Grammatical Optimization

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

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

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.

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

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 ;
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 ) ;
/ / }

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 ) ;

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 " ) ;
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 ( ) ;
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 ()+ " " ) ;
}
}
}
}
}

INITIALIZER I
/∗
∗ I n i t i a l i s e r . java
∗
∗ Created on July 2 , 2007, 6:05 PM
∗
∗/
/∗∗
∗
∗
∗/
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 ) ;
}

GENOTYPE I
/∗
∗ Genotype . java
∗
∗ Created on June 1 , 2007, 11:35 PM
∗
∗/
/∗∗
∗
∗/
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 ;

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

GENOTYPE III
this . addAll ( newVector ) ;
setMaxCodonValue (32767);
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 ) ;
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 ( ) ) ;
}

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 ) {
}
/∗ 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 ) {
}
/∗ Returns the maximum containable value in a codon
∗/
public f i n a l int getMaxCodonValue ( ) {

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

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

GRAMMAR I
/∗
∗ Grammar . java
∗
∗
∗/
/∗∗
∗
∗/
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
∗/

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 ) ;
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 ) ;
startSymbol =0;
}
/∗∗
∗Copy Constructor

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 ( ) {

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;

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 ;
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 ;
return true ;
}

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

CONTEXT-FREE GRAMMAR I
/∗
∗ CFGrammar. java
∗
∗
∗/
/∗∗
∗
∗/
import java . io . ∗ ;
public abstract class CFGrammar extends Grammar {
protected Tree derivationTree ;
/∗∗
∗ Creates a new instance of CFGrammar

CONTEXT-FREE GRAMMAR II
∗/
public CFGrammar ( ) {
super ( ) ;
}
/∗∗
∗/
public CFGrammar( f i n a l Genotype 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 ) {
}
/∗∗
∗ 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 ;

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;
prodIt = r u l e I t ;
symbIt= prodIt . next ( ) . i t e r a t o r ( ) ;
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++;

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 ) ;

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 ) ;
/ / }

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

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 ) ;
}

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
}
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 ’ ;
}

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 ;

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 . " ) ;
}
}
else { / / Normal character
currentChar=stream . charAt ( i i ) ;
}
i f ( ( ! skip )&&(pass >1)){
i f ( currentBuffer . length ()==0){
newSymbol . setType ( SymbolType . TSymbol ) ;
}
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
}

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 ) ;
currentBuffer =Character . t oS tr in g ( currentChar ) ;
}
else {
}
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
}
break ;
case (START_RULE ) : / / Read the lhs Non−terminal symbol
}
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 . " ) ;

CONTEXT-FREE GRAMMAR XII
break ;
case ’> ’ : / / Possible end of non−terminal symbol
}
else {
}
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 ) ;
}
/ / do nothing
}
i f ( tmpRulePtr==null )
insertRule=true ;
else
insertRule=false ;
i f ( insertRule ) {

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
}

CONTEXT-FREE GRAMMAR XIV
}
System . out . p r i n t l n ( e+"ERROR: Grammar changed between parser passes
}
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 + "
}
}
else {

CONTEXT-FREE GRAMMAR XV
}
}
break ;
case (LHS_READ) : / / Must read : : = token
}
break ;
case ’ : ’ : / / Part of : : = token
}
else {
}
break ;
case ’= ’ : / / Should be end of : : = token
try {
}
else {

CONTEXT-FREE GRAMMAR XVI
}
}
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
}
/ / START OF PRODUCTION
newProduction . clear ( ) ;
state=PRODUCTION;
break ;
System . out . p r i n t l n ( "ERROR: Character ’ " + currentChar + " ’ caused an e
}
break ;
case (PRODUCTION) : / / Read everything u n t i l | token or n , or EOL
}
i f ( pass ==1){

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
}
else {
}
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
/ / No symbol exists ; create terminal empty symbol
}
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
}

CONTEXT-FREE GRAMMAR XVIII
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 ) ;
}
/ / 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
}
/ / 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
;
}

CONTEXT-FREE GRAMMAR XIX
/ / END OF PRODUCTION
/ / Add production to current rule
try {
currentRule . add (new Production ( newProduction ) ) ;
}
System . out . p r i n t l n ( e+" But the currentRule i s n u l l . . . i t sucks too "
}
i f ( currentChar== ’ n ’ )
state=START_OF_LINE;
else {
}
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
}
else {

CONTEXT-FREE GRAMMAR XX
}
i f ( ! non_terminal ) newSymbol . setType ( SymbolType . TSymbol ) ;
break ;
}
i f ( currentChar== ’> ’ ) { / / This i s also the end of a non−terminal symbol
}
else {
}
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
}
i f ( ( currentChar== ’ ’ ) | | ( currentChar== ’ t ’ ) ) { / / Token separator
separated =1;
}
i f ( newSymbol . getType ( ) . to St ri ng ( ) . equals ( "NTSymbol" ) ) {
/ / Find rule that defines t h i s symbol
Rule tempRule=null ;
try {

CONTEXT-FREE GRAMMAR XXI
tempRule=findRule ( newSymbol ) ;
}
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
}
}
else { / / Add terminal symbol
}
/ / Reset the symbol
}
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;
}
}

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
}
else {
}
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 ) ) ;

CONTEXT-FREE GRAMMAR XXIII
}
i f ( currentChar== ’ " ’ ) { / / Start ( or end ) quoted section
quoted =! quoted ;
break ;
}
}
}
else {
}
}
break ;
case (START_OF_LINE ) :
}
break ;
case ’ | ’ : / / Start of new production

CONTEXT-FREE GRAMMAR XXIV
state=PRODUCTION;
i f ( pass ==2){
}
break ;
case ’< ’ : / / Start of lhs non−terminal symbol
/ / END OF RULE
i f ( pass ==1){
/ / Add current rule
try {
this . add (new Rule ( newRule ) ) ;
}
}
}
}
/ / START OF RULE
}
else {

CONTEXT-FREE GRAMMAR XXV
}
state=START_RULE;
break ;
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 . " ) ;
}
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 . " ) ;
}
i f ( pass ==1){
/ / Add current rule
this . add (new Rule ( newRule ) ) ;
}
}

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 ;

CONTEXT-FREE GRAMMAR XXVII
}
return true ;
}
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 ( ) ;

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 ;
tmp= r u l e I t . next ( ) ;
i f ( tmp . lhs . get ( tmp . lhs . size () −1).makeComparison ( nonterminal ) )
return tmp ;
}
return null ;
}

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 ( ) ;
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
Production tmp_pd= prodIt . next ( ) ;

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
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
}
/ / 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

CONTEXT-FREE GRAMMAR XXXI
i f ( tmp_pd . getMinimumDepth () <1){
}
}
}
else { / / Terminal symbol
i f ( tmp_pd . getMinimumDepth () <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 ( ) ;
}
/∗∗

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 ( ) ;
clearRuleFields ( ) ;
/ / Go through each rule in the grammar
try {
visitedRules . clear ( ) ;
}
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 ( ) ;
try {
visitedRules . clear ( ) ;
}

CONTEXT-FREE GRAMMAR XXXIII
System . out . p r i n t l n ( e+" UpdateRuleFields sucks " ) ;
}
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 ( ) {
/ / Reset minimum depths and recursion f i e l d s
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 ( ) ;
}

CONTEXT-FREE GRAMMAR XXXIV
}
try {
}
}
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 .

GE GRAMMAR I
/∗
∗ GEGrammar. java
∗
∗ Created on August 2 , 2007, 12:22 AM
∗
∗/
/∗∗
∗
∗/
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
∗/

GE GRAMMAR II
public GEGrammar ( ) {
super ( ) ;
setMaxWraps ( 0 ) ;
}
/∗∗
∗/
public GEGrammar( f i n a l Genotype 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 ) {
setMaxWraps ( 0 ) ;
}
/∗∗
∗ Copy Constructor .
∗/
public GEGrammar( f i n a l GEGrammar copy ) throws Exception {
super ( copy ) ;
setMaxWraps ( copy . getMaxWraps ( ) ) ;

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 ;
}

GE GRAMMAR IV
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 ;
}
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 ;

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 ( ) )
i f ( buildDerivationTree ) {
this . productions . clear ( ) ;
}
/ / Quick safety checks
/ / i f ( ( ! getValidGrammar ( ) ) | | ( ! genotype . getValid ( ) ) | | ( ! getGenotype()−> size ( ) ) ) {
i f ( ! getValidGrammar ( ) ) {

GE GRAMMAR VI
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 ( ) ) ;
/ / Use s t a r t symbol as the derivationTree node
try {
derivationTree . setData ( getStartSymbol ( ) ) ;
}
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 ( ) ) ;

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 . " ) ;

GE GRAMMAR VIII
}
}
/ / 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
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 ;
}
/∗∗

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
try {
r u l e P t r =findRule ( nonterminals . peek ( ) ) ;
}
System . out . p r i n t l n ( e+" genotype2phenotypeStep ( ) s r u l e P t r sucks " ) ;

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){

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;

GE GRAMMAR XII
}
else {
/ / Unknown symbol or special symbol that requires non−empty genotype
/ / Include symbol on phenotype
/ / nonterminals . pop ( ) ;
/ / I n v a l i d a t e mapping
returnValue=−1;
}
}
}
}
/ / 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
/ / nonterminals . pop ( ) ;
returnValue=−1;
}
else {

GE GRAMMAR XIII
nonterminals . pop ( ) ;
/ / Choose production
i f ( codonGenoIt==null&&r u l e P t r . size () >1){
/ / Empty genotype , but symbol requires choice
phenotype . add ( r u l e P t r . lhs . get ( 0 ) ) ;
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 ( ) ;
productions . add ( tmpProd ) ; / / tmpProd i s also used l a t t e r
}

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 ( ) ;
}
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" ) ;

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 ;
}
}
System . out . p r i n t l n ( e+" The whileloop at the end of genotype2phenotypeStep suck
}
catch ( java . u t i l . EmptyStackException e ) {
System . out . p r i n t l n ( e+" GEGrammar sucks . . . Stack i s empty " ) ;
}
}
/ / }
/ / 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 ;
}

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 ( ) ; ;
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 ( ) ;

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 " ) ;
}
/ / t r e e I t ++;
}
}
}

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

PRODUCTION I
/∗
∗ Production . java
∗
∗ Created on June 3 , 2007, 12:24 AM
∗
∗/
/∗∗
∗
∗/
public class Production extends ArrayList <Symbol >{
private boolean recursive ;
private int minimumDepth ;
/∗∗

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 ( ) {

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 ( ) {

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

RULE I
/∗
∗ Rule . java
∗
∗
∗/
/∗∗
∗
∗/
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 ) ;

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
}

RULE III
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 ;
}

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 ;
}
}

MAPPER I
/∗
∗ Mapper . java
∗
∗
∗/
/∗∗
∗
∗/
public abstract class Mapper extends ArrayList <Rule> {
protected Genotype genotype ;
protected Phenotype phenotype ;
public Mapper ( ) {
super ( ) ;

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
∗/

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
∗/

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

SYMBOL I
/∗
∗ Symbol . java
∗
∗
∗/
/∗∗
∗
∗
∗/
import java . lang . String ;
/ /
enum SymbolType {
NTSymbol , TSymbol
} ;
public class Symbol {

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 ( ) ) ;
}

SYMBOL III
}
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 ;
}

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

TREE I
/∗
∗ Tree . java
∗
∗
∗/
/∗∗
∗
∗/
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 ( ) {
}

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 ;
setValid ( true ) ;
}
/∗∗
∗Copy constructor .
∗/
public Tree ( f i n a l Tree copy ) {
super ( copy ) ;
setData ( copy . getData ( ) ) ;
setDepth ( copy . getDepth ( ) ) ;

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 ;
}

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 ) {
}
/∗∗
∗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 ) ;

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

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.

REFERENCES
GO can be found online.
This presentation is developed with Beamer:
Darmstadt, crane.

Grammatical Optimization

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Grammatical Optimization