FormulaParserLL3

java.lang.Object
- org.sbml.jsbml.text.parser.FormulaParserLL3

All Implemented Interfaces:: FormulaParserLL3Constants, IFormulaParser

public class FormulaParserLL3
extends java.lang.Object
implements IFormulaParser, FormulaParserLL3Constants

Class used to parse infix mathematical formula and returns a representation of it as an Abstract Syntax Tree (AST).

Support almost the same syntax as defined in the LibSBML L3 parser. The things not supported for now are the units associated with numbers.

Parsing of the various MathML functions and constants are all case-sensitive by default: names such as Cos and COS are not parsed as the MathML cosine operator, <cos>.

You can change this behaviour by using the setCaseSensitive(boolean) method.

Expression operators and their precedence in the text-string format for mathematical expressions.
Token	Operation	Class	Precedence	Associates
name	symbol reference	operand	8	n/a
`(`expression`)`	expression grouping	operand	8	n/a
`f(`...`)`	function call	prefix	8	left
`^`	power	binary	7	left
`-, !`	negation and boolean 'not'	unary	6	right
`*, /, %`	multiplication, division, and modulo	binary	5	left
`+, -`	addition and subtraction	binary	4	left
`==, <, >, <=, >=, !=`	boolean equality, inequality, and comparison	binary	3	left
`&&, \|\|`	boolean 'and' and 'or'	binary	2	left
`,`	argument delimiter	binary	1	left

In the table above, operand implies the construct is an operand, prefix implies the operation is applied to the following arguments, unary implies there is one argument, and binary implies there are two arguments. The values in the Precedence column show how the order of different types of operation are determined. For example, the expression a + b * c is evaluated as a + (b * c) because the @c * operator has higher precedence. The Associates column shows how the order of similar precedence operations is determined; for example, a && b || c is evaluated as (a && b) || c because the && and || operators are left-associative and have the same precedence.

The function call syntax consists of a function name, followed by an opening parenthesis token, followed by a sequence of zero or more arguments separated by commas (with each comma optionally preceded and/or followed by zero or more white space characters), followed by a closing parenthesis token. The function name must be chosen from one of the pre-defined functions in SBML or a user-defined function in the model. The following table lists the names of certain common mathematical functions; this table corresponds to Table 6 in the SBML Level 1 Version 2 specification with additions based on the functions added in SBML Level 2 and Level 3:

Mathematical functions defined in the text-string formula syntax.
Name	Argument(s)	Formula or meaning	Argument Constraints	Result constraints
`abs`	x	Absolute value of x.
`acos`, `arccos`	x	Arccosine of x in radians.	–1.0 ≤ x ≤ 1.0	0 ≤ acos(x) ≤ π
`acosh`, `arccosh`	x	Hyperbolic arccosine of x in radians.
`acot`, `arccot`	x	Arccotangent of x in radians.
`acoth`, `arccoth`	x	Hyperbolic arccotangent of x in radians.
`acsc`, `arccsc`	x	Arccosecant of x in radians.
`acsch`, `arccsch`	x	Hyperbolic arccosecant of x in radians.
`asec`, `arcsec`	x	Arcsecant of x in radians.
`asech`, `arcsech`	x	Hyperbolic arcsecant of x in radians.
`asin`, `arcsin`	x	Arcsine of x in radians.	–1.0 ≤ x ≤ 1.0	0 ≤ asin(x) ≤ π
`atan`, `arctan`	x	Arctangent of x in radians.		0 ≤ atan(x) ≤ π
`atanh`, `arctanh`	x	Hyperbolic arctangent of x in radians.
`ceil`, `ceiling`	x	Smallest number not less than x whose value is an exact integer.
`cos`	x	Cosine of x
`cosh`	x	Hyperbolic cosine of x.
`cot`	x	Cotangent of x.
`coth`	x	Hyperbolic cotangent of x.
`csc`	x	Cosecant of x.
`csch`	x	Hyperbolic cosecant of x.
`delay`	x, y	The value of x at y time units in the past.
`factorial`	n	The factorial of n. Factorials are defined by n! = n(n–1)* ... * 1*.	n must be an integer.
`exp`	x	e^x, where e is the base of the natural logarithm.
`floor`	x	The largest number not greater than x whose value is an exact integer.
`ln`	x	Natural logarithm of x.	x > 0
`log`	x	By default, the base 10 logarithm of x, but can be set to be the natural logarithm of x, or to be an illegal construct.	x > 0
`log`	x, y	The base x logarithm of y.	y > 0
`log10`	x	Base 10 logarithm of x.	x > 0
`piecewise`	x1, y1, [x2, y2,] [...] [z]	A piecewise function: if (y1), x1. Otherwise, if (y2), x2, etc. Otherwise, z.	y1, y2, y3 [etc] must be boolean
`pow`, `power`	x, y	x^y.
`root`	b, x	The root base b of x.
`sec`	x	Secant of x.
`sech`	x	Hyperbolic secant of x.
`sqr`	x	x².
`sqrt`	x	√x.	x > 0	sqrt(x) ≥ 0
`sin`	x	Sine of x.
`sinh`	x	Hyperbolic sine of x.
`tan`	x	Tangent of x.	x ≠ n*π/2, for odd integer n
`tanh`	x	Hyperbolic tangent of x.
`and`	x, y, z...	Boolean and(x, y, z...): returns `true` if all of its arguments are true. Note that `and` is an n-ary function, taking 0 or more arguments, and that `and()` returns `true`.	All arguments must be boolean
`not`	x	Boolean not(x)	x must be boolean
`or`	x, y, z...	Boolean or(x, y, z...): returns `true` if at least one of its arguments is true. Note that `or` is an n-ary function, taking 0 or more arguments, and that `or()` returns `false`.	All arguments must be boolean
`xor`	x, y, z...	Boolean xor(x, y, z...): returns `true` if an odd number of its arguments is true. Note that `xor` is an n-ary function, taking 0 or more arguments, and that `xor()` returns `false`.	All arguments must be boolean
`eq`	x, y, z...	Boolean eq(x, y, z...): returns `true` if all arguments are equal. Note that `eq` is an n-ary function, but must take 2 or more arguments.
`geq`	x, y, z...	Boolean geq(x, y, z...): returns `true` if each argument is greater than or equal to the argument following it. Note that `geq` is an n-ary function, but must take 2 or more arguments.
`gt`	x, y, z...	Boolean gt(x, y, z...): returns `true` if each argument is greater than the argument following it. Note that `gt` is an n-ary function, but must take 2 or more arguments.
`leq`	x, y, z...	Boolean leq(x, y, z...): returns `true` if each argument is less than or equal to the argument following it. Note that `leq` is an n-ary function, but must take 2 or more arguments.
`lt`	x, y, z...	Boolean lt(x, y, z...): returns `true` if each argument is less than the argument following it. Note that `lt` is an n-ary function, but must take 2 or more arguments.
`neq`	x, y	Boolean x != y: returns `true` unless x and y are equal.
`plus`	x, y, z...	x + y + z + ...: The sum of the arguments of the function. Note that `plus` is an n-ary function taking 0 or more arguments, and that `plus()` returns `0`.
`times`	x, y, z...	x * y * z * ...: The product of the arguments of the function. Note that `times` is an n-ary function taking 0 or more arguments, and that `times()` returns `1`.
`minus`	x, y	x – y.
`divide`	x, y	x / y.

Since:: 1.0
Version:: $Rev$
Author:: Alexander Dörr, Nicolas Rodriguez

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

(package private) static class FormulaParserLL3.JJCalls

private static class FormulaParserLL3.LookaheadSuccess

Nested Classes
Modifier and Type	Class and Description
`(package private) static class`	`FormulaParserLL3.JJCalls`
`private static class`	`FormulaParserLL3.LookaheadSuccess`

Field Summary

Fields
Modifier and Type	Field and Description
`private boolean`	`ignoreCase`
`private FormulaParserLL3.JJCalls[]`	`jj_2_rtns`
`private int`	`jj_endpos`
`private java.util.List<int[]>`	`jj_expentries`
`private int[]`	`jj_expentry`
`private int`	`jj_gc`
`private int`	`jj_gen`
`(package private) SimpleCharStream`	`jj_input_stream`
`private int`	`jj_kind`
`private int`	`jj_la`
`private int[]`	`jj_la1`
`private static int[]`	`jj_la1_0`
`private Token`	`jj_lastpos`
`private int[]`	`jj_lasttokens`
`private FormulaParserLL3.LookaheadSuccess`	`jj_ls`
`Token`	`jj_nt` Next token.
`private int`	`jj_ntk`
`private boolean`	`jj_rescan`
`private Token`	`jj_scanpos`
`static java.util.Properties`	`stringToType`
`Token`	`token` Current token.
`FormulaParserLL3TokenManager`	`token_source` Generated Token Manager.

Fields inherited from interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants
AND, BOOLEAN_LOGIC, CLOSE_PAR, COMPARISON, DEFAULT, DIGIT, DIVIDE, EOF, EOL, EXPNUMBER, IDCHAR, INTEGER, LEFT_BRACES, LEFT_BRACKET, LETTER, LOG, MINUS, MODULO, NOT, NUMBER, OPEN_PAR, OR, PLUS, POWER, RIGHT_BRACES, RIGHT_BRACKET, SPLITTER, STRING, TIMES, tokenImage, XOR

Constructor Summary

Constructors
Constructor and Description
`FormulaParserLL3(FormulaParserLL3TokenManager tm)` Constructor with generated Token Manager.
`FormulaParserLL3(java.io.InputStream stream)` Constructor with InputStream.
`FormulaParserLL3(java.io.InputStream stream, java.lang.String encoding)` Constructor with InputStream and supplied encoding
`FormulaParserLL3(java.io.Reader stream)` Constructor.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`private void`	`checkSize(java.util.ArrayList<ASTNode> arguments, int i)`
`private boolean`	`compareString(java.lang.String str1, java.lang.String str2)`
`private ASTNode`	`createModulo(ASTNode leftChild, ASTNode rightChild)` Returns a piecewise `ASTNode` representing the modulo operation between the left and right child given.
`void`	`disable_tracing()` Disable tracing.
`void`	`enable_tracing()` Enable tracing.
`private ASTNode`	`expression()`
`ParseException`	`generateParseException()` Generate ParseException.
`private java.lang.Integer`	`getInteger(ASTNode node)`
`Token`	`getNextToken()` Get the next Token.
`Token`	`getToken(int index)` Get the specific Token.
`private boolean`	`jj_2_1(int xla)`
`private boolean`	`jj_2_2(int xla)`
`private boolean`	`jj_2_3(int xla)`
`private boolean`	`jj_3_1()`
`private boolean`	`jj_3_2()`
`private boolean`	`jj_3_3()`
`private boolean`	`jj_3R_10()`
`private boolean`	`jj_3R_11()`
`private boolean`	`jj_3R_12()`
`private boolean`	`jj_3R_13()`
`private boolean`	`jj_3R_14()`
`private boolean`	`jj_3R_15()`
`private boolean`	`jj_3R_16()`
`private boolean`	`jj_3R_17()`
`private boolean`	`jj_3R_18()`
`private boolean`	`jj_3R_19()`
`private boolean`	`jj_3R_20()`
`private boolean`	`jj_3R_21()`
`private boolean`	`jj_3R_22()`
`private boolean`	`jj_3R_23()`
`private boolean`	`jj_3R_24()`
`private boolean`	`jj_3R_25()`
`private boolean`	`jj_3R_26()`
`private boolean`	`jj_3R_27()`
`private boolean`	`jj_3R_28()`
`private boolean`	`jj_3R_29()`
`private boolean`	`jj_3R_30()`
`private boolean`	`jj_3R_31()`
`private boolean`	`jj_3R_32()`
`private boolean`	`jj_3R_33()`
`private boolean`	`jj_3R_34()`
`private boolean`	`jj_3R_35()`
`private boolean`	`jj_3R_36()`
`private boolean`	`jj_3R_37()`
`private void`	`jj_add_error_token(int kind, int pos)`
`private Token`	`jj_consume_token(int kind)`
`private static void`	`jj_la1_init_0()`
`private int`	`jj_ntk()`
`private void`	`jj_rescan_token()`
`private void`	`jj_save(int index, int xla)`
`private boolean`	`jj_scan_token(int kind)`
`ASTNode`	`parse()`
`void`	`ReInit(FormulaParserLL3TokenManager tm)` Reinitialise.
`void`	`ReInit(java.io.InputStream stream)` Reinitialise.
`void`	`ReInit(java.io.InputStream stream, java.lang.String encoding)` Reinitialise.
`void`	`ReInit(java.io.Reader stream)` Reinitialise.
`void`	`setCaseSensitive(boolean caseSensitive)` Sets the case sensitivity of the parser, for the mathml elements.
`Token`	`string()`
`private ASTNode`	`termLevel2()`
`private ASTNode`	`termLevel3()`
`private ASTNode`	`termLevel4()`
`private ASTNode`	`termLevel5()`
`private ASTNode`	`termLevel6()`
`private ASTNode`	`termLevel7()`
`private ASTNode`	`termLevel8()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

stringToType

public static java.util.Properties stringToType

ignoreCase
```
private boolean ignoreCase
```

token_source

public FormulaParserLL3TokenManager token_source

Generated Token Manager.

jj_input_stream
```
SimpleCharStream jj_input_stream
```

token
```
public Token token
```
Current token.

jj_nt
```
public Token jj_nt
```
Next token.

jj_ntk
```
private int jj_ntk
```

jj_scanpos
```
private Token jj_scanpos
```

jj_lastpos
```
private Token jj_lastpos
```

jj_la
```
private int jj_la
```

jj_gen
```
private int jj_gen
```

jj_la1
```
private final int[] jj_la1
```

jj_la1_0
```
private static int[] jj_la1_0
```

jj_2_rtns

private final FormulaParserLL3.JJCalls[] jj_2_rtns

jj_rescan
```
private boolean jj_rescan
```

jj_gc
```
private int jj_gc
```

jj_ls

private final FormulaParserLL3.LookaheadSuccess jj_ls

jj_expentries

private java.util.List<int[]> jj_expentries

jj_expentry
```
private int[] jj_expentry
```

jj_kind
```
private int jj_kind
```

jj_lasttokens
```
private int[] jj_lasttokens
```

jj_endpos
```
private int jj_endpos
```

Constructor Detail

FormulaParserLL3

public FormulaParserLL3(java.io.InputStream stream)

Constructor with InputStream.

FormulaParserLL3

public FormulaParserLL3(java.io.InputStream stream,
                        java.lang.String encoding)

Constructor with InputStream and supplied encoding

FormulaParserLL3

public FormulaParserLL3(java.io.Reader stream)

Constructor.

FormulaParserLL3

public FormulaParserLL3(FormulaParserLL3TokenManager tm)

Constructor with generated Token Manager.

Method Detail

setCaseSensitive
```
public void setCaseSensitive(boolean caseSensitive)
```
Sets the case sensitivity of the parser, for the mathml elements.
The default behavior is to be case sensitive, meaning 'cos' would be recognized as the mathematical cosinus but 'Cos', 'cOs' or any other alternatives would be recognized as a name and read as a 'ci' element. If you pass false to this method all the different versions of cos would be recognized as the mathematical cosinus.

Parameters:

caseSensitive - boolean to define if the parser should be case sensitive or not.

checkSize

private void checkSize(java.util.ArrayList<ASTNode> arguments,
                       int i)
                throws ParseException

Throws:: ParseException

getInteger

private java.lang.Integer getInteger(ASTNode node)

createModulo
```
private ASTNode createModulo(ASTNode leftChild,
                             ASTNode rightChild)
```
Returns a piecewise ASTNode representing the modulo operation between the left and right child given.
The formula produced for 'a % b' or modulo(a, b) is 'piecewise(floor(a/b), gt(a/b, 0), ceil(a/b))'

Parameters:

leftChild -

rightChild -

Returns:

a piecewise ASTNode representing the modulo operation between the left and right child given.

See Also:

"http://sbml.org/Documents/FAQ#Why_can.27t_I_use_the_.3Crem.3E_operator_in_SBML_MathML.3F"

compareString

private boolean compareString(java.lang.String str1,
                              java.lang.String str2)

string

public final Token string()
                   throws ParseException

Throws:: ParseException

parse

public final ASTNode parse()
                    throws ParseException

Specified by:: parse in interface IFormulaParser
Throws:: ParseException

expression

private final ASTNode expression()
                          throws ParseException

Throws:: ParseException

termLevel2

private final ASTNode termLevel2()
                          throws ParseException

Throws:: ParseException

termLevel3

private final ASTNode termLevel3()
                          throws ParseException

Throws:: ParseException

termLevel4

private final ASTNode termLevel4()
                          throws ParseException

Throws:: ParseException

termLevel5

private final ASTNode termLevel5()
                          throws ParseException

Throws:: ParseException

termLevel6

private final ASTNode termLevel6()
                          throws ParseException

Throws:: ParseException

termLevel7

private final ASTNode termLevel7()
                          throws ParseException

Throws:: ParseException

termLevel8

private final ASTNode termLevel8()
                          throws ParseException,
                                 java.lang.NumberFormatException

Throws:: ParseException; java.lang.NumberFormatException

jj_2_1
```
private boolean jj_2_1(int xla)
```

jj_2_2
```
private boolean jj_2_2(int xla)
```

jj_2_3
```
private boolean jj_2_3(int xla)
```

jj_3_1
```
private boolean jj_3_1()
```

jj_3R_28
```
private boolean jj_3R_28()
```

jj_3R_22
```
private boolean jj_3R_22()
```

jj_3R_31
```
private boolean jj_3R_31()
```

jj_3R_14
```
private boolean jj_3R_14()
```

jj_3R_29
```
private boolean jj_3R_29()
```

jj_3_3
```
private boolean jj_3_3()
```

jj_3R_12
```
private boolean jj_3R_12()
```

jj_3R_18
```
private boolean jj_3R_18()
```

jj_3R_21
```
private boolean jj_3R_21()
```

jj_3R_37
```
private boolean jj_3R_37()
```

jj_3R_16
```
private boolean jj_3R_16()
```

jj_3R_15
```
private boolean jj_3R_15()
```

jj_3R_34
```
private boolean jj_3R_34()
```

jj_3R_13
```
private boolean jj_3R_13()
```

jj_3R_11
```
private boolean jj_3R_11()
```

jj_3R_36
```
private boolean jj_3R_36()
```

jj_3R_33
```
private boolean jj_3R_33()
```

jj_3R_27
```
private boolean jj_3R_27()
```

jj_3R_25
```
private boolean jj_3R_25()
```

jj_3R_10
```
private boolean jj_3R_10()
```

jj_3R_32
```
private boolean jj_3R_32()
```

jj_3R_30
```
private boolean jj_3R_30()
```

jj_3R_26
```
private boolean jj_3R_26()
```

jj_3R_24
```
private boolean jj_3R_24()
```

jj_3R_20
```
private boolean jj_3R_20()
```

jj_3_2
```
private boolean jj_3_2()
```

jj_3R_17
```
private boolean jj_3R_17()
```

jj_3R_19
```
private boolean jj_3R_19()
```

jj_3R_23
```
private boolean jj_3R_23()
```

jj_3R_35
```
private boolean jj_3R_35()
```

jj_la1_init_0
```
private static void jj_la1_init_0()
```

ReInit
```
public void ReInit(java.io.InputStream stream)
```
Reinitialise.

Specified by:

ReInit in interface IFormulaParser

ReInit

public void ReInit(java.io.InputStream stream,
                   java.lang.String encoding)

Reinitialise.

Specified by:: ReInit in interface IFormulaParser

ReInit
```
public void ReInit(java.io.Reader stream)
```
Reinitialise.

Specified by:

ReInit in interface IFormulaParser

ReInit

public void ReInit(FormulaParserLL3TokenManager tm)

Reinitialise.

jj_consume_token

private Token jj_consume_token(int kind)
                        throws ParseException

Throws:: ParseException

jj_scan_token

private boolean jj_scan_token(int kind)

getNextToken
```
public final Token getNextToken()
```
Get the next Token.

getToken

public final Token getToken(int index)

Get the specific Token.

jj_ntk
```
private int jj_ntk()
```

jj_add_error_token

private void jj_add_error_token(int kind,
                                int pos)

generateParseException

public ParseException generateParseException()

Generate ParseException.

enable_tracing
```
public final void enable_tracing()
```
Enable tracing.

disable_tracing
```
public final void disable_tracing()
```
Disable tracing.

jj_rescan_token
```
private void jj_rescan_token()
```

jj_save

private void jj_save(int index,
                     int xla)

Class FormulaParserLL3

Nested Class Summary

Field Summary

Fields inherited from interface org.sbml.jsbml.text.parser.FormulaParserLL3Constants

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

stringToType

ignoreCase

token_source

jj_input_stream

token

jj_nt

jj_ntk

jj_scanpos

jj_lastpos

jj_la

jj_gen

jj_la1

jj_la1_0

jj_2_rtns

jj_rescan

jj_gc

jj_ls

jj_expentries

jj_expentry

jj_kind

jj_lasttokens

jj_endpos

Constructor Detail

FormulaParserLL3

FormulaParserLL3

FormulaParserLL3

FormulaParserLL3

Method Detail

setCaseSensitive

checkSize

getInteger

createModulo

compareString

string

parse

expression

termLevel2

termLevel3

termLevel4

termLevel5

termLevel6

termLevel7

termLevel8

jj_2_1

jj_2_2

jj_2_3

jj_3_1

jj_3R_28

jj_3R_22

jj_3R_31

jj_3R_14

jj_3R_29

jj_3_3

jj_3R_12

jj_3R_18

jj_3R_21

jj_3R_37

jj_3R_16

jj_3R_15

jj_3R_34

jj_3R_13

jj_3R_11

jj_3R_36

jj_3R_33

jj_3R_27

jj_3R_25

jj_3R_10

jj_3R_32

jj_3R_30

jj_3R_26

jj_3R_24

jj_3R_20