This document contains source code for various components of a Java program that implements grammatical optimization. It includes the main class with the main method that initializes variables and objects. It also includes classes for the genotype, grammar, initializer, and mapper components. The classes define methods for initializing objects, mapping between genotypes and phenotypes, checking validity, and accessing attributes.

1. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GRAMMATICAL OPTIMIZATION
THE SOURCE CODE
Muhammad Adil Raja
Roaming Researchers, Inc.
cbna
April 27, 2015

2. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
OUTLINE I
1 INTRODUCTION
2 GE’S MAIN
3 INITIALIZER
4 GENOTYPE
5 GRAMMAR
6 PRODUCTION
7 RULE
8 MAPPER
9 SYMBOL
10 TREE
11 SUMMARY
12 REFERENCES

3. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
INTRODUCTION I
Grammatical optimization (GO) is an adaptation of
grammatical evolution (GE).
The algorithm is implemented in Java.
The algorithm is aimed at general optimization problems.
With slight modification it can also be used for other types
of problems such as classification.
The source code has many Java files.
In what follows you will find the source code of various
components of Java Beagle.

4. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GE’S MAIN I
/∗
∗ GEsMain . java
∗
∗ Created on August 4 , 2007, 5:31 PM
∗
∗ To change t h i s template , choose Tools | Template Manager
∗ and open the template in the e d i t o r .
∗/
package GrammaticOptimization ;
/∗∗
∗
∗ @author a d i l r a j a
∗/
import java . u t i l . ∗ ;
public class GEsMain {
/∗∗ Creates a new instance of GEsMain ∗/
public GEsMain ( ) {
}
/∗∗
∗ @param args the command l i n e arguments

5. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GE’S MAIN II
∗/
public static void main ( String [ ] args ) {
/ / TODO code a p p l i c a t i o n l o g i c here
Random rand=new Random ( ) ;
int [ ] newArray= new int [ 1 0 ] ;
newArray [ 0 ] = 0 ;
newArray [ 1 ] = 2 ;
newArray [ 2 ] = 1 ;
newArray [ 3 ] = 4 ;
newArray [ 4 ] = 4 ;
newArray [ 5 ] = 4 ;
newArray [ 6 ] = 4 ;
newArray [ 7 ] = 4 ;
newArray [ 8 ] = 4 ;
newArray [ 9 ] = 4 ;
ArrayList <Integer > a r r L i s t =new ArrayList ( ) ;
for ( int i =0; i <10; i ++){
a r r L i s t . add ( ( Integer ) newArray [ i ] ) ;
}
Genotype geno=new Genotype ( newArray , 10 , true , 1 0 ) ;
GEGrammar grammar=new GEGrammar( geno ) ;
grammar . setMaxWraps ( 9 ) ;
grammar . readBNFFile ( " / Users / a d i l r a j a / mywork / adils−java / GrammaticOptimization / d i s t / gram
/ / t r y {
/ / grammar . genotype2phenotype ( true ) ;
/ / }

6. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GE’S MAIN III
/ / catch ( java . lang . Exception e ) {
/ / System . out . p r i n t l n ( e+" In Main " ) ;
/ / }
I t e r a t o r <Symbol> symbIt=grammar . getPhenotype ( ) . i t e r a t o r ( ) ;
I t e r a t o r <Rule> r u l e I t =grammar . i t e r a t o r ( ) ;
System . out . p r i n t l n ( " Here are the r e s u l t s : phenotype sizse= "+grammar . getPhenotype ( ) . si
while ( symbIt . hasNext ( ) ) {
System . out . p r i n t ( symbIt . next ( ) . getSymbol ( ) ) ;
}
i f ( grammar . phenotype . getValid ()== true )
System . out . p r i n t l n ( " nThe above phenotype i s v a l i d " ) ;
else
System . out . p r i n t l n ( " nThe above phenotype i s not v a l i d " ) ;
System . out . p r i n t l n ( " n nHere i s the grammar" ) ;
while ( r u l e I t . hasNext ( ) ) {
Rule tmpRule= r u l e I t . next ( ) ;
System . out . p r i n t ( " n"+tmpRule . lhs . get ( 0 ) . getSymbol ()+ " : : = " ) ;
I t e r a t o r <Production > prodIt =tmpRule . i t e r a t o r ( ) ;
while ( prodIt . hasNext ( ) ) {
I t e r a t o r <Symbol> symbIt2= prodIt . next ( ) . i t e r a t o r ( ) ;
while ( symbIt2 . hasNext ( ) ) {
System . out . p r i n t ( symbIt2 . next ( ) . getSymbol ( ) ) ;
}
}
}
System . out . p r i n t l n ( "My name i s John Rambo "+grammar . size ( ) ) ;
System . out . p r i n t l n ( newArray . length ) ;

7. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GE’S MAIN IV
String str1 =new String ( " Adil " ) ;
String str2 =new String ( " Adil " ) ;
i f ( str1 . equals ( str2 ) )
System . out . p r i n t l n ( " adilRaja " ) ;
Symbol symb=new Symbol ( ) ;
System . out . p r i n t l n (symb . getType ( ) . to Str in g ( ) ) ;
symb . setType ( SymbolType . NTSymbol ) ;
System . out . p r i n t l n (symb . getType ( ) . to Str in g ( ) ) ;
r u l e I t =grammar . i t e r a t o r ( ) ;
System . out . p r i n t l n ( " n nHere i s the grammar ’ s NT/ T i n f o " ) ;
while ( r u l e I t . hasNext ( ) ) {
Rule tmpRule= r u l e I t . next ( ) ;
System . out . p r i n t ( " n"+tmpRule . lhs . get ( 0 ) . getType ( ) . to Str in g ()+ " : : = " ) ;
I t e r a t o r <Production > prodIt =tmpRule . i t e r a t o r ( ) ;
while ( prodIt . hasNext ( ) ) {
I t e r a t o r <Symbol> symbIt2= prodIt . next ( ) . i t e r a t o r ( ) ;
while ( symbIt2 . hasNext ( ) ) {
System . out . p r i n t ( symbIt2 . next ( ) . getType ( ) . to St rin g ()+ " " ) ;
}
}
}
}
}

8. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
INITIALIZER I
/∗
∗ I n i t i a l i s e r . java
∗
∗ Created on July 2 , 2007, 6:05 PM
∗
∗ To change t h i s template , choose Tools | Template Manager
∗ and open the template in the e d i t o r .
∗/
/∗∗
∗
∗ @author a d i l r a j a
∗
∗/
package GrammaticOptimization ;
public interface I n i t i a l i s e r {
public int getPopSize ( ) ;
public void setPopSize ( f i n a l int j ) ;
public int getIndex ( ) ;
public void setIndex ( f i n a l int i ) ;
public boolean i n i t ( f i n a l int i ) ;
}

9. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GENOTYPE I
/∗
∗ Genotype . java
∗
∗ Created on June 1 , 2007, 11:35 PM
∗
∗ To change t h i s template , choose Tools | Template Manager
∗ and open the template in the e d i t o r .
∗/
/∗∗
∗
∗ @author a d i l r a j a
∗/
package GrammaticOptimization ;
import java . u t i l . ∗ ;
import java . u t i l . ArrayList ;
/∗ Default Constructor . Creates a genotype s t r u c t u r e of length newLength , using the elements o
∗ i t s v a l i d f i e l d to newValid and i t s f i t n e s s to newFitness . Non−specified arguments are given
∗, as specified in the function prototype .
∗
∗/
public class Genotype extends ArrayList <Integer >{ / / codonType
private Vector genome ;
private boolean _libGE_Genotype_valid ;

10. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GENOTYPE II
private double _libGE_Genotype_fitness ;
private int _libGE_Genotype_maxCodonValue ;
private int _libGE_Genotype_effectiveSize ;
private int _libGE_Genotype_wraps ;
public Genotype ( ) {
}
/∗∗ Creates a new instance of Genotype ∗/
public Genotype ( f i n a l int [ ] newArray , f i n a l int newLength , f i n a l boolean newValid , f i n a l d
_libGE_Genotype_valid=newValid ;
_libGE_Genotype_fitness=newFitness ;
this . setMaxCodonValue (32767); / / INT_MAX
for ( int i i =0; i i <newLength ; i i ++){
this . add (new Integer ( newArray [ i i ] ) ) ;
}
setEffectiveSize ( 0 ) ;
setWraps ( 0 ) ;
}
/∗ Constructor . Creates a genotype s t r u c t u r e with the contents of newvector , and sets i t s
∗ f i e l d to newValid and i t s f i t n e s s to newFitness .
∗Non−specified arguments are given default values , as specified in he function prototype
∗/
public Genotype ( f i n a l ArrayList <Integer > newVector , f i n a l boolean newValid , f i n a l double n

11. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GENOTYPE III
_libGE_Genotype_valid=newValid ;
_libGE_Genotype_fitness=newFitness ;
this . addAll ( newVector ) ;
setMaxCodonValue (32767);
setEffectiveSize ( 0 ) ;
setWraps ( 0 ) ;
}
/∗ Constructor . Creates an empty genotype structure , and sets maCodonValue to the value
∗specified as argument
∗/
public Genotype ( f i n a l int maxCodonValue ) {
setMaxCodonValue ( maxCodonValue ) ;
setEffectiveSize ( 0 ) ;
setWraps ( 0 ) ;
}
/∗Copy constructor
∗/
public Genotype ( f i n a l Genotype copy ) {
setValid ( copy . getValid ( ) ) ;
setFitness ( copy . getFitness ( ) ) ;
setMaxCodonValue ( copy . getMaxCodonValue ( ) ) ;
setEffectiveSize ( copy . getEffectiveSize ( ) ) ;
setWraps ( copy . getWraps ( ) ) ;
}

12. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GENOTYPE IV
/∗ Returns the current v a l i d f i e l d
∗/
public f i n a l boolean getValid ( ) {
return _libGE_Genotype_valid ;
}
/∗ Set a new value f o r the v a l i d f i e l d
∗/
public void setValid ( f i n a l boolean newValid ) {
_libGE_Genotype_valid=newValid ;
}
/∗ Returns the current f i t n e s s score
∗/
public f i n a l double getFitness ( ) {
return _libGE_Genotype_fitness ;
}
/∗ Sets a new f i t n e s s score
∗/
public void setFitness ( f i n a l double newFitness ) {
_libGE_Genotype_fitness=newFitness ;
}
/∗ Returns the maximum containable value in a codon
∗/
public f i n a l int getMaxCodonValue ( ) {

13. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GENOTYPE V
return _libGE_Genotype_maxCodonValue ;
}
/∗ Sets the maximum containable value in a codon
∗/
public void setMaxCodonValue ( f i n a l int newMaxCodonValue ) {
_libGE_Genotype_maxCodonValue=newMaxCodonValue ;
}
/∗ Returns e f f e c t i v e length of Genotype
∗/
public f i n a l int getEffectiveSize ( ) {
return _libGE_Genotype_effectiveSize ;
}
/∗ Sets e f f e c t i v e length of genotype
∗/
public void setEffectiveSize ( f i n a l int newEffectiveSize ) {
_libGE_Genotype_effectiveSize=newEffectiveSize ;
}
/∗ Returns number of wrapping events
∗/
public f i n a l int getWraps ( ) {
return _libGE_Genotype_wraps ;
}
/∗ Sets the number of wrapping events

14. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GENOTYPE VI
∗/
public void setWraps ( f i n a l int newWraps ) {
_libGE_Genotype_wraps=newWraps ;
}
/∗Used to p r i n t the genome as a s t r i n g
∗/
public String printContents ( ) {
/ / String s=new String ( ) ;
return this . toArray ( ) . toS tr in g ( ) ;
}
}
/ / complete

15. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GRAMMAR I
/∗
∗ Grammar . java
∗
∗ Created on July 26 , 2007, 6:09 PM
∗
∗ To change t h i s template , choose Tools | Template Manager
∗ and open the template in the e d i t o r .
∗/
package GrammaticOptimization ;
/∗∗
∗
∗ @author a d i l r a j a
∗/
import java . u t i l . I t e r a t o r ;
public abstract class Grammar extends Mapper {
private boolean validGrammar ;
private int startSymbol ;
protected abstract boolean genotype2phenotype ( ) ;
protected abstract boolean phenotype2genotype ( ) ;
/∗∗
∗ Creates a new instance of Grammar
∗/

16. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GRAMMAR II
public Grammar ( ) {
super ( ) ;
setValidGrammar ( false ) ;
startSymbol =0;
}
/∗∗
∗Constructor s e t t i n g the genotype s t r u c t u r e of t h i s mapper to newGenotype .
∗/
public Grammar( f i n a l Genotype newGenotype ) {
super ( newGenotype ) ;
setValidGrammar ( false ) ;
startSymbol =0;
}
/∗∗
∗Constructor s e t t i n g the phenotype s t r u c t u r e of t h i s mapper to newPhenotype .
∗/
public Grammar( f i n a l Phenotype newPhenotype ) {
super ( newPhenotype ) ;
setValidGrammar ( false ) ;
startSymbol =0;
}
/∗∗
∗Copy Constructor

17. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GRAMMAR III
∗/
public Grammar( f i n a l Grammar copy ) {
super ( ) ;
setValidGrammar ( copy . getValidGrammar ( ) ) ;
startSymbol=copy . startSymbol ;
}
/∗∗
∗ Return the v a l i d i t y of the current grammar .
∗/
public f i n a l boolean getValidGrammar ( ) {
return validGrammar ;
}
/∗∗
∗Set the v a l i d i t y of the grammar .
∗/
protected void setValidGrammar ( f i n a l boolean newValidGrammar ) {
validGrammar=newValidGrammar ;
}
/∗∗
∗Return current s t a r t symbol .
∗/
public f i n a l Symbol getStartSymbol ( ) {

18. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GRAMMAR IV
/ / return f r o n t ( ) . lhs . f r o n t ( ) ;
/ / return (∗ t h i s ) [ startSymbol ] . lhs . f r o n t ( ) ;
Symbol symb=null ;
i f ( startSymbol <this . size ( ) )
{
symb=this . get ( startSymbol ) . lhs . get ( 0 ) ;
}
return symb ;
}
/∗∗
∗Change s t a r t symbol by index on Vector of rules .
∗/
public boolean setStartSymbol ( f i n a l int index ) {
i f ( index <this . size ( ) ) { / / Check boundaries .
startSymbol=index ;
genotype2phenotype ( ) ; / / Update phenotype .
return true ;
}
return false ;
}
/∗∗
∗Change s t a r t symbol by symbol pointer .
∗/
public boolean setStartSymbol ( f i n a l Symbol newStartSymbol ) {
int i i =0;

19. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GRAMMAR V
I t e r a t o r <Rule> i t =this . i t e r a t o r ( ) ;
while ( i t . hasNext ( ) ) {
/ / Work by ∗pointer ∗.
i f ( i t . next ( ) . lhs . get ( 0 ) . getSymbol ( ) . compareTo ( newStartSymbol . getSymbol ( ) ) = = 0 ) {
startSymbol= i i ;
genotype2phenotype ( ) ; / / Update phenotype .
return true ;
}
i i ++;
}
return false ;
}
/∗∗
∗Change s t a r t symbol by s t r i n g .
∗/
public boolean setStartSymbol ( f i n a l String newStartSymbol ) {
int i i =0;
I t e r a t o r <Rule> i t =this . i t e r a t o r ( ) ;
while ( i t . hasNext ( ) ) {
/ / Work by ∗s t r i n g ∗.
String currentStartSymbol= i t . next ( ) . lhs . get ( 0 ) . getSymbol ( ) ;
i f ( currentStartSymbol . compareTo ( newStartSymbol )==0){
startSymbol= i i ;
genotype2phenotype ( ) ; / / Update phenotype .
return true ;
}

20. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GRAMMAR VI
i i ++;
}
return false ;
}
/∗∗
∗Return pointer to current s t a r t rule .
∗/
public f i n a l Rule getStartRule ( ) {
return this . get ( 0 ) ;
}
}
/ / complete

21. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR I
/∗
∗ CFGrammar. java
∗
∗ Created on July 26 , 2007, 12:21 PM
∗
∗ To change t h i s template , choose Tools | Template Manager
∗ and open the template in the e d i t o r .
∗/
package GrammaticOptimization ;
/∗∗
∗
∗ @author a d i l r a j a
∗/
import java . u t i l . ∗ ;
import java . u t i l . ArrayList ;
import java . u t i l . I t e r a t o r ;
import java . io . ∗ ;
public abstract class CFGrammar extends Grammar {
protected Tree derivationTree ;
protected abstract boolean genotype2phenotype ( ) ;
protected abstract boolean phenotype2genotype ( ) ;
/∗∗
∗ Creates a new instance of CFGrammar

22. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR II
∗/
public CFGrammar ( ) {
super ( ) ;
}
/∗∗
∗Constructor s e t t i n g the genotype s t r u c t u r e of t h i s mapper to newGenotype .
∗/
public CFGrammar( f i n a l Genotype newGenotype ) {
super ( newGenotype ) ;
}
/∗∗
∗ Constructor s e t t i n g the phenotype s t r u c t u r e of t h i s mapper to newPhenotype .
∗/
public CFGrammar( f i n a l Phenotype newPhenotype ) {
super ( newPhenotype ) ;
}
/∗∗
∗ Copy Constructor .
∗/
public CFGrammar( f i n a l CFGrammar copy ) {
super ( copy ) ;
/ / Now must go through the copied grammar , and replace references to
/ / the copy ’ s lhs symbols with references to the new lhs symbols .
I t e r a t o r r u l e I t =this . i t e r a t o r ( ) ; / / i t e r a t o r of Rule
I t e r a t o r <Rule> prodIt ;

23. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR III
I t e r a t o r <Production > symbIt ;
Rule r u l e P t r =null ;
int ruleCt =0 , prodCt =0 , symbCt=0;
while ( r u l e I t . hasNext ( ) ) {
prodIt = r u l e I t ;
while ( prodIt . hasNext ( ) ) {
symbIt= prodIt . next ( ) . i t e r a t o r ( ) ;
while ( symbIt . hasNext ( ) ) {
Symbol symb=symbIt . next ( ) . get ( 0 ) ;
i f (symb . getType ( ) . t oSt ri ng ( ) . compareTo ( "NTSymbol" )==0){
try {
r u l e P t r =findRule (symb ) ;
}
catch ( Exception e ) {
/ / do nothing
}
i f ( r u l e P t r ==null ) {
/∗ Undefined NTSymbol − create new symbol ∗/
symb=new Symbol (symb . getSymbol ( ) , null ) ;
}
else {
/∗ Point to symbol ’ s d e f i n i t i o n ∗/
symb= r u l e P t r . lhs . get ( r u l e P t r . lhs . size () −1);
}
this . get ( ruleCt ) . get ( prodCt ) . insertSymbol (symb , symbCt ) ;
}
symbIt . next ( ) ;
symbCt++;

24. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR IV
}
prodIt . next ( ) ;
prodCt ++;
}
r u l e I t . next ( ) ;
ruleCt ++;
}
/ / I n v a l i d a t e phenotype − lower classes in hierarchy can always c a l l
/ / genotype2Phenotype ( ) to regenerate i t
phenotype . clear ( ) ;
phenotype . setValid ( false ) ;
/ / Don ’ t copy d e r i v a t i o n tree : procedure i s too complex and expensive .
/ / I f tree i s requested , i t w i l l be regenerated .
}
/∗∗
∗ Opens the f i l e whose name i s passed as an argument , reads i t s contents onto
∗a character string , and c a l l s readBNFString .
∗/
public boolean readBNFFile ( f i n a l String filename ) {
/∗
FILE ∗pFile ;
i f ( ! ( pFile=fopen ( filename , " r " ) ) ) {
cerr << " Could not open grammar f i l e " << filename << " . nExecution aborted . n
e x i t ( 1 ) ;
}
fseek ( pFile ,0 ,SEEK_END) ;
i n t size = f t e l l ( pFile ) ;

25. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR V
char program [ size +1];
strncpy ( program , " " , size ) ;
char l i n e [1024];
rewind ( pFile ) ;
while ( fgets ( line ,1024 , pFile ) )
s t r c a t ( program , l i n e ) ;
fclose ( pFile ) ;
s t r c a t ( program , " n " ) ;
return readBNFString ( program ) ;
∗/
String program=new String ( ) ;
/ / t r y
/ / {
/ / Open the f i l e that i s the f i r s t
/ / command l i n e parameter
/ / FileInputStream fstream = new FileInputStream ( " a d i l . bnf " ) ;
/ / Convert our input stream to a
/ / DataInputStream
/ / BufferedReader in = new BufferedReader (new InputStreamReader ( fstream ) ) ;
/ / Continue to read l i n e s while
/ / there are s t i l l some l e f t to read
/ / DataInput s = new DataInputStream (new FileInputStream ( " ~ / mywork /GE/ libGE −0.26/E
/ / String th is Li ne ;
/ / while ( ( th is Li ne =s . readLine ( ) ) != n u l l )
/ / {
/ / program . concat ( th is Li ne ) ;
/ / }

26. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR VI
/ / s . close ( ) ;
/ / }
/ / catch ( Exception e )
/ / {
/ / System . out . p r i n t l n ( e+" F i l e input error " ) ;
/ / }
/ / program . concat ( " n " ) ;
program="<expr > : : = (<expr > <op> <expr > ) n | DIV(<expr > , <expr > ) n | ABS(<expr > ) n | GT(
return readBNFString ( program ) ;
}
/∗∗
∗ Reads in the BNF grammar specified by i t s argument t e x t . Returns true i f
∗ loading of grammar was successful , false otherwise .
∗/
public boolean readBNFString ( String stream ) { / / the stream was f i n a l
/ / Delete the current grammar , i f any
this . clear ( ) ;
Rule newRule=new Rule ( 0 ) ; / / Used to create new rules f o r gramm
boolean insertRule=false ; / / I f newRule i s to be inserted onto grammar
Rule currentRule=null ; / / Used in pass 2 to add productions to current rule
Production newProduction=new Production ( 1 ) ;
newProduction . clear ( ) ; / / Used to create new productions f o r grammar
Symbol newSymbol=new Symbol ( ) ; / / Used to create new symbols f o r grammar
Symbol newTokenSeparator=new Symbol ( ) ; / / Used to create token separators f o r gramma

27. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR VII
int stream_size=stream . length ( ) ;
int i i , j j ; / / Working variables
char currentChar ; / / Current char of input
boolean skip=false ; / / SKip an i t e r a t i o n on parser ( f o r escaped newlines )
boolean quoted=false ; / / I f current char i s quoted
boolean non_terminal=false ; / / I f current t e x t i s a non−terminal symbol
char separated =0; / / I f there was a separator between previous token and
ArrayList <Symbol> nonTerminals=new ArrayList ( ) ;
nonTerminals . clear ( ) ; / / Contains pointers to a l l defined non−terminals
I t e r a t o r <Symbol> nonTerminalsIt ;
String currentBuffer =new String ( ) ; / / Buffer used to add new symbols to g
/ / States of parser
f i n a l int START = 0;
f i n a l int START_RULE = 1;
f i n a l int LHS_READ = 2;
f i n a l int PRODUCTION = 3;
f i n a l int START_OF_LINE = 4;
int state=START; / / Current state of parser
/ / #define libGE_DEBUG_CFGRAMMAR_PARSER
stream+=" n" ;
for ( int pass =1;pass <=2;pass ++){
i i = j j =0;
while ( i i <=stream_size ) {
i f ( i i <stream_size ) {
currentChar=stream . charAt ( i i ) ;
}

28. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR VIII
else {
/ / Simulate presence of endl at end of grammar
currentChar= ’ n ’ ;
}
System . out . p r i n t l n ( " I am here "+ i i ) ;
i f ( stream . charAt ( i i )== ’ ’ ) { / / Escape sequence
i i ++;
i f ( i i >=stream_size ) {
/ / Escape sequence as l a s t char i s i n v a l i d
ERROR_IN_GRAMMAR( ) ;
}
else i f ( ( non_terminal )&&( stream . charAt ( i i ) ! = ’ n ’ ) ) {
/ / Only escaped newline allowed inside non−terminal
System . out . p r i n t l n ( "ERROR: Escape sequence detected inside non−terminal s
ERROR_IN_GRAMMAR( ) ;
}
i f ( stream . charAt ( i i )== ’ ’ ’ ) { / / Single quote
currentChar= ’ ’ ’ ;
}
else i f ( stream . charAt ( i i )== ’ " ’ ) { / / Double quote
currentChar= ’ " ’ ;
}
else i f ( stream . charAt ( i i )== ’ ’ ) { / / Backslash
currentChar= ’ ’ ;
}
else i f ( stream . charAt ( i i )== ’0 ’ ) { / / Null character
currentChar= ’ 0 ’ ;
}

29. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR IX
/ / else i f ( stream . charAt ( i i )== ’a ’ ) { / / Audible b e l l
/ / currentChar = ’ a ’ ;
/ / }
else i f ( stream . charAt ( i i )== ’b ’ ) { / / Backspace
currentChar= ’ b ’ ;
}
else i f ( stream . charAt ( i i )== ’ f ’ ) { / / Formfeed
currentChar= ’ f ’ ;
}
else i f ( stream . charAt ( i i )== ’n ’ ) { / / Newline
currentChar= ’ n ’ ;
}
else i f ( stream . charAt ( i i )== ’ r ’ ) { / / Carriage return
currentChar= ’ r ’ ;
}
else i f ( stream . charAt ( i i )== ’ t ’ ) { / / Horizontal tab
currentChar= ’ t ’ ;
}
/ / else i f ( stream [ i i ]== ’ v ’ ) { / / V e r t i c a l tab
/ / currentChar = ’ v ’ ;
/ / }
else i f ( stream . charAt ( i i )== ’ n ’ ) { / / Escaped newline
/ / Ignore newline
skip=true ;
}
else i f ( stream . charAt ( i i )== ’ r ’ ) { / / Escaped DOS return
/ / Ignore newline
skip=true ;

30. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR X
i f ( stream . charAt (++ i i ) ! = ’ n ’ ) {
System . out . p r i n t l n ( "ERROR: r character not followed by n . " ) ;
ERROR_IN_GRAMMAR( ) ;
}
}
else { / / Normal character
currentChar=stream . charAt ( i i ) ;
}
i f ( ( ! skip )&&(pass >1)){
i f ( currentBuffer . length ()==0){
newSymbol . setType ( SymbolType . TSymbol ) ;
}
i f ( currentBuffer . length ()==0){
currentBuffer =Character . t oS tr ing ( currentChar ) ;
}
else {
/ / currentBuffer . concat ( Character . to St ri ng ( currentChar ) ) ;
currentBuffer +=currentChar ;
}
}
}
else {
switch ( state ) {
case (START) :
i f ( currentChar== ’ r ’ ) {
break ; / / Ignore DOS newline f i r s t char
}

31. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR XI
switch ( currentChar ) {
case ’ ’ : / / Ignore whitespaces
case ’ t ’ : / / Ignore tabs
case ’ n ’ : / / Ignore newlines
break ;
case ’< ’ : / / START OF RULE
newSymbol . setType ( SymbolType . NTSymbol ) ;
i f ( currentBuffer . length ()==0){
currentBuffer =Character . t oS tr in g ( currentChar ) ;
}
else {
/ / currentBuffer . concat ( Character . to St ri ng ( currentChar ) ) ;
currentBuffer +=currentChar ;
}
state=START_RULE;
break ;
default : / / I l l i g a l
System . out . p r i n t l n ( "ERROR: Character "+ currentChar + " caused an erro
ERROR_IN_GRAMMAR( ) ;
}
break ;
case (START_RULE ) : / / Read the lhs Non−terminal symbol
i f ( currentChar== ’ r ’ ) {
break ; / / Ignore DOS newline f i r s t char
}
switch ( currentChar ) {
case ’ n ’ : / / Newlines are i l l i g a l here
System . out . p r i n t l n ( "ERROR: Newline inside non−terminal . " ) ;

32. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR XII
ERROR_IN_GRAMMAR( ) ;
break ;
case ’> ’ : / / Possible end of non−terminal symbol
i f ( currentBuffer . length ()==0){
currentBuffer =Character . t oS tr ing ( currentChar ) ;
}
else {
/ / currentBuffer . concat ( Character . to St ri ng ( currentChar ) ) ;
currentBuffer +=currentChar ;
}
newSymbol . setSymbol ( currentBuffer ) ;
/ / newSymbol . setType ( SymbolType . NTSymbol ) ; / / t h i s was added a d i l
i f ( pass ==1){
/ / F i r s t pass
/ / Check i f new symbol d e f i n i t i o n
/ / insertRule = ! ( findRule ( newSymbol ) ) ;
Rule tmpRulePtr=null ;
try {
tmpRulePtr=findRule ( newSymbol ) ;
}
catch ( Exception e ) {
/ / do nothing
}
i f ( tmpRulePtr==null )
insertRule=true ;
else
insertRule=false ;
i f ( insertRule ) {

33. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR XIII
/ / Create new rule f o r symbol
newRule . clear ( ) ;
try {
newRule . lhs . add (new Symbol ( newSymbol ) ) ;
}
catch ( java . lang . Exception e ) {
System . out . p r i n t l n ( e + " newRule sucks " ) ;
}
/ / Add to grammar
try {
nonTerminals . add ( newRule . lhs . get ( newRule . lhs . size () −1));
}
catch ( java . lang . NullPointerException e ) {
System . out . p r i n t l n ( e+ " nonTerminals suck " ) ;
}
}
else { / / Existing symbol , do nothing
}
}
else {
/ / Second pass
/ / Point currentRule to previously defined rule
try {
i f ( ( currentRule=findRule ( newSymbol))== null ) {
System . out . p r i n t l n ( "ERROR: Grammar changed between parser pass
ERROR_IN_GRAMMAR( ) ;
}

34. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR XIV
}
catch ( java . lang . NullPointerException e ) {
System . out . p r i n t l n ( e+"ERROR: Grammar changed between parser passes
ERROR_IN_GRAMMAR( ) ;
}
catch ( java . lang . Exception e ) {
System . out . p r i n t l n ( e+"ERROR: Grammar changed between parser passes
}
/ / i f ( ( currentRule=findRule ( newSymbol))== n u l l ) {
/ / System . out . p r i n t l n ( "ERROR: Grammar changed between parser pa
/ / ERROR_IN_GRAMMAR( ) ;
/ / }
}
/ / Reset the buffer
currentBuffer =" " ;
/ / lhs f o r t h i s rule has been read
state=LHS_READ;
break ;
default : / / Check f o r non−escaped special characters
i f ( ( ( currentChar== ’ " ’ ) | | ( currentChar== ’ | ’ ) | | ( currentChar== ’< ’ ) ) ) {
System . out . p r i n t l n ( "ERROR: I n v a l i d character ’ " + currentChar + "
ERROR_IN_GRAMMAR( ) ;
}
i f ( currentBuffer . length ()==0){
currentBuffer =Character . t oS tr ing ( currentChar ) ;
}
else {
/ / currentBuffer . concat ( Character . to St ri ng ( currentChar ) ) ;

35. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR XV
currentBuffer +=currentChar ;
}
}
break ;
case (LHS_READ) : / / Must read : : = token
i f ( currentChar== ’ r ’ ) {
break ; / / Ignore DOS newline f i r s t char
}
switch ( currentChar ) {
case ’ ’ : / / Ignore whitespaces
case ’ t ’ : / / Ignore tabs
case ’ n ’ : / / Ignore newlines
break ;
case ’ : ’ : / / Part of : : = token
i f ( currentBuffer . length ()==0){
currentBuffer =Character . t oS tr in g ( currentChar ) ;
}
else {
/ / currentBuffer . concat ( Character . to St ri ng ( currentChar ) ) ;
currentBuffer +=currentChar ;
}
break ;
case ’= ’ : / / Should be end of : : = token
try {
i f ( currentBuffer . length ()==0){
currentBuffer =Character . t oS tr ing ( currentChar ) ;
}
else {

36. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR XVI
/ / currentBuffer . concat ( Character . to St ri ng ( currentChar ) ) ;
currentBuffer +=currentChar ;
}
/ / currentBuffer . concat ( Character . to St ri ng ( currentChar ) ) ;
}
catch ( java . lang . NullPointerException e ) {
System . out . p r i n t l n ( e ) ;
}
i f ( currentBuffer . equals ( " : : = " )== false ) { / / Something other than : : = was
System . out . p r i n t l n ( "ERROR: Token ’ " + currentBuffer + " ’ cause
ERROR_IN_GRAMMAR( ) ;
}
/ / Reset the buffer
currentBuffer =" " ;
/ / START OF PRODUCTION
newProduction . clear ( ) ;
state=PRODUCTION;
break ;
default : / / I l l i g a l
System . out . p r i n t l n ( "ERROR: Character ’ " + currentChar + " ’ caused an e
ERROR_IN_GRAMMAR( ) ;
}
break ;
case (PRODUCTION) : / / Read everything u n t i l | token or n , or EOL
i f ( currentChar== ’ r ’ ) {
break ; / / Ignore DOS newline f i r s t char
}
i f ( pass ==1){

37. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR XVII
i f ( currentChar== ’ n ’ )
state=START_OF_LINE;
}
else switch ( currentChar ) {
case ’ | ’ : / / Possible end of production
i f ( quoted ) { / / Normal character
/ / currentBuffer . concat ( Character . to St ri ng ( currentChar ) ) ;
i f ( currentBuffer . length ()==0){
currentBuffer =Character . t oS tr ing ( currentChar ) ;
}
else {
currentBuffer +=currentChar ;
}
break ;
}
case ’ n ’ : / / End of production ( and possibly rule )
/ / Reset separator marker
separated =0;
i f ( ( currentBuffer . length ( ) ! = 0 ) | | ( newProduction . size ( ) ! = 0 ) ) { / / The
System . out . p r i n t l n ( "A symbol ’ " + currentBuffer + " ’ " + newSym
i f ( currentBuffer . length ()==0){
/ / No symbol exists ; create terminal empty symbol
newSymbol . setType ( SymbolType . TSymbol ) ;
}
i f ( non_terminal ) { / / Current non−terminal symbol isn ’ t f in is hed
System . out . p r i n t l n ( "ERROR: Symbol ’ " + currentBuffer + " ’ caus
ERROR_IN_GRAMMAR( ) ;
}

38. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR XVIII
newSymbol . setSymbol ( currentBuffer ) ;
i f ( newSymbol . getType ( ) . t oSt ri ng ( ) . equals ( "NTSymbol" ) ) {
/ / Find rule that defines t h i s symbol
Rule tempRule=null ;
try {
tempRule=findRule ( newSymbol ) ;
}
catch ( Exception e ) {
/ / do nothing again
}
i f ( tempRule != null ) {
newProduction . add (new Symbol ( tempRule . lhs . get ( tempRule . lhs
}
else {
/ / Undefined symbol , i n s e r t anyway
newProduction . add (new Symbol ( newSymbol ) ) ;
}
}
else { / / Add terminal symbol
newProduction . add (new Symbol ( newSymbol ) ) ;
}
/ / Reset the symbol
/ / newSymbol . clear ( ) ; / / t h i s i s not required , the garbage c o l l e c t o r does
newSymbol . clear ( ) ;
}
else { / / Empty token ; ignored
;
}

39. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR XIX
/ / END OF PRODUCTION
/ / Add production to current rule
try {
currentRule . add (new Production ( newProduction ) ) ;
}
catch ( Exception e ) {
System . out . p r i n t l n ( e+" But the currentRule i s n u l l . . . i t sucks too "
}
/ / Reset the buffer
currentBuffer =" " ;
i f ( currentChar== ’ n ’ )
state=START_OF_LINE;
else {
/ / START OF PRODUCTION
newProduction . clear ( ) ;
}
break ;
case ’< ’ : / / Possible s t a r t of non−terminal symbol
case ’> ’ : / / Possible end of non−terminal symbol
case ’ ’ : / / Possible token separator
case ’ t ’ : / / Possible token separator
i f ( ( quoted ) / / Normal character
| | ( ( ( currentChar== ’ ’ ) | | ( currentChar== ’ t ’ ))&&( non_terminal ) ) ) { / / Spaces i
i f ( currentBuffer . length ()==0){
currentBuffer =Character . t oS tr in g ( currentChar ) ;
}
else {
/ / currentBuffer . concat ( Character . to St ri ng ( currentChar ) ) ;

40. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR XX
currentBuffer +=currentChar ;
}
i f ( ! non_terminal ) newSymbol . setType ( SymbolType . TSymbol ) ;
break ;
}
i f ( currentChar== ’> ’ ) { / / This i s also the end of a non−terminal symbol
i f ( currentBuffer . length ()==0){
currentBuffer =Character . t oS tr ing ( currentChar ) ;
}
else {
/ / currentBuffer . concat ( Character . to St ri ng ( currentChar ) ) ;
currentBuffer +=currentChar ;
}
non_terminal=false ;
}
i f ( currentBuffer . length () >0){
i f ( non_terminal ) { / / Current non−terminal symbol isn ’ t f in is hed
System . out . p r i n t l n ( "ERROR: Symbol " + currentBuffer + " ’ caused an
ERROR_IN_GRAMMAR( ) ;
}
i f ( ( currentChar== ’ ’ ) | | ( currentChar== ’ t ’ ) ) { / / Token separator
separated =1;
}
newSymbol . setSymbol ( currentBuffer ) ;
i f ( newSymbol . getType ( ) . to St ri ng ( ) . equals ( "NTSymbol" ) ) {
/ / Find rule that defines t h i s symbol
Rule tempRule=null ;
try {

41. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR XXI
tempRule=findRule ( newSymbol ) ;
}
catch ( java . lang . Exception e ) {
System . out . p r i n t l n ( e+" Finding the rule sucks . . . " ) ;
}
i f ( tempRule != null ) {
newProduction . add (new Symbol ( tempRule . lhs . get ( tempRule . lhs . siz
}
else {
/ / Undefined symbol , i n s e r t anyway
newProduction . add (new Symbol ( newSymbol ) ) ;
}
}
else { / / Add terminal symbol
newProduction . add (new Symbol ( newSymbol ) ) ;
}
/ / Reset the symbol
newSymbol . clear ( ) ;
}
else { / / Empty buffer
i f ( ( ( currentChar== ’ ’ ) | | ( currentChar== ’ t ’ ) ) / / Token separator
&&(newProduction . size ( ) > 0 ) ) {
/ / Probably a token separator a f t e r a non−terminal symbol
separated =1;
}
}
/ / Reset the buffer
currentBuffer =" " ;

42. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR XXII
i f ( currentChar== ’< ’ ) { / / This i s also the s t a r t of a non−terminal symbol
/ / Special case ; must create new Symbol here
newSymbol . clear ( ) ;
newSymbol . setType ( SymbolType . NTSymbol ) ;
i f ( currentBuffer . length ()==0){
currentBuffer =Character . t oS tr ing ( currentChar ) ;
}
else {
/ / currentBuffer . concat ( Character . to St ri ng ( currentChar ) ) ;
currentBuffer +=currentChar ;
}
non_terminal=true ; / / Now reading a non−terminal symbol
i f ( separated ! = 0 ) { / / I n s e r t a token separator
separated =0;
newTokenSeparator=new Symbol ( ) ;
newTokenSeparator . setSymbol ( " " ) ;
newTokenSeparator . setType ( SymbolType . TSymbol ) ;
newProduction . add (new Symbol ( newTokenSeparator ) ) ;
}
}
break ;
default : / / Add character to current buffer
i f ( separated ! = 0 ) { / / I n s e r t a token separator
separated =0;
newTokenSeparator=new Symbol ( ) ;
newTokenSeparator . setSymbol ( " " ) ;
newTokenSeparator . setType ( SymbolType . TSymbol ) ;
newProduction . add (new Symbol ( newTokenSeparator ) ) ;

43. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR XXIII
}
i f ( currentChar== ’ " ’ ) { / / Start ( or end ) quoted section
quoted =! quoted ;
newSymbol . setType ( SymbolType . TSymbol ) ;
break ;
}
i f ( currentBuffer . length ()==0){
newSymbol . setType ( SymbolType . TSymbol ) ;
}
i f ( currentBuffer . length ()==0){
currentBuffer =Character . t oS tr ing ( currentChar ) ;
}
else {
/ / currentBuffer . concat ( Character . to St ri ng ( currentChar ) ) ;
currentBuffer +=currentChar ;
}
}
break ;
case (START_OF_LINE ) :
i f ( currentChar== ’ r ’ ) {
break ; / / Ignore DOS newline f i r s t char
}
switch ( currentChar ) {
case ’ ’ : / / Ignore whitespaces
case ’ t ’ : / / Ignore tabs
case ’ n ’ : / / Ignore newlines
break ;
case ’ | ’ : / / Start of new production

44. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR XXIV
state=PRODUCTION;
i f ( pass ==2){
/ / START OF PRODUCTION
newProduction . clear ( ) ;
}
break ;
case ’< ’ : / / Start of lhs non−terminal symbol
/ / END OF RULE
i f ( pass ==1){
/ / Add current rule
i f ( insertRule ) {
try {
this . add (new Rule ( newRule ) ) ;
}
catch ( java . lang . NullPointerException e ) {
System . out . p r i n t l n ( e ) ;
}
}
}
/ / START OF RULE
newSymbol . setType ( SymbolType . NTSymbol ) ;
i f ( currentBuffer . length ()==0){
currentBuffer =Character . t oS tr ing ( currentChar ) ;
}
else {
/ / currentBuffer . concat ( Character . to St ri ng ( currentChar ) ) ;
currentBuffer +=currentChar ;

45. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR XXV
}
state=START_RULE;
break ;
default : / / I l l i g a l
System . out . p r i n t l n ( "ERROR: Detected l i n e s t a r t i n g with terminal symbol . " ) ;
ERROR_IN_GRAMMAR( ) ;
}
break ;
default : / / Impossible error , q u i t the program now !
System . out . p r i n t l n ( " I n t e r n a l error . nPlease report error ’ Impossible state in
System . e x i t ( 0 ) ;
}
}
skip=false ;
i i ++;
}
/ / END OF PASS
i f ( state !=START_OF_LINE ) { / / This must be the state of the parser
System . out . p r i n t l n ( " Parsing error reading grammar . " ) ;
ERROR_IN_GRAMMAR( ) ;
}
i f ( pass ==1){
/ / Add current rule
i f ( insertRule ) {
this . add (new Rule ( newRule ) ) ;
}
}

46. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR XXVI
}
updateRuleFields ( ) ;
setValidGrammar ( true ) ;
genotype2phenotype ( ) ;
return true ;
}
/∗∗
∗ Reads in the BNF grammar−part specified by i t s argument text , and adds i t to
∗the current grammar . Returns true i f loading of new grammar part was
∗successful , false otherwise .
∗/
public boolean addBNFString ( f i n a l String stream ) {
/ / FIXME Slow implementation .
/ / Copy current grammar
ArrayList <Rule> grammarCopy=this ;
/ / Create appended grammar s t r i n g
String newGrammarStream=outputBNF ( ) ;
String newGrammar=new String ( newGrammarStream ) ;
newGrammar=stream ;
/ / Read new grammar
try {
i f ( ! readBNFString (newGrammar ) ) {
/ / Restore previous state of Mapper
readBNFString ( newGrammarStream ) ;
return false ;

47. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR XXVII
}
return true ;
}
catch ( java . lang . Exception e ) {
return false ;
}
}
/∗∗
∗ Pretty p r i n t the current BNF grammar .
∗/
public String outputBNF ( ) {
String stream=null ;
i f ( ! getValidGrammar ( ) ) {
return null ;
}
I t e r a t o r <Rule> r _ i t =this . i t e r a t o r ( ) ;
while ( r _ i t . hasNext ( ) ) {
Rule tmp ;
tmp= r _ i t . next ( ) ;
stream . concat ( tmp . lhs . get ( tmp . lhs . size () −1). getSymbol ( ) + " : : = " ) ;
/ / go through productions
I t e r a t o r <Production > p _ i t =tmp . i t e r a t o r ( ) ;
while ( p _ i t . hasNext ( ) ) {
/ / go through symbols
I t e r a t o r <Symbol> s _ i t = p _ i t . next ( ) . i t e r a t o r ( ) ;

48. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR XXVIII
while ( s _ i t . hasNext ( ) ) {
stream . concat ( s _ i t . next ( ) . getSymbol ( ) ) ;
}
stream . concat ( " | " ) ;
}
stream=stream . trim ( ) ;
stream . concat ( " n" ) ;
/ / get next rule
}
return stream ;
}
/∗∗
∗ Returns the address of the rule defining the argument non−terminal symbol ,
∗ i f i t exists ; otherwise returns NULL.
∗/
public Rule findRule ( f i n a l Symbol nonterminal ) throws Exception {
I t e r a t o r <Rule> r u l e I t =this . i t e r a t o r ( ) ;
Rule tmp ;
while ( r u l e I t . hasNext ( ) ) {
tmp= r u l e I t . next ( ) ;
i f ( tmp . lhs . get ( tmp . lhs . size () −1).makeComparison ( nonterminal ) )
return tmp ;
}
return null ;
}

49. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR XXIX
/∗∗
∗Returns the calculated recursive nature of the Rule passed as argument ,
∗and updates i t s minimum mapping depth ( minimumDepth )
∗/
private boolean isRecursive ( ArrayList <Symbol> visitedRules , Rule currentRule ) {
I t e r a t o r <Production > prodIt =currentRule . i t e r a t o r ( ) ;
I t e r a t o r <Symbol> symbIt ;
I t e r a t o r <Symbol> v i s i t e d R u l e s I t =visitedRules . i t e r a t o r ( ) ;
Rule r u l e P t r =null ;
boolean r e s u l t ;
/ / DON’T DO IT − otherwise minimumDepth i s not updated properly
/ / I f t h i s rule has already been labeled , e x i t
/ / i f ( currentRule−>getRecursive ( ) ! = SI_Undef ) {
/ / return currentRule−>getRecursive ( ) ;
/ / }
/ / Check i f t h i s i s a recursive c a l l to a previously v i s i t e d rule
while ( v i s i t e d R u l e s I t . hasNext ( ) ) {
i f ( v i s i t e d R u l e s I t . next ( ) . makeComparison ( currentRule . lhs . get ( currentRule . lhs . si
currentRule . setRecursive ( true ) ;
return true ;
}
}
/ / Go through each production in the rule
while ( prodIt . hasNext ( ) ) {
Production tmp_pd= prodIt . next ( ) ;

50. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR XXX
tmp_pd . setMinimumDepth ( 0 ) ;
symbIt=tmp_pd . i t e r a t o r ( ) ;
/ / Go through each symbol in the production
while ( symbIt . hasNext ( ) ) {
Symbol tmp_symb=symbIt . next ( ) ;
i f ( tmp_symb . getType ( ) . to St ri ng ( ) . equals ( "NTSymbol" ) ) { / / Symbol i s non−
try {
r u l e P t r =findRule ( tmp_symb ) ; / / Find defining rule
}
catch ( java . lang . Exception e ) {
/ / do nothing
}
i f ( r u l e P t r != null ) { / / Symbol i s defined
/ / Recursive c a l l
visitedRules . add ( currentRule . lhs . get ( currentRule . lhs . s
r e s u l t =isRecursive ( visitedRules , r u l e P t r ) ;
visitedRules . remove ( visitedRules . size () −1);
i f ( r e s u l t ) { / / Production i s recursive
/ / Mark production as recursive
tmp_pd . setRecursive ( true ) ;
/ / Mark current rule also as recursive
currentRule . setRecursive ( true ) ;
}
i f ( tmp_pd . getMinimumDepth () <( r u l e P t r . getMinimumDepth ( )
tmp_pd . setMinimumDepth ( r u l e P t r . getMinimumDepth
}
}
else { / / Non−defined non−terminal symbols are considered term

51. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR XXXI
i f ( tmp_pd . getMinimumDepth () <1){
tmp_pd . setMinimumDepth ( 1 ) ;
}
}
}
else { / / Terminal symbol
i f ( tmp_pd . getMinimumDepth () <1){
tmp_pd . setMinimumDepth ( 1 ) ;
}
}
}
/ / i f ( prodIt −>getRecursive ()== SI_Undef ) { / / Production i s not recursive
/ / prodIt −>setRecursive ( SI_NonRec ) ;
/ / }
i f ( currentRule . getMinimumDepth () >tmp_pd . getMinimumDepth ( ) ) { / / Update rule mini
currentRule . setMinimumDepth ( tmp_pd . getMinimumDepth ( ) ) ;
}
/ / prodIt ++;
}
/ / i f ( currentRule−>getRecursive ( ) ! = SI_Rec ) { / / Rule i s not recursive , as i t contains no
/ / currentRule−>setRecursive ( SI_NonRec ) ;
/ / return SI_NonRec ;
/ / }
/ / return SI_Rec ;
return currentRule . getRecursive ( ) ;
}
/∗∗

52. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR XXXII
∗ Update recursive and minimumDepth f i e l d s f o r every Rule
∗/
/ / and Production in grammar .
private void updateRuleFields ( ) {
ArrayList <Symbol> visitedRules=new ArrayList ( ) ;
I t e r a t o r <Rule> r u l e I t =this . i t e r a t o r ( ) ;
clearRuleFields ( ) ;
/ / Go through each rule in the grammar
while ( r u l e I t . hasNext ( ) ) {
try {
visitedRules . clear ( ) ;
}
catch ( java . lang . NullPointerException e ) {
System . out . p r i n t l n ( e+" UpdateRuleFields sucks " ) ;
}
Rule tmp_rule= r u l e I t . next ( ) ;
tmp_rule . setRecursive ( isRecursive ( visitedRules , tmp_rule ) ) ;
}
/ / Second pass , to c o r r e c t l y update a l l recursive rules
r u l e I t =this . i t e r a t o r ( ) ;
while ( r u l e I t . hasNext ( ) ) {
try {
visitedRules . clear ( ) ;
}
catch ( java . lang . NullPointerException e ) {

53. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR XXXIII
System . out . p r i n t l n ( e+" UpdateRuleFields sucks " ) ;
}
Rule tmp_rule= r u l e I t . next ( ) ;
tmp_rule . setRecursive ( isRecursive ( visitedRules , tmp_rule ) ) ;
}
}
/∗∗
∗ Update recursive and minimumDepth f i e l d s f o r every Rule
∗/
/ / and Production in grammar .
private void clearRuleFields ( ) {
I t e r a t o r <Rule> r u l e I t =this . i t e r a t o r ( ) ;
/ / Reset minimum depths and recursion f i e l d s
while ( r u l e I t . hasNext ( ) ) {
Rule tmp_rule= r u l e I t . next ( ) ;
tmp_rule . setMinimumDepth(32767 > >1);
tmp_rule . setRecursive ( false ) ;
}
}
/ / ERROR FUNCTION
private boolean ERROR_IN_GRAMMAR( ) {
System . out . p r i n t l n ( "Grammar not loaded ; " ) ;
try {
this . clear ( ) ;
}
catch ( java . lang . NullPointerException e ) {

54. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
CONTEXT-FREE GRAMMAR XXXIV
System . out . p r i n t l n ( e ) ;
}
setValidGrammar ( false ) ;
try {
phenotype . clear ( ) ;
phenotype . setValid ( false ) ;
}
catch ( java . lang . NullPointerException e ) {
System . out . p r i n t l n ( e ) ;
}
return false ;
}
}
/ / F i r s t implementation i s complete , t h i s f i l e may pose a l o t of bugs .

55. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GE GRAMMAR I
/∗
∗ GEGrammar. java
∗
∗ Created on August 2 , 2007, 12:22 AM
∗
∗ To change t h i s template , choose Tools | Template Manager
∗ and open the template in the e d i t o r .
∗/
package GrammaticOptimization ;
/∗∗
∗
∗ @author a d i l r a j a
∗/
import java . u t i l . ∗ ;
import java . u t i l . L i s t I t e r a t o r ;
public class GEGrammar extends CFGrammar {
private int maxWraps ;
protected ArrayList <Production > productions ;
/∗∗
∗ Creates a new instance of GEGrammar
∗/

56. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GE GRAMMAR II
public GEGrammar ( ) {
super ( ) ;
setMaxWraps ( 0 ) ;
}
/∗∗
∗Constructor s e t t i n g the genotype s t r u c t u r e of t h i s mapper to newGenotype .
∗/
public GEGrammar( f i n a l Genotype newGenotype ) {
super ( newGenotype ) ;
setMaxWraps ( 0 ) ;
productions=new ArrayList ( ) ;
}
/∗∗
∗Constructor s e t t i n g the phenotype s t r u c t u r e of t h i s mapper to newPhenotype .
∗/
public GEGrammar( f i n a l Phenotype newPhenotype ) {
super ( newPhenotype ) ;
setMaxWraps ( 0 ) ;
}
/∗∗
∗ Copy Constructor .
∗/
public GEGrammar( f i n a l GEGrammar copy ) throws Exception {
super ( copy ) ;
setMaxWraps ( copy . getMaxWraps ( ) ) ;

57. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GE GRAMMAR III
/ / Call genotype2Phenotype ( ) to regenerate phenotype structure ,
/ / and productions and derivationTree structures .
genotype2phenotype ( true ) ;
}
/∗∗
∗ Return number of maximum allowed wrapping events .
∗/
public f i n a l int getMaxWraps ( ) {
return maxWraps ;
}
/∗∗
∗ Set the new number of maximum allowed wrapping events .
∗/
public void setMaxWraps ( f i n a l int newMaxWraps ) {
maxWraps=newMaxWraps ;
}
/∗∗
∗ Builds the the current d e r i v a t i o n tree , and returns i t s address ;
∗ i f d e r i v a t i o n tree i s impossible to build , returns NULL.
∗/
public f i n a l Tree getTree ( ) throws Exception {
i f ( ( ! getValidGrammar ( ) ) | | ( ! genotype . getValid ( ) ) | | ( getGenotype ( ) . size ( ) ! = 0 ) ) {
return null ;
}

58. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GE GRAMMAR IV
genotype2phenotype ( true ) ;
return this . derivationTree ;
}
/∗∗
∗ Returns a vector of a l l productions used during the mapping process .
∗/
public f i n a l ArrayList <Production > getProductions ( ) throws Exception {
i f ( ( ! getValidGrammar ( ) ) | | ( ! genotype . getValid ( ) ) | | ( getGenotype ( ) . size ( ) ! = 0 ) ) {
return null ;
}
genotype2phenotype ( true ) ;
return productions ;
}
/∗∗
∗ S t r i c t implementation of genotype2Phenotype i n t e r f a c e . Calls l o c a l
∗ genotype2phenotype ( bool ) method , with bool= false .
∗/
public boolean genotype2phenotype ( ) {
/ / t r y {
return genotype2phenotype ( false ) ;
/ / }
/ / catch ( Exception e ) {
/ / System . out . p r i n t l n ( e+" genotype2phenotype ( ) " ) ;
/ / return false ;

59. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GE GRAMMAR V
/ / }
}
/∗∗
∗ Updates the contents of the phenotype structure , based on the current
∗ genotype and the current grammar , and according to the standard GE
∗ mapping process . Returns true upon a successful mapping , and false
∗ otherwise , and also updates the v a l i d f i e l d of the phenotype .
∗ With argument set to true , also updates derivationTree .
∗/
public boolean genotype2phenotype ( f i n a l boolean buildDerivationTree ) {
this . derivationTree=new Tree ( ) ; / / I n i t i a l i z e the tree
boolean returnValue=true ;
int newEffectiveSize =0;
/ / Start by s e t t i n g e f f e c t i v e S i z e to 0
genotype . setEffectiveSize ( newEffectiveSize ) ;
this . phenotype=new Phenotype ( true , 1 ) ;
i f ( ! phenotype . isEmpty ( ) )
phenotype . clear ( ) ;
i f ( buildDerivationTree ) {
this . productions . clear ( ) ;
}
/ / Quick safety checks
/ / i f ( ( ! getValidGrammar ( ) ) | | ( ! genotype . getValid ( ) ) | | ( ! getGenotype()−> size ( ) ) ) {
i f ( ! getValidGrammar ( ) ) {
phenotype . clear ( ) ;

60. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GE GRAMMAR VI
phenotype . setValid ( false ) ;
return false ;
}
/ / Wraps counter and nonterminals stack
int wraps =0;
Stack <Symbol> nonterminals=new Stack ( ) ;
/ / I t e r a t o r s
I t e r a t o r <Rule> r u l e I t ;
L i s t I t e r a t o r <Production > prodIt ;
I t e r a t o r <Integer > genoIt=genotype . i t e r a t o r ( ) ;
Integer tmpInt ; / / s h a l l contain the values in Genotype
/ / Start with the s t a r t symbol
nonterminals . push ( getStartSymbol ( ) ) ;
i f ( buildDerivationTree ) {
/ / Use s t a r t symbol as the derivationTree node
try {
derivationTree . setData ( getStartSymbol ( ) ) ;
}
catch ( java . lang . NullPointerException e ) {
System . out . p r i n t l n ( e+" The c a l l : derivationTree . setData ( getStartSymbol ( ) ) ; in
}
}
boolean gotToUseWrap=true ;
Integer codonGenoIt=new Integer ( genoIt . next ( ) . intValue ( ) ) ;

61. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GE GRAMMAR VII
/ / Get r i d of a l l non−terminal symbols
while ( ( ! nonterminals . empty ())&&( wraps<=getMaxWraps ( ) ) ) {
/ / Do a mapping step
switch ( genotype2phenotypeStep ( nonterminals , codonGenoIt , buildDerivationTree ) )
case −1:returnValue=false ;
break ;
case 0: ;
break ;
case 1: codonGenoIt=new Integer ( genoIt . next ( ) . intValue ( ) ) ;
/ / genoIt ++;
newEffectiveSize ++;
i f ( gotToUseWrap ) {
wraps++;
gotToUseWrap=false ;
}
/ / Check i f wrap i s needed
i f ( ! genoIt . hasNext ( ) ) {
/ / newEffectiveSize+=genotype . size ( ) ;
genoIt=genotype . i t e r a t o r ( ) ;
codonGenoIt=new Integer ( genoIt . next ( ) . intValue ( ) ) ;
gotToUseWrap=true ;
}
break ;
default : System . out . p r i n t l n ( " I n t e r n a l error in genotype2Phenotype ( ) " ) ;
System . out . p r i n t l n ( " Execution aborted . " ) ;

62. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GE GRAMMAR VIII
System . e x i t ( 0 ) ;
}
}
/ / newEffectiveSize +=( genoIt−genotype . begin ( ) ) ;
/ / Was the mapping successful?
i f ( ( wraps>getMaxWraps ( ) ) | | ( ! nonterminals . empty ( ) ) ) {
returnValue=false ;
/ / Add remaining symbols in nonterminals queue to phenotype
while ( ! nonterminals . empty ( ) ) {
phenotype . add ( nonterminals . pop ( ) ) ;
}
}
phenotype . setValid ( returnValue ) ;
genotype . setEffectiveSize ( newEffectiveSize ) ;
genotype . setWraps ( wraps ) ;
/ / Now build d e r i v a t i o n tree , based on productions vector
i f ( buildDerivationTree ) {
derivationTree . clear ( ) ;
derivationTree . setData ( getStartSymbol ( ) ) ;
derivationTree . setCurrentLevel ( 1 ) ;
derivationTree . setDepth ( 1 ) ;
prodIt =productions . l i s t I t e r a t o r ( ) ; / / something wrong here
buildDTree ( derivationTree , prodIt ) ;
}
return returnValue ;
}
/∗∗

63. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GE GRAMMAR IX
∗ Updates the contents of the genotype structure , based on the current
∗ phenotype and the current grammar , and according to a mapping process
∗ corresponding to the inverse of the standard GE mapping process .
∗ Returns true upon a successful inverse mapping , and false otherwise .
∗/
public boolean phenotype2genotype ( ) {
return false ;
/ / FIXME
}
/∗∗
∗ Performs one step of the mapping process , that is , maps the next
∗non−terminal symbol on the nonterminals stack passed as argument , using the
∗codon at the pos it io n pointed by genoIt .
∗Returns number of codons consumed , −1 i f not successful
∗/
public int genotype2phenotypeStep ( Stack <Symbol> nonterminals , Integer codonGenoIt , boolean bu
L i s t I t e r a t o r <Production > prodIt ;
int returnValue=−1;
/ / Find the rule f o r the current non−terminal
Rule r u l e P t r =null ;
try {
r u l e P t r =findRule ( nonterminals . peek ( ) ) ;
}
catch ( java . lang . Exception e ) {
System . out . p r i n t l n ( e+" genotype2phenotypeStep ( ) s r u l e P t r sucks " ) ;

64. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GE GRAMMAR X
}
/ / cerr << " mapping " << ∗( nonterminals . top ( ) ) << " with " << ∗genoIt << " n " ;
i f ( r u l e P t r ==null ) { / / Undefined symbol − could be an extension symbol
try {
i f ( nonterminals . peek ( ) . getSymbol ( ) . startsWith ( "<GECodonValue" )&&( codonGenoIt !=
/ / I n s e r t codon value
/ / Extract range f o r value from non−terminal s p e c i f i c a t i o n
int low =0 , high=−1,pointer ="<GECodonValue" . length ( ) ;
/ / currentChar i s the f i r s t character a f t e r "<GECodonValue"
char currentChar=nonterminals . peek ( ) . getSymbol ( ) . substring ( pointer , po
/ / Look f o r range d e f i n i t i o n s
while ( Character . to St ri ng ( currentChar ) . compareTo ( ">" ) ! = 0 ) {
i f ( Character . t oSt ri ng ( currentChar ) . compareTo ( "−" )==0){
/ / Low range s p e c i f i c a t i o n
currentChar=nonterminals . peek ( ) . getSymbol ( ) . substring (
while ( Character . i s D i g i t ( currentChar ) ) {
low =( low ∗10)+( currentChar−’0 ’ ) ;
currentChar=nonterminals . peek ( ) . getSymbol ( ) . s
}
}
else i f ( Character . t oSt ri ng ( currentChar ) . compareTo ( "+" )==0){
/ / High range s p e c i f i c a t i o n
currentChar=nonterminals . peek ( ) . toS tr in g ( ) . substring (+
while ( Character . i s D i g i t ( currentChar ) ) {
i f ( high==−1){

65. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GE GRAMMAR XI
high =0;
}
high =( high ∗10)+( currentChar−’0 ’ ) ;
currentChar=nonterminals . peek ( ) . toS tr in g ( ) . su
}
}
else { / / Ignore errors
currentChar=nonterminals . peek ( ) . toS tr in g ( ) . substring (+
}
}
/ / High range was not specified , so set i t to maximum
i f ( high==−1){
high=genotype . getMaxCodonValue ( ) ;
}
/ / Remove non−terminal
nonterminals . pop ( ) ;
/ / P r i n t value onto " codon "
String codon ;
i f ( high==low ) {
/ / Catch d i v i s i o n by zero
codon=Integer . toS tr in g ( low ) ;
}
else {
codon=Integer . toS tr in g ( codonGenoIt . intValue ()%( high−low+1)+low
}
/ / I n s e r t symbol with value onto phenotype
phenotype . add (new Symbol ( codon , null ) ) ;
returnValue =1;

66. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GE GRAMMAR XII
}
else {
/ / Unknown symbol or special symbol that requires non−empty genotype
/ / Include symbol on phenotype
phenotype . add ( nonterminals . pop ( ) ) ;
/ / Remove non−terminal
/ / nonterminals . pop ( ) ;
/ / I n v a l i d a t e mapping
returnValue=−1;
}
}
catch ( java . lang . NullPointerException e ) {
System . out . p r i n t l n ( e ) ;
}
}
/ / else i f ( rulePtr −>getMinimumDepth() >=INT_MAX> >1){// Stuck on recursive rule
/ / Allow recursive rules , but only i f they consume a codon
else i f ( ( r u l e P t r . getMinimumDepth() >=(32767 > >1)) / / Stuck on recursive rule
&&( r u l e P t r . size () <=1)){ / / No codon w i l l be consumed
/ / Include symbol on phenotype
phenotype . add ( nonterminals . pop ( ) ) ;
/ / Remove non−terminal
/ / nonterminals . pop ( ) ;
/ / I n v a l i d a t e mapping
returnValue=−1;
}
else {

67. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GE GRAMMAR XIII
/ / Remove non−terminal
nonterminals . pop ( ) ;
/ / Choose production
i f ( codonGenoIt==null&&r u l e P t r . size () >1){
/ / Empty genotype , but symbol requires choice
/ / Include symbol on phenotype
phenotype . add ( r u l e P t r . lhs . get ( 0 ) ) ;
/ / I n v a l i d a t e mapping
returnValue=−1;
}
else {
i f ( codonGenoIt==null ) { / / Empty genotype
prodIt = r u l e P t r . l i s t I t e r a t o r ( 0 ) ;
}
else {
prodIt = r u l e P t r . l i s t I t e r a t o r ( 0 ) ;
int tmp=0;
tmp=codonGenoIt . intValue ()% r u l e P t r . size ( ) ;
for ( int i =0; i <tmp ; i ++)
prodIt . next ( ) ;
/ / i f ( prodIt . hasPrevious ( ) )
/ / prodIt . previous ( ) ;
}
/ / Place production on productions vector
Production tmpProd= prodIt . next ( ) ;
i f ( buildDerivationTree ) {
productions . add ( tmpProd ) ; / / tmpProd i s also used l a t t e r
}

68. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GE GRAMMAR XIV
/ / Put a l l terminal symbols at s t a r t of production onto phenotype
int s_start =0;
int s_stop =0;
try {
s_stop=tmpProd . size ( ) ; / / Instead of prodIt . size ( ) ;
}
catch ( java . lang . NullPointerException e ) {
System . out . p r i n t l n ( e+" tmpProd i s n u l l in GEGrammar" ) ;
}
while ( ( s_start <s_stop)&&tmpProd . get ( s_start ) . getType ( ) . to Str in g ( ) . com
phenotype . add ( tmpProd . get ( s_start ++));
/ / s_start ++;
}
/ / Push a l l remaining symbols from production onto nonterminals queue
for ( ; s_stop > s_start ; s_stop−−){
nonterminals . push ( tmpProd . get ( s_stop −1));
}
/ / 0 or 1 choice f o r current rule , didn ’ t consume genotype codon
i f ( r u l e P t r . size () <=1){
returnValue =0;
}
else {
returnValue =1;
}
}
}
i f ( phenotype==null ) System . out . p r i n t l n ( " Phenotype i s messy" ) ;

69. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GE GRAMMAR XV
/ / Finally , pop a l l terminal symbols on top of stack and i n s e r t onto phenotype
/ / t r y {
while ( true ) {
try {
i f ( ( nonterminals . empty ( ) ) | | ( ! nonterminals . peek ( ) . getType ( ) . to St rin g ( ) . equals
break ;
}
phenotype . add ( nonterminals . pop ( ) ) ;
}
catch ( java . lang . NullPointerException e ) {
System . out . p r i n t l n ( e+" The whileloop at the end of genotype2phenotypeStep suck
System . e x i t ( 0 ) ;
}
catch ( java . u t i l . EmptyStackException e ) {
System . out . p r i n t l n ( e+" GEGrammar sucks . . . Stack i s empty " ) ;
System . e x i t ( 0 ) ;
}
}
/ / }
/ / catch ( java . lang . NullPointerException e ) {
/ / System . out . p r i n t l n ( e+" The whileloop at the end of genotype2phenotypeStep sucks
/ / }
return returnValue ;
}

70. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GE GRAMMAR XVI
/∗∗
∗ Builds the d e r i v a t i o n tree , based on the productions vector .
∗Arguments are current tree node , and i t e r a t o r on productions vector .
∗/
public void buildDTree ( Tree currentNode , L i s t I t e r a t o r <Production > prodIt ) {
/ / I f current symbol i s not a non−terminal , or i f a l l productions have been treated
i f ( currentNode . getData ( ) . getType ( ) . t oS tri ng ( ) . compareTo ( "NTSymbol" ) ! = 0 | | ! prodIt . hasNe
/ / Correct productions i t e r a t o r , as no production was read from i t
prodIt . previous ( ) ;
return ;
}
/ / Create new tree l e v e l
I t e r a t o r <Symbol> symbIt= prodIt . next ( ) . i t e r a t o r ( ) ; ;
while ( symbIt . hasNext ( ) ) {
currentNode . add (new Tree ( symbIt . next ( ) , currentNode . getCurrentLevel ()+1 , curre
/ / symbIt ++;
}
/ / Expand each c h i l d node
I t e r a t o r <Tree> t r e e I t =currentNode . i t e r a t o r ( ) ;
while ( t r e e I t . hasNext ( ) ) {
try {
buildDTree ( t r e e I t . next ( ) , prodIt ) ;
/ / prodIt . next ( ) ;

71. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
GE GRAMMAR XVII
}
catch ( java . u t i l . NoSuchElementException e ) {
System . out . p r i n t l n ( e+" The l a s t l i n e s of buildTree suck " ) ;
System . e x i t ( 0 ) ;
}
/ / t r e e I t ++;
}
}
}

72. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
BACKUS NAUR FORM I
<expr > : : = mymul(<expr > , <expr >) | mysub(<expr > , <expr >) | myadd(<expr > , <expr >) | pdiv (<expr >
| (<expr >)
| sin (<expr >) | cos(<expr >) | tan (<expr >) | exp(<expr >)
| x | y | 1.000 | <const> | −<const>
<const> : : = 0. < d i g i t >< d i g i t >< d i g i t >
< d i g i t > : : = 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

73. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
PRODUCTION I
/∗
∗ Production . java
∗
∗ Created on June 3 , 2007, 12:24 AM
∗
∗ To change t h i s template , choose Tools | Template Manager
∗ and open the template in the e d i t o r .
∗/
/∗∗
∗
∗ @author a d i l r a j a
∗/
package GrammaticOptimization ;
import java . u t i l . ∗ ;
import java . u t i l . ArrayList ;
import java . u t i l . I t e r a t o r ;
public class Production extends ArrayList <Symbol >{
private boolean recursive ;
private int minimumDepth ;
/∗∗

74. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
PRODUCTION II
∗Creates a new production with newLength elements
∗/
public Production ( f i n a l int newLength ) {
super ( ) ;
this . ensureCapacity ( newLength ) ;
setRecursive ( false ) ;
setMinimumDepth(32767 > >1);
}
/∗∗
∗Copy constructor ; copy a l l symbols
∗/
public Production ( f i n a l Production copy ) {
I t e r a t o r <Symbol> i t r = copy . i t e r a t o r ( ) ;
while ( i t r . hasNext ( ) ) {
Symbol tmpsymb= i t r . next ( ) ;
i f ( tmpsymb . getType ( ) . to St ri ng ( ) . compareTo ( " TSymbol " )==0){
this . add (new Symbol ( tmpsymb ) ) ; / / Terminal symbol , create new one
}
else
this . add ( tmpsymb ) ;
}
setRecursive ( copy . recursive ) ;
setMinimumDepth ( copy . minimumDepth ) ;
}
/∗∗
∗Delete a l l terminal symbols and a l l symbol references
∗/
public void clearTerminals ( ) {

75. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
PRODUCTION III
I t e r a t o r <Symbol> i t r = this . i t e r a t o r ( ) ;
while ( i t r . hasNext ( ) ) {
Symbol tmpsymb= i t r . next ( ) ;
i f ( tmpsymb . getType ( ) . to St ri ng ( ) . compareTo ( " TSymbol " )==0){
this . remove ( tmpsymb ) ;
}
}
}
/∗∗
∗Return the recursive nature of t h i s production
∗/
public f i n a l boolean getRecursive ( ) {
return this . recursive ;
}
/∗∗
∗Update the recursive nature of t h i s production
∗/
public void setRecursive ( f i n a l boolean newRecursive ) {
this . recursive=newRecursive ;
}
/∗∗
∗Return the minimum mapping depth of t h i s production
∗/
public f i n a l int getMinimumDepth ( ) {

76. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
PRODUCTION IV
return this . minimumDepth ;
}
/∗∗
∗Update the minimum mapping depth of t h i s production
∗/
public void setMinimumDepth ( f i n a l int newMinimumDepth ) {
this . minimumDepth=newMinimumDepth ;
}
/∗∗
∗P r i n t the contents of t h i s production
∗/
/∗∗
∗This removes and adds a symbol at a p a r t i c u l a r l oc at io n in t h i s object . To be called l a
∗/
public void insertSymbol ( f i n a l Symbol symb , int pos ) {
this . remove ( pos ) ;
this . add ( pos , symb ) ;
}
}
/ / f i l e complete

77. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
RULE I
/∗
∗ Rule . java
∗
∗ Created on June 21 , 2007, 12:06 PM
∗
∗ To change t h i s template , choose Tools | Template Manager
∗ and open the template in the e d i t o r .
∗/
package GrammaticOptimization ;
/∗∗
∗
∗ @author a d i l r a j a
∗/
import java . u t i l . ∗ ;
import java . u t i l . ArrayList ; / / The l e f t −hand side of the rule
public class Rule extends ArrayList <Production >{
private boolean recursive ; / / Recursive nature of rule
private int minimumDepth ; / / Minimum depth of parse tree f o r production to map to termin
public ArrayList <Symbol> lhs ;
/∗∗
∗Creates a new rule with newLength elements .
∗/
public Rule ( f i n a l int newLength ) {
super ( newLength ) ;
this . ensureCapacity ( newLength ) ;
setRecursive ( false ) ;

78. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
RULE II
setMinimumDepth(32767 > >1);
lhs =new ArrayList ( ) ;
}
/∗∗
∗Copy constructor
∗/
public Rule ( f i n a l Rule copy ) {
super ( ) ;
lhs=new ArrayList ( ) ;
I t e r a t o r <Symbol> l h s I t =copy . lhs . i t e r a t o r ( ) ;
while ( l h s I t . hasNext ( ) ) {
Symbol tmpsymb= l h s I t . next ( ) ;
lhs . add (new Symbol ( tmpsymb ) ) ;
}
setRecursive ( copy . getRecursive ( ) ) ;
setMinimumDepth ( copy . getMinimumDepth ( ) ) ;
}
/∗∗
∗Delete a l l productions , and a l l symbols stored in lhs .
∗/
public void clear ( ) {
try {
lhs . clear ( ) ; / / clear the lhs vector
super . clear ( ) ; / / Clear production vector
}

79. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
RULE III
catch ( java . lang . Exception e ) {
System . out . p r i n t ( e ) ;
}
}
/∗∗
∗Return the recursive nature of t h i s rule .
∗/
public f i n a l boolean getRecursive ( ) {
return recursive ;
}
/∗∗
∗Update the recursive nature of t h i s rule .
∗/
public void setRecursive ( f i n a l boolean newRecursive ) {
recursive=newRecursive ;
}
/∗∗
∗Return the minimum mapping depth of t h i s rule .
∗/
public f i n a l int getMinimumDepth ( ) {
return minimumDepth ;
}

80. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
RULE IV
/∗∗
∗ Update the minimum mapping depth of t h i s Rule .
∗/
public void setMinimumDepth ( f i n a l int newMinimumDepth ) {
minimumDepth=newMinimumDepth ;
}
}

81. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
MAPPER I
/∗
∗ Mapper . java
∗
∗ Created on June 1 , 2007, 11:24 PM
∗
∗ To change t h i s template , choose Tools | Template Manager
∗ and open the template in the e d i t o r .
∗/
/∗∗
∗
∗ @author a d i l r a j a
∗/
package GrammaticOptimization ;
import java . u t i l . ∗ ;
import java . u t i l . ArrayList ;
public abstract class Mapper extends ArrayList <Rule> {
protected Genotype genotype ;
protected Phenotype phenotype ;
protected abstract boolean genotype2phenotype ( ) ;
protected abstract boolean phenotype2genotype ( ) ;
public Mapper ( ) {
super ( ) ;

82. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
MAPPER II
phenotype=new Phenotype ( ) ;
genotype=new Genotype ( ) ;
}
/∗∗
∗Constructor with genotype s t r u c t u r e . set to new newGenotype
∗/
public Mapper ( f i n a l Genotype newGenotype ) {
super ( ) ;
this . genotype=newGenotype ;
}
/∗∗
∗Constructor with phenotype s t r u c t o r . set phenotype to newPhenotype
∗/
public Mapper ( f i n a l Phenotype newPhenotype ) {
super ( ) ;
this . phenotype=new Phenotype ( newPhenotype ) ;
}
/∗∗
∗Copy Constructor
∗/
public Mapper ( f i n a l Mapper copy ) {
this . genotype=new Genotype ( copy . genotype ) ;
this . phenotype=new Phenotype ( copy . phenotype ) ;
}
/∗∗
∗returns the genotype s t r u c t u r e of t h i s mapper
∗/

83. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
MAPPER III
public f i n a l Genotype getGenotype ( ) {
return this . genotype ;
}
/∗∗
∗Sets t h i s mapper ’ s genotype s t r u c t u r e to be a copy of the argument , newgenotype ,
∗and c a l l s the genotype2phenotype private method .
∗/
public void setGenotype ( f i n a l Genotype newGenotype ) {
this . genotype=new Genotype ( newGenotype ) ;
genotype2phenotype ( ) ;
}
/∗∗
∗returns a pointer to the phenotype s t r u c t u r e of t h i s mapper
∗/
public f i n a l Phenotype getPhenotype ( ) {
return phenotype ;
}
/∗∗
∗Sets t h i s mapper ’ s phenotype s t r u c t u r e to be a copy of the argument phenotype
∗structure , and c a l l s the phenotype2genotype private method
∗/
public void setPhenotype ( f i n a l Phenotype newPhenotype ) {
phenotype=new Phenotype ( newPhenotype ) ;
phenotype2genotype ( ) ;
}
/∗∗
∗Sets the maximum codon value of the genotype s t r u c t u r e
∗/

84. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
MAPPER IV
public void setGenotypeMaxCodonValue ( f i n a l int newMaxCodonValue ) { / / CodonType= i n t
this . genotype . setMaxCodonValue ( newMaxCodonValue ) ;
}
/ / something l e f t here
}
/ / f i l e complete

85. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
SYMBOL I
/∗
∗ Symbol . java
∗
∗ Created on June 2 , 2007, 6:05 PM
∗
∗ To change t h i s template , choose Tools | Template Manager
∗ and open the template in the e d i t o r .
∗/
/∗∗
∗
∗ @author a d i l r a j a
∗
∗/
package GrammaticOptimization ;
import java . u t i l . ∗ ;
import java . lang . String ;
/ /
enum SymbolType {
NTSymbol , TSymbol
} ;
public class Symbol {

86. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
SYMBOL II
private SymbolType type ;
private String symbol ;
/∗∗ Creates a new instance of Symbol ∗/
/∗ Creat a new symbol object as a copy of newArry and with type newType , i f specified
∗/
public Symbol ( ) {
setType ( SymbolType . TSymbol ) ;
this . symbol=new String ( ) ;
}
public Symbol ( f i n a l String newArray , f i n a l SymbolType newType ) {
i f ( newArray != null )
this . symbol=new String ( newArray ) ;
else
this . symbol=new String ( " " ) ;
i f ( newType!= null )
setType ( newType ) ;
else
setType ( SymbolType . TSymbol ) ;
}
/∗∗
∗ Copy Constructor
∗/
public Symbol ( f i n a l Symbol copy ) {
try {
this . symbol=new String ( copy . getSymbol ( ) ) ;
}
catch ( java . lang . NullPointerException e ) {

87. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
SYMBOL III
System . out . p r i n t l n ( e ) ;
}
setType ( copy . getType ( ) ) ;
}
/∗∗
∗ Get the type of the symbol
∗/
public f i n a l SymbolType getType ( ) {
return this . type ;
}
/∗ Set the type of the symbol
∗/
public void setType ( f i n a l SymbolType newType ) {
this . type=newType ;
}
/∗∗
∗Returns the symbol
∗/
public f i n a l String getSymbol ( ) {
return this . symbol ;
}
/∗∗
∗Sets the symbol
∗/
public void setSymbol ( f i n a l String newSymbol ) {
this . symbol=newSymbol ;
}

88. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
SYMBOL IV
/∗∗
∗
∗/
public boolean makeComparison ( f i n a l Symbol newSymbol ) {
i f ( this . symbol . compareTo ( newSymbol . symbol)==0 && this . getType ( ) . t oS tr in g ( ) . compareTo ( n
return true ;
return false ;
}
public void clear ( ) {
this . symbol=" " ;
}
}
/ / under consideration

89. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
TREE I
/∗
∗ Tree . java
∗
∗ Created on July 27 , 2007, 3:53 PM
∗
∗ To change t h i s template , choose Tools | Template Manager
∗ and open the template in the e d i t o r .
∗/
package GrammaticOptimization ;
/∗∗
∗
∗ @author a d i l r a j a
∗/
import java . u t i l . ∗ ;
import java . u t i l . ArrayList ;
public class Tree extends ArrayList <Tree> {
private Symbol data ; / / Tree i s made of objects of type symbol as opposed to a r b i t r a r y type
private int depth ;
private int currentLevel ;
private boolean v a l i d ;
/∗∗ Creates a new instance of Tree ∗/
public Tree ( ) {
}

90. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
TREE II
/∗∗
∗ Constructor ; i n i t i a l i s e s depth and current l e v e l .
∗/
public Tree ( f i n a l int newDepth , f i n a l int newCurrentLevel ) {
depth=newDepth ;
currentLevel=newCurrentLevel ;
setValid ( false ) ;
}
/∗∗
∗Constructor ; i n i t i a l i s e s data to match arguments .
∗/
public Tree ( f i n a l Symbol newData , f i n a l int newCurrentLevel , f i n a l int newDepth ) {
data=newData ;
depth=newDepth ;
currentLevel=newCurrentLevel ;
setValid ( true ) ;
}
/∗∗
∗Copy constructor .
∗/
public Tree ( f i n a l Tree copy ) {
super ( copy ) ;
setData ( copy . getData ( ) ) ;
setDepth ( copy . getDepth ( ) ) ;

91. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
TREE III
setCurrentLevel ( copy . getCurrentLevel ( ) ) ;
setValid ( copy . getValid ( ) ) ;
}
/∗∗
∗ Return depth from t h i s node u n t i l the deepest l e a f .
∗/
/ / template <class T>
public f i n a l int getDepth ( ) {
return depth ;
}
/∗∗
∗Set new depth of t h i s node .
∗/
public void setDepth ( f i n a l int newDepth ) {
depth=newDepth ;
}
/∗∗
∗Return l e v e l of t h i s node .
∗/
public f i n a l int getCurrentLevel ( ) {
return currentLevel ;
}

92. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
TREE IV
/∗∗
∗Set new current l e v e l of t h i s node .
∗/
public void setCurrentLevel ( f i n a l int newCurrentLevel ) {
currentLevel=newCurrentLevel ;
}
/∗∗
∗Return data stored in t h i s node .
∗/
public f i n a l Symbol getData ( ) {
i f ( getValid ( ) ) {
return data ;
}
else {
return null ;
}
}
/∗∗
∗ Set data to store in t h i s node .
∗/
public void setData ( f i n a l Symbol newData ) {
data=new Symbol ( newData ) ;
setValid ( true ) ;

93. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
TREE V
}
/∗∗
∗Return v a l i d i t y of t h i s node .
∗/
public f i n a l boolean getValid ( ) {
return v a l i d ;
}
/∗∗
∗ Set v a l i d i t y of t h i s node .
∗/
public void setValid ( f i n a l boolean newValid ) {
v a l i d =newValid ;
}
}
/ / complete

94. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
SUMMARY
Java Beagle implements a simple genetic algorithm in
Java.
Implementation was focused at efficiency, ease of use and
simplicity.
Much of it is based on Beagle Puppy.
It is open source and can be found online.

95. Introduction GE’s Main Initializer Genotype Grammar Production Rule Mapper Symbol Tree Summary Referen
REFERENCES
GO can be found online.
This presentation is developed with Beamer:
Darmstadt, crane.