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gentech.cpp
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gentech.cpp
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/*
* Author: Sven Gothel <[email protected]>
* Copyright (c) 1994-2022 Gothel Software e.K.
* Copyright (c) 1994 Christian Mueller
*
* Proprietary licenses are available
* via Gothel Software e.K. <[email protected]>.
*
* This library is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public
* License as published by the Free Software Foundation; either
* version 2 of the License, or (at your option) any later version.
*
* This library is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* General Public License for more details.
*
* You should have received a copy of the GNU General Public
* License along with this library; if not, write to the
* Free Software Foundation, Inc., 59 Temple Place - Suite 330,
* Boston, MA 02111-1307, USA.
*
* You can also check the GNU General Public License
* in the internet at http://www.gnu.org/copyleft/gpl.html !
*/
#include <gentech/gentech.hpp>
#include <gentech/random.hpp>
#include <jau/basic_algos.hpp>
#include <climits>
#include <limits>
#include <iostream>
#include <cassert>
using namespace jau::gentech;
#define THIS (*this)
std::ostream& std::operator<< (std::ostream& os, const jau::gentech::nucleotide_array_t& list)
{
const nucleotide_array_t::size_type Zeilenlaenge = 10;
os << "( " << list.size() << " ) < ";
for (nucleotide_array_t::size_type i=0; i<list.size(); i++) {
if (i % Zeilenlaenge == 0 && i) os << "\n\t";
os << list[i];
if (i % Zeilenlaenge != Zeilenlaenge-1 && i != list.size()-1) {
os << ", ";
}
}
os << " >";
return os;
}
// *******************************************************************
// *******************************************************************
// C H R O M O S O M
// *******************************************************************
// *******************************************************************
// STATISCHE-KLASSEN-GLOBALE VARIABLEN !!!
Chromosom::Chromosom ( Chromosomen & env, size_type initial_length )
: nucleotide_array_t(initial_length), m_env(env), m_fitness(0)
// Zufaellig erzeugte Chromosomen
{
for ( Chromosom::size_type i=initial_length; i > 0; --i) {
push_back( Random<size_type>(env.m_min_nucleotide_value,env.m_max_nucleotide_value) );
}
assert (size() == initial_length);
}
Chromosom::Chromosom ( Chromosomen & env, const std::string& FileName )
: nucleotide_array_t(), m_env(env), m_fitness(0)
{
Load(FileName);
}
void Chromosom::Copy (const Chromosom &a)
{
m_fitness = a.m_fitness;
assert (size() == a.size());
}
Chromosom& Chromosom::operator=(const Chromosom& m)
{
if (this == &m) { return *this; }
// Neue Liste der Nukleotide anlegen.
// In Liste<NukleoTyp> wird der *this-Zeiger auf Gleichheit ueberprueft
// Das Environment env (Chromosomen) bleibt !
nucleotide_array_t::operator=(m);
Copy(m);
return *this;
}
bool Chromosom::operator==(const Chromosom& ch) const noexcept
{
if (this == &ch) { return true; }; // gleiches Chromosom
if (size() != ch.size()) { // garantiert Ungleich
return false;
}
size_type i;
for(i=0; i < size() && THIS[i] == ch[i]; ++i ) ; // Ueberprufung
return i == size();
}
void Chromosom::Save(const std::string& FileName) const
{
FILE *file;
if( ( file=fopen(FileName.c_str(),"wb") ) == nullptr ) {
ABORT("Couldn't open file '%s'", FileName.c_str());
}
{
// 4-7-94, 2:51 PM
// Speichert die Groesse des NukleoDatenTyps als erstes in der Datei
const uint16_t NukleoLen = sizeof(nucleotide_t);
if( fwrite (&NukleoLen, sizeof (NukleoLen), 1, file) != 1 ) {
ABORT("Couldn't write to file '%s'", FileName.c_str());
}
// 4-7-94, 2:51 PM
}
const size_type len=size();
if( fwrite (&len, sizeof(len), 1, file) != 1 ) {
ABORT("Couldn't write to file '%s'", FileName.c_str());
}
for(size_type i=0; i<len; ++i) {
if( fwrite (&(THIS[i]), sizeof (nucleotide_t), 1, file) != 1 ) {
ABORT("Couldn't write to file '%s'", FileName.c_str());
}
}
fclose(file);
}
void Chromosom::Load(const std::string& FileName) {
FILE *file;
if ((file=fopen(FileName.c_str(), "rb")) == nullptr) {
ABORT("Couldn't open file '%s'", FileName.c_str());
}
{
// 4-7-94, 3:3 PM
// Liest als erstes die Groesse des abgespeicherten NukleoTyps
// aus dem File
uint16_t NukleoLen;
if( fread (&NukleoLen, sizeof (NukleoLen), 1, file) != 1 ) {
ABORT("Couldn't read file '%s'", FileName.c_str());
}
if( NukleoLen != sizeof(nucleotide_t) ) {
std::cerr << "!! ERROR !!\n"
<< " Laenge des Datentyps der gespeicherten Nuklotide\n"
<< " ist kleiner als das abgespeicherte Format\n";
exit (0);
}
// 4-7-94, 3:3 PM
}
// Puffer der richtigen Laenge bereit stellen
nucleotide_t value;
size_type len;
if (fread (&len, sizeof (len), 1, file) == 0) {
ABORT("Couldn't read file '%s'", FileName.c_str());
}
reserve(len);
for(size_type i=0; i<len; ++i) {
if( fread (&value, sizeof(value), 1, file) == 0 ) {
ABORT("Couldn't read file '%s'", FileName.c_str());
}
insert(i, value);
}
fclose(file);
}
Chromosom::size_type Chromosom::GetNukleotidNumber(size_type nuckleotide_idx) const noexcept
{
nucleotide_t nuckleotide_value=THIS[nuckleotide_idx];
if( m_env.m_nucleotide_value_scale * (m_env.m_nucleotide_count-1) <= nuckleotide_value &&
nuckleotide_value <= m_env.m_max_nucleotide_value )
{
// Trifft auch fuer Nukleotide gleich nullptr zu !!!
return m_env.m_nucleotide_count;
}
for (size_type n=m_env.m_nucleotide_count-1; n > 0; --n) { // FIXME: Double '-1' here and on 'n'?
if( m_env.m_nucleotide_value_scale * (n-1) <= nuckleotide_value &&
nuckleotide_value < m_env.m_nucleotide_value_scale * n ) {
return n;
}
}
ABORT("Failed to determine nucleotide number of nucleotide[%zu]=%zu", (size_t)nuckleotide_idx, (size_t)nuckleotide_value);
return 0;
}
nucleotide_t Chromosom::GetUserNukleotidValue(size_type i) const noexcept
{
return m_env.m_nucleotide_value_scale*(i-1);
}
bool Chromosom::FindIntron(size_type &von, size_type &bis) const noexcept
{
bool done = false;
size_type i, i2, i3;
if (bis-von+1 >= m_env.m_splice_code_ptr->Length)
{
// Spleissen..Anfang suchen
i=von; i2=0;
while (i <= bis && m_env.m_splice_code_ptr->SpliceCode[i2] != 0) {
if (GetNukleotidNumber (i) == m_env.m_splice_code_ptr->SpliceCode[i2]) {
++i2;
++i;
} else {
i2=0;
von=++i;
}
}
if (i < bis) {
assert (m_env.m_splice_code_ptr->SpliceCode[i2] == 0) ;
// von gefunden...
// Spleissen..Ende suchen
i3=i;
i=++i2;
while (i3 <= bis && m_env.m_splice_code_ptr->SpliceCode[i2] != 0) {
if (GetNukleotidNumber(i3) == m_env.m_splice_code_ptr->SpliceCode[i2]) {
i2++;
} else {
i2=i;
}
i3++;
}
if (m_env.m_splice_code_ptr->SpliceCode[i2] == 0) {
// bis gefunden...
bis=i3-1;
done=true;
}
}
}
return done;
}
Chromosom::size_type Chromosom::Splicing()
{
size_type NNukleotide=0, IntronStart=0, IntronEnd=size()-1;
#ifndef NDEBUG
size_type len_old;
#endif
// Die Bedingung fuer den SpliceCode ist Nukleotide > 1 !
// Nukleotide wird in Chromosomen::CalcParameter gesetzt !
if (m_env.m_nucleotide_count <= 1) {
// Kein Splicing , da kein SpliceCode !!!
return 0;
}
while( FindIntron(IntronStart, IntronEnd) ) {
#ifndef NDEBUG
len_old=size();
#endif
assert( IntronStart <= IntronEnd );
erase( IntronStart, IntronEnd+1 );
assert ( len_old - ( IntronEnd - IntronStart + 1 ) == size() );
NNukleotide+=IntronEnd-IntronStart+1;
IntronEnd=size()-1;
}
return NNukleotide;
}
void Chromosom::InsertIntrons (size_type von, size_type length)
{
size_type i, iRumpf;
if (m_env.m_splice_code_ptr != nullptr &&
m_env.m_splice_code_ptr->SpliceCode[0] != 0 &&
von <= size() &&
length >= m_env.m_splice_code_ptr->Length)
{
// StartSequenz einfuegen.
for (i=0; m_env.m_splice_code_ptr->SpliceCode[i] != 0; ++i, ++von, --length) {
insert(von, GetUserNukleotidValue(m_env.m_splice_code_ptr->SpliceCode[i]));
}
// Stelle fuer Rumpf merken.
iRumpf=von;
// EndSequenz einfuegen.
for (++i; m_env.m_splice_code_ptr->SpliceCode[i] != 0; ++i, ++von, --length) {
insert(von, GetUserNukleotidValue (m_env.m_splice_code_ptr->SpliceCode[i]));
}
// Rumpf fuellen.
while (length > 0) {
insert(iRumpf, Random (m_env.m_min_nucleotide_value, m_env.m_max_nucleotide_value));
length--;
}
}
}
void Chromosom::Inversion()
{
const size_type start = Random<size_type>(0, size()-2);
assert (start < size()-1);
const size_type end = Random(start+1, size()-1) ;
assert (end < size());
assert (end > start);
const size_type length = end-start+1;
nucleotide_array_t save(length);
/**
* S E
* 0123456789 01234
* abcdefghij -> cdefg
*
* S E
* 0123456789 43210
* abgfedchij <- gfedc
*/
for (size_type i=start; i <= end; ++i) {
save.push_back( THIS[i] );
}
assert( save.size() == length );
for (size_type i=start; i <= end; ++i) {
THIS[i]=save[end-i];
}
}
void Chromosom::Translocation()
{
const size_type start = Random<size_type>(0, size()-2);
assert (start < size()-1);
const size_type end = Random (start+1, size()-1) ;
assert (end < size());
assert (end > start);
const size_type length = end-start+1;
nucleotide_array_t save(length);
for(size_type i=start; i <= end; ++i) {
save.push_back(THIS[i]);
}
erase(start, end+1);
assert( save.size() == length );
const size_type dest = Random<size_type>( 0, size()-1 );
for(size_type i=0; i<save.size(); ++i) {
THIS.insert(dest+i, save[i]);
}
}
// *******************************************************************
// *******************************************************************
// C H R O M O S O M E N
// *******************************************************************
// *******************************************************************
// STATISCHE-KLASSEN-GLOBALE VARIABLEN !!!
const Chromosomen::size_type Chromosomen::m_mutation_freq_variance=1000;
Chromosomen::Chromosomen (nucleotide_t UserNukleoMinVal,
nucleotide_t UserNukleoMaxVal,
size_type max_chromosom_count,
const std::string& StartGenFile,
size_type Nukleotide,
SpliceCodeInfo *PtrSpliceCodeInfo,
size_type InversionFreq,
size_type TranslocationFreq,
size_type AsymXOverFreq,
size_type CrossVal,
size_type MutationFreq,
size_type max_no_improving_gens)
: chromosom_array_t(max_chromosom_count),
m_all_time_best_gen(1),
m_all_time_best_avrg_fitness(0),
m_all_time_best(*this),
m_avrg_fitness(0),
m_best_fitness(0),
m_fitness_sum(0),
m_max_no_improving_gens(max_no_improving_gens),
m_no_improving_gens(0),
m_generation(1),
m_max_chromosom_count(max_chromosom_count),
m_intro_code_len_sum(0),
m_spliced_chromosom_count(0),
m_file_ptk_ptr(nullptr),
m_generation_start(0),
m_generation_end(0),
m_evolution_start(0),
m_evolution_end(0),
m_min_chromosom_len(0),
m_max_chromosom_len(0),
m_avrg_chromosom_len(0),
m_chromosom_above_zero_count(0),
m_mutations_this_gen(0),
m_inversions_this_gen(0),
m_translocations_this_gen(0),
m_mutation_freq(MutationFreq),
m_inversion_freq(InversionFreq),
m_translocation_freq(TranslocationFreq),
m_asymxover_freq(AsymXOverFreq),
m_cross_val(CrossVal),
m_xover_number(0), // FIXME
m_splice_code_ptr(PtrSpliceCodeInfo),
m_min_nucleotide_value(UserNukleoMinVal),
m_max_nucleotide_value(UserNukleoMaxVal),
m_nucleotide_value_scale(1),
m_nucleotide_count(Nukleotide)
{
// StartGene aus dem File holen ! ....
FILE *file;
CalcParameter();
if ((file=fopen(StartGenFile.c_str(),"rb") ) == nullptr ) {
ABORT("Couldn't open file '%s'", StartGenFile.c_str());
}
{
// 4-7-94, 3:3 PM
// Liest als erstes die Groesse des abgespeicherten NukleoTyps
// aus dem File
uint16_t NukleoLen;
if (fread (&NukleoLen, sizeof(NukleoLen), 1, file)!=1) {
ABORT("can't read file %s\n", StartGenFile.c_str());
}
if( NukleoLen != sizeof(nucleotide_t) ) {
std::cerr << "!! ERROR !!\n"
<< " Laenge des Datentyps der gespeicherten Nuklotide\n"
<< " ist kleiner als das abgespeicherte Format\n";
exit (0);
}
// 4-7-94, 3:3 PM
}
// int ChromLen, ChromQuantity, i, j;
size_type ChromQuantity;
if (fread(&ChromQuantity, sizeof(ChromQuantity), 1, file)==0) {
ABORT("can't read file %s\n", StartGenFile.c_str());
}
// Puffer der richtigen Laenge bereitstellen
nucleotide_t value;
for(size_type j=0; j<ChromQuantity; ++j ) {
Chromosom Gamma( *this, 0 );
assert (Gamma.size()==0);
size_type ChromLen;
if (fread(&ChromLen, sizeof(ChromLen), 1, file) == 0) {
ABORT("can't read file %s\n", StartGenFile.c_str());
} // FIXME: Use fixed width type
for(size_type i=0; i<ChromLen; ++i) {
if (fread(&value, sizeof(value), 1, file) == 0) {
ABORT("can't read file %s\n", StartGenFile.c_str());
}
Gamma.push_back(value);
}
assert (Gamma.size()==ChromLen);
push_back(Gamma);
}
assert (size()==ChromQuantity);
fclose (file);
}
Chromosomen::Chromosomen ( nucleotide_t UserNukleoMinVal, nucleotide_t UserNukleoMaxVal,
size_type max_chromosom_count,
size_type StartChromosomNumber,
size_type StartChromosomLength,
size_type Nukleotide,
SpliceCodeInfo *PtrSpliceCodeInfo,
size_type InversionFreq,
size_type TranslocationFreq,
size_type AsymXOverFreq,
size_type CrossVal,
size_type MutationFreq,
size_type max_no_improving_gens)
: chromosom_array_t(max_chromosom_count),
m_all_time_best_gen(1),
m_all_time_best_avrg_fitness(0),
m_all_time_best(*this),
m_avrg_fitness(0),
m_best_fitness(0),
m_fitness_sum(0),
m_max_no_improving_gens(max_no_improving_gens),
m_no_improving_gens(0),
m_generation(1),
m_max_chromosom_count(max_chromosom_count),
m_intro_code_len_sum(0),
m_spliced_chromosom_count(0),
m_file_ptk_ptr(nullptr),
m_generation_start(0),
m_generation_end(0),
m_evolution_start(0),
m_evolution_end(0),
m_min_chromosom_len(0),
m_max_chromosom_len(0),
m_avrg_chromosom_len(0),
m_chromosom_above_zero_count(0),
m_mutations_this_gen(0),
m_inversions_this_gen(0),
m_translocations_this_gen(0),
m_mutation_freq(MutationFreq),
m_inversion_freq(InversionFreq),
m_translocation_freq(TranslocationFreq),
m_asymxover_freq(AsymXOverFreq),
m_cross_val(CrossVal),
m_xover_number(0), // FIXME
m_splice_code_ptr(PtrSpliceCodeInfo),
m_min_nucleotide_value(UserNukleoMinVal),
m_max_nucleotide_value(UserNukleoMaxVal),
m_nucleotide_value_scale(1),
m_nucleotide_count(Nukleotide)
{
CalcParameter();
// StartGene zufaellig setzen !
for (size_type i=0; i<StartChromosomNumber ; ++i) {
Chromosom Gamma (*this, StartChromosomLength);
assert (Gamma.size() == StartChromosomLength);
push_back(Gamma);
}
assert (size()==StartChromosomNumber);
}
void Chromosomen::Save (const std::string& FileName) const
{
FILE *file;
if((file=fopen(FileName.c_str(), "wb")) == nullptr) {
ABORT("Couldn't open file '%s'", FileName.c_str());
}
{
// 4-7-94, 2:51 PM
// Speichert die Groesse des NukleoTyps als erstes im File ab
const uint16_t NukleoLen=sizeof(nucleotide_t);
if (fwrite (&NukleoLen, sizeof (NukleoLen), 1, file) != 1) {
ABORT("can't write to file %s\n", FileName.c_str());
}
// 4-7-94, 2:51 PM
}
size_type ChromQuantity = size();
if (fwrite (&ChromQuantity, sizeof (ChromQuantity), 1, file) != 1 ) {
ABORT("can't write to file %s\n", FileName.c_str());
}
for (size_type j=0; j<ChromQuantity; j++ ) {
const size_type ChromLen = THIS[j].size();
if (fwrite (&ChromLen, sizeof (ChromLen), 1, file) != 1) {
ABORT("can't write to file %s\n", FileName.c_str());
}
for(size_type i=0; i<ChromLen; ++i) {
nucleotide_t value = THIS[j][i];
if (fwrite (&value, sizeof (nucleotide_t), 1, file) != 1) {
ABORT("can't write to file %s\n", FileName.c_str());
}
}
}
fclose(file);
}
Chromosomen::size_type Chromosomen::Evolution (double GoalFitness, const std::string& chrptrPtkFile,
double BirthRate, int Bigamie )
{
double BestEverAverageFitness = -1,
Cut = 0; // Der Cut beim Sterben
bool stop = false;
InitFitness() ;
if( !chrptrPtkFile.empty() ) {
if ((m_file_ptk_ptr=fopen (chrptrPtkFile.c_str(), "wt")) == nullptr) {
ABORT("Couldn't open file '%s'", chrptrPtkFile.c_str());
}
} else {
m_file_ptk_ptr = nullptr;
}
m_evolution_start=time(nullptr);
m_generation=1;
m_spliced_chromosom_count=0;
m_intro_code_len_sum=0;
m_no_improving_gens = 0;
Protokoll();
if( !Echo() ) { stop = true; }
if( BirthRate <= 0.0 || BirthRate > 1.0 ) { stop = true; }
while( m_best_fitness < GoalFitness &&
m_no_improving_gens < m_max_no_improving_gens &&
!stop )
{
m_generation++;
m_spliced_chromosom_count=0;
m_intro_code_len_sum=0;
if( BirthRate < 1.0 ) {
NewGeneration(BirthRate, Bigamie);
// Fuer LetDie !!!
Cut = GetXWorstFitness( size() - m_max_chromosom_count );
} else {
NewGeneration(Bigamie);
Cut = -.5; // Eltern Fitness auf -1 gesetzt
}
// Sterben !!!
LetDie(Cut);
// Die Mutation
Mutation();
// Fitness berechnen
CalcWholeFitness();
// Weitere Mutationen
InversionsMutation();
TranslocationsMutation();
m_generation_end=time(nullptr);
if( BestEverAverageFitness < m_avrg_fitness ) {
m_no_improving_gens=0;
BestEverAverageFitness = m_avrg_fitness ;
} else {
m_no_improving_gens++ ;
}
Protokoll();
if(!Echo()) { stop = true; }
}
m_evolution_end=time(nullptr);
Echo();
Protokoll();
if (m_file_ptk_ptr != nullptr) { fclose (m_file_ptk_ptr); }
return m_generation;
}
void Chromosomen::InitFitness()
{
for (size_type i = 0; i < size(); ++i) {
Chromosom Neu = THIS[i];
Neu.Splicing();
THIS[i].SetFitness(Fitness(Neu));
}
CalcWholeFitness();
}
void Chromosomen::NewGeneration(double BirthRate, bool Bigamie)
{
indexlist_t ElternPaare;
size_type l = (size_type) ( (double)size() * BirthRate );
size_type i;
m_generation_start=time(nullptr);
// Gerade Anzahl der ElternPaare !!!
if( l%2 > 0 ) {
--l;
}
// ooops, die letzten beiden Elternpaare sind nicht-bigamistisch SCHLECHT
// zu finden !!!
if( 2 <= m_chromosom_above_zero_count && m_chromosom_above_zero_count <= l ) {
m_chromosom_above_zero_count -= 2;
}
// Neue Partner in die ElternPaare-Menge einfuegen
// "Bigamistische Beziehung" werden, wenn moeglich, nicht erlaubt.
while(l>0) {
// Nur NEUE Partner !!!
if (!Bigamie && ElternPaare.size() < m_chromosom_above_zero_count) {
do {
i=RouletteSelect();
} while( jau::contains(ElternPaare, i) ) ;
ElternPaare.push_back(i);
l--;
} else {
if (!Bigamie) {
// the hard way ...
do {
i = Random<size_type>(0, size()-1);
} while( jau::contains(ElternPaare, i) ) ;
ElternPaare.push_back(i);
l--;
} else {
// Bigamistische Beziehung JA, aber sexuell !!!
size_type w, m;
ElternPaare.push_back((w = Random<size_type>(0, size()-1))) ;
while (w == (m=Random<size_type>(0, size()-1))) ;
ElternPaare.push_back(m) ;
l-=2;
}
}
};
l=ElternPaare.size();
#ifndef NDEBUG
// alles ok ?? GERADE ELTERNPAARE ????
assert( l%2==0 );
assert( l== ( (size_type)( size() * BirthRate ) % 2 ) ?
(size_type)( size() * BirthRate ) - 1 :
(size_type)( size() * BirthRate )
);
#endif
// Fortpflanzen !!!
while (l > 1) {
CrossingOver (ElternPaare[l-1], ElternPaare[l-2]);
l -= 2 ;
}
assert (l == 0);
}
void Chromosomen::NewGeneration(bool Bigamie)
{
indexlist_t ElternPaare;
size_type l = m_max_chromosom_count;
m_generation_start=time(nullptr);
// Gerade Anzahl der ElternPaare !!!
if( l%2 > 0 ) {
--l;
}
// ooops, die letzten beiden Elternpaare sind nicht-bigamistisch SCHLECHT
// zu finden !!!
if( 2 <= m_chromosom_above_zero_count && m_chromosom_above_zero_count <= l ) {
m_chromosom_above_zero_count -= 2;
}
// Neue Partner in die ElternPaare-Menge einfuegen
// "Bigamistische Beziehung" werden, wenn moeglich, nicht erlaubt.
while( l > 0 ) {
// Nur NEUE Partner !!!
if( !Bigamie && ElternPaare.size() < m_chromosom_above_zero_count ) {
size_type i;
do {
i = RouletteSelect();
} while ( jau::contains(ElternPaare, i) ) ;
ElternPaare.push_back(i);
l--;
} else {
if( !Bigamie ) {
size_type i;
do {
i = Random<size_type>(0, size()-1);
} while( jau::contains(ElternPaare, i) ) ;
ElternPaare.push_back(i);
l--;
} else { // Bigamistische Beziehung JA, aber sexuell !!!
size_type w, m;
ElternPaare.push_back( ( w = Random<size_type>(0, size()-1) ) );
while( w == ( m = Random<size_type>(0, size()-1) ) ) ;
ElternPaare.push_back(m);
l-=2;
}
}
};
l=ElternPaare.size();
// alles ok ?? GERADE ANZAHL DER ELTERN !!!
assert (l%2==0);
(void)l;
// Neue Population...
l=ElternPaare.size();
while (l > 1) {
// Beim Crossing Over werden die Nachkommen am Ende der Populations-Liste
// eingefuegt.
// Die Indizes fuer die ElternPaare bleiben somit aktuell !!!
CrossingOver (ElternPaare[l-1], ElternPaare[l-2]);
l-=2;
}
// Eltern markieren, damit sie "getoetet" werden koennen !!!
// Das geschied in 'LetDie', Aufruf in Evolution
l=ElternPaare.size()-1;
while (l > 0) {
const size_type w=ElternPaare[l-1];
// markieren !!!
THIS[w].SetFitness(-1);
l--;
}
}
void Chromosomen::LetDie(double cut)
{
size_type i=0;
while (i < size() && size() > m_max_chromosom_count) {
if (THIS[i].GetFitness() <= cut) {
Kill (i);
} else {
++i;
}
}
// Sicherheitsabfrage
if (size() > m_max_chromosom_count) {
cut = GetXWorstFitness (size()-m_max_chromosom_count);
i = 0;
while (i < size() && size() > m_max_chromosom_count) {
if (THIS[i].GetFitness() <= cut) {
Kill (i);
} else {
++i;
}
}
}
assert (size() <= m_max_chromosom_count);
}
Chromosomen::size_type Chromosomen::RouletteSelect() const
// Chris: geaendert
{
size_type i;
double Sum = 0.0;
const double Threshold = Random (0.0, 1.0) * GetFitnessSum();
// Aufgrund der Ungenauigkeit der Flieskommaoperatoren
// muss auch das Ende der Liste abgefragt werden.
for (i=0; Sum < Threshold && i<size(); ++i) {
Sum += THIS[i].GetFitness();
}
return ( i < size() ) ? i : size()-1;
}
void Chromosomen::CreateNewSymChromosom ( Chromosom &dest, size_type m, size_type w,
crosspoints_t &CrossPoints )
{
// i : Indize des Crosspoints
// von, bis : Zu Uebertragender Chromosomenabschnitt [von..bis[
// ch : Alternierendes Indize zwischen den beiden Chromosomen
// mit den Geschlechtern 'm' und 'w'
// done : Abbruch Indikator
bool done = false;
size_type i, von, bis, ch;
// Startwerte !!
i = bis = 0;
ch = w;
dest.reserve( THIS[ch].size() );
do {
// An dem letzten exklusiven Ende fortfahren
von = bis;
if ( i < CrossPoints.size() ) {
// Chromosomenabschnitt-Ende holen.
if( CrossPoints[i] < THIS[ch].size() ) bis = CrossPoints[i];
else bis = THIS[ch].size();
++i;
} else {
// ...und den Rest uebertragen
bis = THIS[ch].size();
done = true;
}
assert ( bis <= THIS[ch].size() );
assert ( von == dest.size() );
// Chromosomenabschnitt uebertragen [von..bis[
for (size_type n=von; n<bis; n++) {
dest.insert(n, THIS[ch][n]);
}
// Indize zwischen den Geschlechtern alternieren
ch = ( ch==m ? w : m ) ;
} while ( !done );
// ...sonst Fehler !!!
assert( dest.size() > 0 );
}
void Chromosomen::CrossingOver (size_type m, size_type w)
{
if ( m_cross_val == 0 ) { return; }
size_type shortest=( ( THIS[m].size() < THIS[w].size() ) ? m : w);
if ( m_xover_number++ < m_asymxover_freq || m_asymxover_freq==0 ) {
// Symmetrisches XOver !!!
crosspoints_t CrossPoints;
assert( CrossPoints.size()==0 );
// Kreuzungspunkte sortiert eintragen.
for ( size_type i = 0; i < m_cross_val; ++i ) {
CrossPoints.insert( Random<size_type>(0 , THIS[shortest].size()) );
}
Chromosom NeuA (*this, 0);
Chromosom NeuB (*this, 0);
size_type SplicedCode;
CreateNewSymChromosom ( NeuA, m, w, CrossPoints );
push_back( NeuA );
SplicedCode=NeuA.Splicing();
if(SplicedCode>0) {
m_spliced_chromosom_count++;
m_intro_code_len_sum+=SplicedCode;
}
// Die Fitness des gespleissten Chromosomes in das ungespleisste
// eingebundene Chromosom einsetzen !!!
THIS[size()-1].SetFitness(Fitness(NeuA));
CreateNewSymChromosom ( NeuB, w, m, CrossPoints );
push_back( NeuB );
SplicedCode=NeuB.Splicing();
if(SplicedCode>0) {
m_spliced_chromosom_count++;
m_intro_code_len_sum+=SplicedCode;
}
// Die Fitness des gespleissten Chromosomes in das ungespleisste
// eingebundene Chromosom einsetzen !!!
THIS[size()-1].SetFitness(Fitness(NeuB));
} else {
m_xover_number = 0;
// Assymetrisches XOver : Nur ein neues Element !
Chromosom Neu (*this, 0);
// Kopieren
Neu=THIS[m];
// anhaengen
for (size_type n=0; n<THIS[w].size(); n++) {
Neu.push_back( THIS[w][n] );
}
Neu.SetFitness(Fitness(Neu));
push_back( Neu );
}
}
void Chromosomen::Mutation()
{
static size_type next_nukleotide_idx = m_mutation_freq + Random<size_type>( 0, (size_type)(m_mutation_freq/m_mutation_freq_variance) ) ;
m_mutations_this_gen=0;
if ( m_mutation_freq > 0 ) {
size_type nukleotide_idx = next_nukleotide_idx;
for(size_type chromosom_idx = 0; chromosom_idx < size(); ++chromosom_idx ) {
bool mutated = false;
const size_type chromosom_len = THIS[chromosom_idx].size();
while( nukleotide_idx < chromosom_len ) {
// Die Mutation.
(THIS[chromosom_idx])[nukleotide_idx] = Random<size_type>( m_min_nucleotide_value, m_max_nucleotide_value);
m_mutations_this_gen++;
mutated=true;
nukleotide_idx += m_mutation_freq + Random<size_type>( 0, (size_type)(m_mutation_freq/m_mutation_freq_variance) );
}
if( nukleotide_idx >= chromosom_len ) {
nukleotide_idx -= chromosom_len;
}
if(mutated) {
// Fitness neuberechnen ...
// ... this is a social event - we are hard folks :-)
Chromosom Neu (THIS[chromosom_idx]);
Neu.Splicing();
THIS[chromosom_idx].SetFitness(Fitness(Neu));
}
}
next_nukleotide_idx = nukleotide_idx;
}
}
void Chromosomen::InversionsMutation()
{
static size_type next_chromosomen_idx = m_inversion_freq;
m_inversions_this_gen=0;
size_type chromosomen_idx = next_chromosomen_idx;
while( chromosomen_idx < size() ) {
m_inversions_this_gen++;
THIS[chromosomen_idx].Inversion();
// Fitness neuberechnen ...
Chromosom Neu (THIS[chromosomen_idx]);
Neu.Splicing();
THIS[chromosomen_idx].SetFitness(Fitness(Neu));
chromosomen_idx += m_inversion_freq;