- Throws:
ScriptException
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atomCenterOrCoordinateParameter
public javajs.util.P3 atomCenterOrCoordinateParameter(int i, Object[] ret) throws ScriptException
- Parameters:
i
-ret
- return P3 or BS to ret[0]; on input, passing a BS as ret[1] indicates that it should be ANDED with this BS prior to calculation (SHOW/DRAW SYMOP)- Returns:
- point -- ORIGINAL, non-copied atom, if a single atom
- Throws:
ScriptException
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isCenterParameter
public boolean isCenterParameter(int i)
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centerParameter
public javajs.util.P3 centerParameter(int i, Object[] ret) throws ScriptException
- Throws:
ScriptException
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centerParameterForModel
protected javajs.util.P3 centerParameterForModel(int i, int modelIndex, Object[] ret) throws ScriptException
- Throws:
ScriptException
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planeParameter
public javajs.util.P4 planeParameter(int i) throws ScriptException
- Throws:
ScriptException
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getPointOrCenterVector
public javajs.util.Lst<javajs.util.P3> getPointOrCenterVector(T t) throws ScriptException
- Throws:
ScriptException
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hklParameter
public javajs.util.P4 hklParameter(int i) throws ScriptException
- Throws:
ScriptException
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getHklPlane
public javajs.util.P4 getHklPlane(javajs.util.P3 pt)
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getPointOrPlane
public Object getPointOrPlane(int index, boolean integerOnly, boolean allowFractional, boolean doConvert, boolean implicitFractional, int minDim, int maxDim, boolean throwE) throws ScriptException
- Throws:
ScriptException
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isPoint3f
public boolean isPoint3f(int i)
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getPoint3f
public javajs.util.P3 getPoint3f(int i, boolean allowFractional, boolean throwE) throws ScriptException
- Throws:
ScriptException
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getPoint4f
public javajs.util.P4 getPoint4f(int i) throws ScriptException
- Throws:
ScriptException
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xypParameter
public javajs.util.P3 xypParameter(int index) throws ScriptException
- Throws:
ScriptException
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xyzpParameter
public javajs.util.P4 xyzpParameter(int index) throws ScriptException
- Throws:
ScriptException
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optParameterAsString
public String optParameterAsString(int i) throws ScriptException
- Throws:
ScriptException
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intParameter
public int intParameter(int index) throws ScriptException
- Throws:
ScriptException
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isFloatParameter
public boolean isFloatParameter(int index)
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floatParameter
public float floatParameter(int index) throws ScriptException
- Throws:
ScriptException
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getPointArray
public javajs.util.P3[] getPointArray(int i, int nPoints, boolean allowNull) throws ScriptException
may return null values in some cases- Parameters:
i
-nPoints
- -1 for unspecified number of pointsallowNull
- if allowing null values (as in setting atom properties such as vxyz or xyz)- Returns:
- array of P3, with possible null values
- Throws:
ScriptException
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listParameter
public javajs.util.Lst<Object> listParameter(int i, int nMin, int nMax) throws ScriptException
- Throws:
ScriptException
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listParameter4
public javajs.util.Lst<Object> listParameter4(int i, int nMin, int nMax, boolean allowString) throws ScriptException
- Throws:
ScriptException
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floatParameterSet
public float[] floatParameterSet(int i, int nMin, int nMax) throws ScriptException
process a general string or set of parameters as an array of floats, allowing for relatively free form input- Parameters:
i
-nMin
-nMax
-- Returns:
- array of floats
- Throws:
ScriptException
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isArrayParameter
public boolean isArrayParameter(int i)
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getQuaternionParameter
public javajs.util.Quat getQuaternionParameter(int i, javajs.util.BS bsAtoms, boolean divideByCurrent) throws ScriptException
- Throws:
ScriptException
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checkLast
public int checkLast(int i) throws ScriptException
- Throws:
ScriptException
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checkLength
public int checkLength(int length) throws ScriptException
- Throws:
ScriptException
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checkLengthErrorPt
public int checkLengthErrorPt(int length, int errorPt) throws ScriptException
- Throws:
ScriptException
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checkLength23
public int checkLength23() throws ScriptException
- Throws:
ScriptException
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checkLength34
protected int checkLength34() throws ScriptException
- Throws:
ScriptException
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modelNumberParameter
public int modelNumberParameter(int index) throws ScriptException
- Throws:
ScriptException
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getMadParameter
public int getMadParameter() throws ScriptException
- Throws:
ScriptException
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intParameterRange
public int intParameterRange(int i, int min, int max) throws ScriptException
- Throws:
ScriptException
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floatParameterRange
protected float floatParameterRange(int i, float min, float max) throws ScriptException
- Throws:
ScriptException
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getPointVector
public javajs.util.Lst<javajs.util.P3> getPointVector(T t, int i) throws ScriptException
- Throws:
ScriptException
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getFloatEncodedInt
static int getFloatEncodedInt(String strDecimal)
Encodes a string such as "2.10" as an integer instead of a float so as to distinguish "2.1" from "2.10" used for model numbers and partial bond orders. 2147483647 is maxvalue, so this allows loading simultaneously up to 2147 files, each with 999999 models (or trajectories)- Parameters:
strDecimal
-- Returns:
- float encoded as an integer
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getPartialBondOrderFromFloatEncodedInt
public static int getPartialBondOrderFromFloatEncodedInt(int bondOrderInteger)
reads standard n.m float-as-integer n*1000000 + m and returns (n % 7) << 5 + (m % 0x1F)- Parameters:
bondOrderInteger
-- Returns:
- Bond order partial mask
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getBondOrderFromString
public static int getBondOrderFromString(String s)
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getPartialBondOrderFromString
private static int getPartialBondOrderFromString(String s)
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isColorParam
public boolean isColorParam(int i)
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getArgbParam
public int getArgbParam(int index) throws ScriptException
- Throws:
ScriptException
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getArgbParamLast
protected int getArgbParamLast(int index, boolean allowNone) throws ScriptException
- Throws:
ScriptException
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getArgbParamOrNone
protected int getArgbParamOrNone(int index, boolean allowNone) throws ScriptException
- Throws:
ScriptException
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getColorTriad
private int getColorTriad(int i) throws ScriptException
- Throws:
ScriptException
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tickParamAsStr
public TickInfo tickParamAsStr(int index, boolean allowUnitCell, boolean allowScale, boolean allowFirst) throws ScriptException
- Parameters:
index
-allowUnitCell
- IGNOREDallowScale
-allowFirst
-- Returns:
- TickInfo
- Throws:
ScriptException
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setBooleanProperty
public void setBooleanProperty(String key, boolean value)
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setIntProperty
protected boolean setIntProperty(String key, int value)
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setFloatProperty
protected boolean setFloatProperty(String key, float value)
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