org.jmol.script

Class ScriptMathProcessor

java.lang.Object

org.jmol.script.ScriptMathProcessor

 class ScriptMathProcessor
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
private boolean	asBitSet
private boolean	asVector
private int	braceCount
private boolean	chk Reverse Polish Notation Engine for IF, SET, and %{...} -- Bob Hanson 2/16/2007 Just a (not so simple?) RPN processor that can handle boolean, int, float, String, Point3f, BitSet, Array, Hashtable, Matrix3f, Matrix4f hansonr@stolaf.edu
private int	equalCount
private ScriptEvaluator	eval
private boolean	haveSpaceBeforeSquare
private int	ifPt
private char[]	ifStack
private int	incrementX
private boolean	isArrayItem
private boolean	logMessages
private int	oPt
private T[]	oStack
private int	parenCount
private int	ptid
private int	ptx
private boolean	skipping
private int	squareCount
private Viewer	viewer
private boolean	wasSyntaxCheck
private boolean	wasX
private int	xPt
private SV[]	xStack

Constructor Summary

Constructors

Constructor and Description
ScriptMathProcessor(ScriptEvaluator eval, boolean isArrayItem, boolean asVector, boolean asBitSet)

Method Summary

Methods

Modifier and Type	Method and Description
(package private) boolean	addOp(T op) addOp The primary driver of the Reverse Polish Notation evaluation engine.
(package private) boolean	addOpAllowMath(T op, boolean allowMathFunc)
(package private) boolean	addXAD(double[] x)
(package private) boolean	addXAF(float[] x)
(package private) boolean	addXAFF(float[][] x)
(package private) boolean	addXAI(int[] x)
(package private) boolean	addXAII(int[][] x)
(package private) boolean	addXAS(java.lang.String[] x)
(package private) boolean	addXAV(SV[] x)
private boolean	addXBool(boolean x)
(package private) boolean	addXBs(BS bs)
private boolean	addXFloat(float x)
private boolean	addXInt(int x)
private boolean	addXList(JmolList<?> x)
private boolean	addXM3(Matrix3f x)
private boolean	addXM4(Matrix4f x)
private boolean	addXMap(java.util.Map<java.lang.String,?> x)
(package private) boolean	addXNum(SV x)
(package private) boolean	addXObj(java.lang.Object x)
(package private) boolean	addXPt(P3 pt)
(package private) boolean	addXPt4(P4 pt)
(package private) boolean	addXStr(java.lang.String x)
(package private) boolean	addXVar(SV x)
private boolean	doBitsetSelect()
(package private) void	dumpStacks(java.lang.String message)
private boolean	evaluateArray(SV[] args, boolean allowMatrix)
private boolean	evaluateBin(SV[] args)
private boolean	evaluateCache(SV[] args)
private boolean	evaluateColor(SV[] args)
private boolean	evaluateCompare(SV[] args)
private boolean	evaluateConnected(SV[] args)
private boolean	evaluateContact(SV[] args)
private boolean	evaluateCross(SV[] args)
private boolean	evaluateData(SV[] args)
private boolean	evaluateDot(SV[] args, int tok, int intValue) distance, dot
private boolean	evaluateFind(SV[] args)
private boolean	evaluateFunction(int tok)
private boolean	evaluateGetProperty(SV[] args)
private boolean	evaluateHelix(SV[] args)
private boolean	evaluateLabel(int intValue, SV[] args)
private boolean	evaluateList(int tok, SV[] args)
private boolean	evaluateLoad(SV[] args, int tok)
private boolean	evaluateMath(SV[] args, int tok)
private boolean	evaluateMeasure(SV[] args, int tok)
private boolean	evaluatePlane(SV[] args, int tok)
private boolean	evaluatePoint(SV[] args)
private boolean	evaluatePrompt(SV[] args)
private boolean	evaluateQuaternion(SV[] args, int tok)
private boolean	evaluateRandom(SV[] args)
private boolean	evaluateReplace(SV[] args)
private boolean	evaluateRowCol(SV[] args, int tok)
private boolean	evaluateScript(SV[] args, int tok)
private boolean	evaluateSort(SV[] args, int tok)
private boolean	evaluateString(int tok, SV[] args)
private boolean	evaluateSubstructure(SV[] args, int tok)
private boolean	evaluateSymop(SV[] args, boolean haveBitSet) {xxx}.symop() symop({xxx}
private boolean	evaluateTensor(SV[] args)
private boolean	evaluateUserFunction(java.lang.String name, SV[] args, int tok, boolean isSelector)
private boolean	evaluateWithin(SV[] args)
private boolean	evaluateWrite(SV[] args)
private boolean	getAllProperties(SV x2, java.lang.String abbr)
private boolean	getBoundBox(SV x2)
private float	getDistance(SV x1, SV x2, int tok)
(package private) static Matrix4f	getMatrix4f(Matrix3f matRotate, Tuple3f vTranslate)
private static java.lang.Object	getMinMax(java.lang.Object floatOrSVArray, int tok)
private static java.lang.Object	getMinMaxPoint(java.lang.Object pointOrSVArray, int tok) calculates the statistical value for x, y, and z independently
private static java.lang.Object	getMinMaxQuaternion(JmolList<SV> svData, int tok)
private boolean	getPointOrBitsetOperation(T op, SV x2)
protected static Quaternion[]	getQuaternionArray(java.lang.Object quaternionOrSVData, int itype)
(package private) SV	getResult(boolean allowUnderflow)
private static void	getTorsions(Atom[] atoms, int[][] bondMap, float[][] diff, int pt)
private SV	getX()
private static boolean	isOpFunc(T op)
private boolean	operate()
private P4	planeValue(T x)
P3	ptValue(SV x, boolean allowFloat)
private void	putIf(char c)
private void	putOp(T op)
private void	putX(SV x)
private static java.lang.String	typeOf(SV x)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

chk

private boolean chk

Reverse Polish Notation Engine for IF, SET, and %{...} -- Bob Hanson 2/16/2007 Just a (not so simple?) RPN processor that can handle boolean, int, float, String, Point3f, BitSet, Array, Hashtable, Matrix3f, Matrix4f hansonr@stolaf.edu

wasSyntaxCheck

private boolean wasSyntaxCheck

logMessages

private boolean logMessages

eval

private ScriptEvaluator eval

viewer

private Viewer viewer

oStack

private T[] oStack

xStack

private SV[] xStack

ifStack

private char[] ifStack

ifPt

private int ifPt

oPt

private int oPt

xPt

private int xPt

parenCount

private int parenCount

squareCount

private int squareCount

braceCount

private int braceCount

wasX

private boolean wasX

incrementX

private int incrementX

isArrayItem

private boolean isArrayItem

asVector

private boolean asVector

asBitSet

private boolean asBitSet

ptid

private int ptid

ptx

private int ptx

skipping

private boolean skipping

haveSpaceBeforeSquare

private boolean haveSpaceBeforeSquare

equalCount

private int equalCount

Constructor Detail

ScriptMathProcessor

ScriptMathProcessor(ScriptEvaluator eval,
                   boolean isArrayItem,
                   boolean asVector,
                   boolean asBitSet)

Method Detail

getResult

SV getResult(boolean allowUnderflow)
       throws ScriptException

Throws:

ScriptException

putX

private void putX(SV x)

putOp

private void putOp(T op)

putIf

private void putIf(char c)

addXVar

boolean addXVar(SV x)

addXObj

boolean addXObj(java.lang.Object x)

addXStr

boolean addXStr(java.lang.String x)

addXBool

private boolean addXBool(boolean x)

addXInt

private boolean addXInt(int x)

addXList

private boolean addXList(JmolList<?> x)

addXMap

private boolean addXMap(java.util.Map<java.lang.String,?> x)

addXM3

private boolean addXM3(Matrix3f x)

addXM4

private boolean addXM4(Matrix4f x)

addXFloat

private boolean addXFloat(float x)

addXBs

boolean addXBs(BS bs)

addXPt

boolean addXPt(P3 pt)

addXPt4

boolean addXPt4(P4 pt)

addXNum

boolean addXNum(SV x)
          throws ScriptException

Throws:

ScriptException

addXAV

boolean addXAV(SV[] x)

addXAD

boolean addXAD(double[] x)

addXAS

boolean addXAS(java.lang.String[] x)

addXAI

boolean addXAI(int[] x)

addXAII

boolean addXAII(int[][] x)

addXAF

boolean addXAF(float[] x)

addXAFF

boolean addXAFF(float[][] x)

isOpFunc

private static boolean isOpFunc(T op)

addOp

boolean addOp(T op)
        throws ScriptException

addOp The primary driver of the Reverse Polish Notation evaluation engine. This method loads operators onto the oStack[] and processes them based on a precedence system. Operands are added by addX() onto the xStack[]. We check here for syntax issues that were not caught in the compiler. I suppose that should be done at compilation stage, but this is how it is for now. The processing of functional arguments and (___?___:___) constructs is carried out by pushing markers onto the stacks that later can be used to fill argument lists or turn "skipping" on or off. Note that in the case of skipped sections of ( ? : ) no attempt is made to do syntax checking. [That's not entirely true -- when syntaxChecking is true, that is, when the user is typing at the Jmol application console, then this code is being traversed with dummy variables. That could be improved, for sure. Actually, there's plenty of room for improvement here. I did this based on what I learned in High School in 1974 -- 35 years ago! -- when I managed to build a mini FORTRAN compiler from scratch in machine code. That was fun. (This was fun, too.) -- Bob Hanson, hansonr@stolaf.edu 6/9/2009

Parameters:

op -

Returns:

false if an error condition arises

Throws:

ScriptException

addOpAllowMath

boolean addOpAllowMath(T op,
                     boolean allowMathFunc)
                 throws ScriptException

Throws:

ScriptException

doBitsetSelect

private boolean doBitsetSelect()

dumpStacks

void dumpStacks(java.lang.String message)

getX

private SV getX()
         throws ScriptException

Throws:

ScriptException

evaluateFunction

private boolean evaluateFunction(int tok)
                          throws ScriptException

Throws:

ScriptException

evaluateTensor

private boolean evaluateTensor(SV[] args)
                        throws ScriptException

Throws:

ScriptException

evaluateCache

private boolean evaluateCache(SV[] args)

evaluateCompare

private boolean evaluateCompare(SV[] args)
                         throws ScriptException

Throws:

ScriptException

getTorsions

private static void getTorsions(Atom[] atoms,
               int[][] bondMap,
               float[][] diff,
               int pt)

evaluateSort

private boolean evaluateSort(SV[] args,
                   int tok)
                      throws ScriptException

Throws:

ScriptException

evaluateSymop

private boolean evaluateSymop(SV[] args,
                    boolean haveBitSet)
                       throws ScriptException

{xxx}.symop() symop({xxx}

Parameters:

args -

haveBitSet -

Returns:

true/false

Throws:

ScriptException

evaluateBin

private boolean evaluateBin(SV[] args)
                     throws ScriptException

Throws:

ScriptException

evaluateHelix

private boolean evaluateHelix(SV[] args)
                       throws ScriptException

Throws:

ScriptException

evaluateDot

private boolean evaluateDot(SV[] args,
                  int tok,
                  int intValue)
                     throws ScriptException

distance, dot

Parameters:

args -

tok -

intValue -

Returns:

variable

Throws:

ScriptException

getDistance

private float getDistance(SV x1,
                SV x2,
                int tok)
                   throws ScriptException

Throws:

ScriptException

ptValue

public P3 ptValue(SV x,
         boolean allowFloat)
           throws ScriptException

Throws:

ScriptException

planeValue

private P4 planeValue(T x)

evaluateMeasure

private boolean evaluateMeasure(SV[] args,
                      int tok)
                         throws ScriptException

Throws:

ScriptException

evaluateUserFunction

private boolean evaluateUserFunction(java.lang.String name,
                           SV[] args,
                           int tok,
                           boolean isSelector)
                              throws ScriptException

Throws:

ScriptException

evaluateFind

private boolean evaluateFind(SV[] args)
                      throws ScriptException

Throws:

ScriptException

evaluateGetProperty

private boolean evaluateGetProperty(SV[] args)

evaluatePlane

private boolean evaluatePlane(SV[] args,
                    int tok)
                       throws ScriptException

Throws:

ScriptException

evaluatePoint

private boolean evaluatePoint(SV[] args)

evaluatePrompt

private boolean evaluatePrompt(SV[] args)

evaluateReplace

private boolean evaluateReplace(SV[] args)
                         throws ScriptException

Throws:

ScriptException

evaluateString

private boolean evaluateString(int tok,
                     SV[] args)
                        throws ScriptException

Throws:

ScriptException

evaluateList

private boolean evaluateList(int tok,
                   SV[] args)
                      throws ScriptException

Throws:

ScriptException

evaluateRowCol

private boolean evaluateRowCol(SV[] args,
                     int tok)
                        throws ScriptException

Throws:

ScriptException

evaluateArray

private boolean evaluateArray(SV[] args,
                    boolean allowMatrix)

evaluateMath

private boolean evaluateMath(SV[] args,
                   int tok)

evaluateQuaternion

private boolean evaluateQuaternion(SV[] args,
                         int tok)
                            throws ScriptException

Throws:

ScriptException

evaluateRandom

private boolean evaluateRandom(SV[] args)

evaluateCross

private boolean evaluateCross(SV[] args)

evaluateLoad

private boolean evaluateLoad(SV[] args,
                   int tok)

evaluateWrite

private boolean evaluateWrite(SV[] args)
                       throws ScriptException

Throws:

ScriptException

evaluateScript

private boolean evaluateScript(SV[] args,
                     int tok)
                        throws ScriptException

Throws:

ScriptException

evaluateData

private boolean evaluateData(SV[] args)

evaluateLabel

private boolean evaluateLabel(int intValue,
                    SV[] args)
                       throws ScriptException

Throws:

ScriptException

evaluateWithin

private boolean evaluateWithin(SV[] args)
                        throws ScriptException

Throws:

ScriptException

evaluateContact

private boolean evaluateContact(SV[] args)

evaluateColor

private boolean evaluateColor(SV[] args)

evaluateConnected

private boolean evaluateConnected(SV[] args)

evaluateSubstructure

private boolean evaluateSubstructure(SV[] args,
                           int tok)
                              throws ScriptException

Throws:

ScriptException

operate

private boolean operate()
                 throws ScriptException

Throws:

ScriptException

typeOf

private static java.lang.String typeOf(SV x)

getAllProperties

private boolean getAllProperties(SV x2,
                       java.lang.String abbr)
                          throws ScriptException

Throws:

ScriptException

getMatrix4f

static Matrix4f getMatrix4f(Matrix3f matRotate,
                   Tuple3f vTranslate)

getBoundBox

private boolean getBoundBox(SV x2)

getPointOrBitsetOperation

private boolean getPointOrBitsetOperation(T op,
                                SV x2)
                                   throws ScriptException

Throws:

ScriptException

getMinMax

private static java.lang.Object getMinMax(java.lang.Object floatOrSVArray,
                         int tok)

getMinMaxPoint

private static java.lang.Object getMinMaxPoint(java.lang.Object pointOrSVArray,
                              int tok)

calculates the statistical value for x, y, and z independently

Parameters:

pointOrSVArray -

tok -

Returns:

Point3f or "NaN"

getMinMaxQuaternion

private static java.lang.Object getMinMaxQuaternion(JmolList<SV> svData,
                                   int tok)

getQuaternionArray

protected static Quaternion[] getQuaternionArray(java.lang.Object quaternionOrSVData,
                              int itype)