FormulaParser

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

All Implemented Interfaces:

FormulaParserConstants, IFormulaParser
```
public class FormulaParser
extends java.lang.Object
implements IFormulaParser, FormulaParserConstants
```
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 C-inspired infix notation taken from SBML Level 1 parser.

Since:

0.8

Version:

$Rev$

Author:

Alexander Dörr, Nicolas Rodriguez

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

(package private) static class FormulaParser.JJCalls

private static class FormulaParser.LookaheadSuccess

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

Field Summary

Fields
Modifier and Type	Field and Description
`private FormulaParser.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 FormulaParser.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.
`FormulaParserTokenManager`	`token_source` Generated Token Manager.

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

Constructor Summary

Constructors
Constructor and Description
`FormulaParser(FormulaParserTokenManager tm)` Constructor with generated Token Manager.
`FormulaParser(java.io.InputStream stream)` Constructor with InputStream.
`FormulaParser(java.io.InputStream stream, java.lang.String encoding)` Constructor with InputStream and supplied encoding
`FormulaParser(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 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_8()`
`private boolean`	`jj_3R_9()`
`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()`
`private ASTNode`	`Primary()`
`void`	`ReInit(FormulaParserTokenManager 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.
`Token`	`string()`
`private ASTNode`	`TermLvl1()`
`private ASTNode`	`TermLvl2()`
`private ASTNode`	`TermLvl3()`

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

token_source

public FormulaParserTokenManager 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 FormulaParser.JJCalls[] jj_2_rtns

jj_rescan
```
private boolean jj_rescan
```

jj_gc
```
private int jj_gc
```

jj_ls

private final FormulaParser.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

FormulaParser

public FormulaParser(java.io.InputStream stream)

Constructor with InputStream.

FormulaParser

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

Constructor with InputStream and supplied encoding

FormulaParser

public FormulaParser(java.io.Reader stream)

Constructor.

FormulaParser

public FormulaParser(FormulaParserTokenManager tm)

Constructor with generated Token Manager.

Method Detail

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"

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

TermLvl3

private final ASTNode TermLvl3()
                        throws ParseException

Throws:: ParseException

TermLvl2

private final ASTNode TermLvl2()
                        throws ParseException

Throws:: ParseException

TermLvl1

private final ASTNode TermLvl1()
                        throws ParseException

Throws:: ParseException

Primary

private final ASTNode Primary()
                       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_3R_12
```
private boolean jj_3R_12()
```

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

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

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

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

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

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

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

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

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

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

jj_3R_9
```
private boolean jj_3R_9()
```

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

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

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

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

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

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

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

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

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

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

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

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

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

jj_3R_8
```
private boolean jj_3R_8()
```

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

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

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

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

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(FormulaParserTokenManager 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 FormulaParser

Nested Class Summary

Field Summary

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

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

stringToType

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

FormulaParser

FormulaParser

FormulaParser

FormulaParser

Method Detail

checkSize

getInteger

createModulo

string

parse

Expression

TermLvl3

TermLvl2

TermLvl1

Primary

jj_2_1

jj_2_2

jj_2_3

jj_3R_12

jj_3R_15

jj_3R_14

jj_3R_21

jj_3R_25

jj_3R_28

jj_3R_10

jj_3_2

jj_3R_11

jj_3R_24

jj_3R_19

jj_3R_9

jj_3R_18

jj_3R_23

jj_3R_32

jj_3R_34

jj_3_1

jj_3R_31

jj_3_3

jj_3R_33

jj_3R_20

jj_3R_17

jj_3R_30

jj_3R_13

jj_3R_27

jj_3R_8

jj_3R_16

jj_3R_29

jj_3R_22

jj_3R_26

jj_la1_init_0

ReInit