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source: cpp/frams/genetics/genman.cpp @ 950

Last change on this file since 950 was 896, checked in by Maciej Komosinski, 5 years ago
Replaced #defined macros for popular random-related operations with functions
Property svn:eol-style set to `native`
File size: 22.5 KB

Rev	Line
[286]	1	// This file is a part of Framsticks SDK. http://www.framsticks.com/
[761]	2	// Copyright (C) 1999-2018 Maciej Komosinski and Szymon Ulatowski.
[286]	3	// See LICENSE.txt for details.
[138]	4
	5	#include "genman.h"
	6	#include <frams/vm/classes/genoobj.h>
	7	#include GEN_CONFIG_FILE //configuration of active genetic operators
[375]	8	#include "common/log.h"
[138]	9	#include "common/nonstd_math.h"
[841]	10	#include "common/util-string.h"
[391]	11	#include <common/loggers/loggers.h>
[138]	12
	13
[768]	14	#define GENMAN_REPEAT_FAILED 100 //how many times GenMan tries to repeat a mutation or crossover when the operator does not return acceptable genotype
[761]	15	#define STRINGIFY_1(x) #x
	16	#define STRINGIFY(x) STRINGIFY_1(x) //this second-level macro allows the parameter to be a macro itself and to stringify its value, not its name
	17	#define GENMAN_REPEAT_FAILED_STR STRINGIFY(GENMAN_REPEAT_FAILED)
	18
	19
[139]	20	#ifdef USE_GENMAN_f0
[779]	21	#include "f0/f0_oper.h"
[138]	22	#endif
[139]	23	#ifdef USE_GENMAN_f0FUZZY
[779]	24	#include "f0/f0Fuzzy_oper.h"
[138]	25	#endif
[139]	26	#ifdef USE_GENMAN_f1
[779]	27	#include "f1/f1_oper.h"
[138]	28	#endif
[139]	29	#ifdef USE_GENMAN_f2
[779]	30	#include "f2/f2_oper.h"
[138]	31	#endif
[139]	32	#ifdef USE_GENMAN_f2
[779]	33	#include "f3/f3_oper.h"
[138]	34	#endif
[139]	35	#ifdef USE_GENMAN_f4
[779]	36	#include "f4/f4_oper.h"
[138]	37	#endif
[139]	38	#ifdef USE_GENMAN_f5
[779]	39	#include "f5/f5_oper.h"
[138]	40	#endif
[139]	41	#ifdef USE_GENMAN_f6
[779]	42	#include "f6/f6_oper.h"
[138]	43	#endif
[139]	44	#ifdef USE_GENMAN_f7
[779]	45	#include "f7/f7_oper.h"
[138]	46	#endif
[139]	47	#ifdef USE_GENMAN_f8
[779]	48	#include "f8/f8_oper.h"
[138]	49	#endif
[139]	50	#ifdef USE_GENMAN_f9
[779]	51	#include "f9/f9_oper.h"
[138]	52	#endif
[139]	53	#ifdef USE_GENMAN_fF
[779]	54	#include "fF/fF_oper.h"
[139]	55	#endif
[748]	56	#ifdef USE_GENMAN_fn
[779]	57	#include "fn/fn_oper.h"
[748]	58	#endif
[194]	59	#ifdef USE_GENMAN_fT
[779]	60	#include "fT/fTest_oper.h"
[194]	61	#endif
[780]	62	#ifdef USE_GENMAN_fB
	63	#include "fB/fB_oper.h"
	64	#endif
	65	#ifdef USE_GENMAN_fH
	66	#include "fH/fH_oper.h"
	67	#endif
	68	#ifdef USE_GENMAN_fL
	69	#include "fL/fL_oper.h"
	70	#endif
[138]	71
	72	using namespace std; //string, vector
	73
	74	//old code needs update:
	75	//#include "gengroups.h"
	76	//extern GenGroup *listaGen;
	77	// GENGROUP(0)->l_del.add(sim->GM.onDelGen,&sim->GM); //before delete
	78	// GENGROUP(0)->l_del.remove(sim->GM.onDelGen,&sim->GM); //before delete
	79
	80
	81	#define FIELDSTRUCT GenMan
	82
	83	static ParamEntry GMparam_tab[] =
	84	{
	85	{ "Genetics", 1, 10, "GenMan", },
	86	{ "gen_hist", 0, PARAM_DONTSAVE, "Remember history of genetic operations", "d 0 1 0", FIELD(history), "Required for phylogenetic analysis", },
	87	{ "gen_hilite", 0, 0, "Use syntax highlighting", "d 0 1 1", FIELD(hilite), "Use colors for genes?\n(slows down viewing/editing of huge genotypes)", },
	88	{ "gen_extmutinfo", 0, 0, "Extended mutation info", "d 0 2 0 ~Off~Method ID~Method description", FIELD(extmutinfo), "If active, information about employed mutation method will be stored in the 'info' field of each mutated genotype.", },
	89	{ "operReport", 0, PARAM_DONTSAVE, "Operators report", "p()", PROCEDURE(p_report), "Show available genetic operators", },
	90	{ "toHTML", 0, PARAM_DONTSAVE, "HTMLize a genotype", "p s(s)", PROCEDURE(p_htmlize), "returns genotype expressed as colored HTML", },
	91	{ "toHTMLshort", 0, PARAM_DONTSAVE, "HTMLize a genotype, shorten if needed", "p s(s)", PROCEDURE(p_htmlizeshort), "returns genotype (abbreviated if needed) expressed as colored HTML", },
[240]	92	{ "validate", 0, PARAM_DONTSAVE \| PARAM_USERHIDDEN, "Validate", "p oGeno(oGeno)", PROCEDURE(p_validate), "returns validated (if possible) Geno object from supplied Geno", },
	93	{ "mutate", 0, PARAM_DONTSAVE \| PARAM_USERHIDDEN, "Mutate", "p oGeno(oGeno)", PROCEDURE(p_mutate), "returns mutated Geno object from supplied Geno", },
	94	{ "crossOver", 0, PARAM_DONTSAVE \| PARAM_USERHIDDEN, "Crossover", "p oGeno(oGeno,oGeno)", PROCEDURE(p_crossover), "returns crossed over genotype", },
[668]	95	{ "getSimplest", 0, PARAM_DONTSAVE \| PARAM_USERHIDDEN, "Get simplest genotype", "p oGeno(s format)", PROCEDURE(p_getsimplest), "returns the simplest genotype for a given encoding (format). \"0\" means f0, \"4\" means f4, etc.", },
[138]	96	{ 0, },
	97	};
	98
	99	static ParamEntry GMstats_tab[] =
	100	{
	101	{ "Genetics", 1, 12, "GenManStats", "Statistics for genetic operations." },
	102	{ "gen_count", 0, PARAM_READONLY, "Number of genetic operations so far", "d", FIELD(count), "", },
	103	{ "gen_mvalid", 0, PARAM_READONLY, "Mutations valid", "d", FIELD(valid_m), "", },
	104	{ "gen_mvalidated", 0, PARAM_READONLY, "Mutations validated", "d", FIELD(validated_m), "", },
	105	{ "gen_minvalid", 0, PARAM_READONLY, "Mutations invalid", "d", FIELD(invalid_m), "couldn't be repaired", },
	106	{ "gen_mfailed", 0, PARAM_READONLY, "Mutations failed", "d", FIELD(failed_m), "couldn't be performed", },
	107	{ "gen_xovalid", 0, PARAM_READONLY, "Crossovers valid", "d", FIELD(valid_xo), "", },
	108	{ "gen_xovalidated", 0, PARAM_READONLY, "Crossovers validated", "d", FIELD(validated_xo), "", },
	109	{ "gen_xoinvalid", 0, PARAM_READONLY, "Crossovers invalid", "d", FIELD(invalid_xo), "couldn't be repaired", },
	110	{ "gen_xofailed", 0, PARAM_READONLY, "Crossovers failed", "d", FIELD(failed_xo), "couldn't be performed", },
	111	{ "gen_mutimpr", 0, PARAM_READONLY, "Mutations total effect", "f", FIELD(mutchg), "total cumulative mutation change", },
	112	{ "gen_xoimpr", 0, PARAM_READONLY, "Crossovers total effect", "f", FIELD(xochg), "total cumulative crossover change", },
	113	{ "clrstats", 0, PARAM_DONTSAVE, "Clear stats and history", "p()", PROCEDURE(p_clearStats), "", },
	114	{ 0, },
	115	};
	116
	117	#undef FIELDSTRUCT
	118
	119	GenMan::GenMan() : localpar(GMparam_tab, this), localstats(GMstats_tab, this),
	120	seloperpar("GenOperators", "Genetics: Active operators"),
[319]	121	neuronsparam("Genetics: Neurons to add", "neuronsAdd", "neuadd_"),
	122	par("GenMan", "Manages various genetic operations, using appropriate operators for the argument genotype format.")
[138]	123	{
	124	history = 0;
	125	hilite = 1;
	126	clearStats();
	127
[139]	128	#ifdef USE_GENMAN_f0
[145]	129	oper_fx_list.push_back(new Geno_f0);
[138]	130	#endif
[139]	131	#ifdef USE_GENMAN_f0FUZZY
[145]	132	oper_fx_list.push_back(new Geno_f0Fuzzy);
[138]	133	#endif
[139]	134	#ifdef USE_GENMAN_f1
[145]	135	oper_fx_list.push_back(new Geno_f1);
[138]	136	#endif
[139]	137	#ifdef USE_GENMAN_f2
[145]	138	oper_fx_list.push_back(new Geno_f2);
[138]	139	#endif
[139]	140	#ifdef USE_GENMAN_f3
[145]	141	oper_fx_list.push_back(new Geno_f3);
[138]	142	#endif
[139]	143	#ifdef USE_GENMAN_f4
[145]	144	oper_fx_list.push_back(new Geno_f4);
[138]	145	#endif
[139]	146	#ifdef USE_GENMAN_f5
[145]	147	oper_fx_list.push_back(new Geno_f5);
[138]	148	#endif
[139]	149	#ifdef USE_GENMAN_f6
[145]	150	oper_fx_list.push_back(new Geno_f6);
[138]	151	#endif
[139]	152	#ifdef USE_GENMAN_f7
[145]	153	oper_fx_list.push_back(new Geno_f7);
[138]	154	#endif
[139]	155	#ifdef USE_GENMAN_f8
[145]	156	oper_fx_list.push_back(new Geno_f8);
[138]	157	#endif
[139]	158	#ifdef USE_GENMAN_f9
[145]	159	oper_fx_list.push_back(new GenoOper_f9);
[138]	160	#endif
[139]	161	#ifdef USE_GENMAN_fF
[145]	162	oper_fx_list.push_back(new GenoOper_fF);
[139]	163	#endif
[748]	164	#ifdef USE_GENMAN_fn
	165	oper_fx_list.push_back(new GenoOper_fn);
	166	#endif
[194]	167	#ifdef USE_GENMAN_fT
	168	oper_fx_list.push_back(new GenoOper_fTest);
	169	#endif
[780]	170	#ifdef USE_GENMAN_fB
	171	oper_fx_list.push_back(new Geno_fB);
	172	#endif
	173	#ifdef USE_GENMAN_fH
	174	oper_fx_list.push_back(new Geno_fH);
	175	#endif
	176	#ifdef USE_GENMAN_fL
	177	oper_fx_list.push_back(new Geno_fL);
	178	#endif
[138]	179
[145]	180	seloper = new int[oper_fx_list.size()]; //may result in a little overhead if some of the operators on the oper_fx_list concern the same genetic format
[138]	181	int selopercount = 0;
[145]	182	for (unsigned int i = 0; i < oper_fx_list.size(); i++)
[138]	183	{
[145]	184	if (operformats.find(oper_fx_list[i]->supported_format) != -1) continue;
[200]	185	string type = string("~") + oper_fx_list[i]->name;
[138]	186	int dup = 0;
[145]	187	for (unsigned int j = i + 1; j < oper_fx_list.size(); j++)
	188	if (oper_fx_list[i]->supported_format == oper_fx_list[j]->supported_format)
[138]	189	{
[761]	190	type += "~";
	191	type += oper_fx_list[j]->name;
	192	dup++;
[138]	193	}
[200]	194	type = ssprintf("d 0 %d ", dup) + type;
	195	string id = ssprintf("genoper_f%c", oper_fx_list[i]->supported_format);
	196	string name = ssprintf("Operators for f%c", oper_fx_list[i]->supported_format);
[138]	197	seloper[selopercount] = 0;
[145]	198	operformats += oper_fx_list[i]->supported_format;
[138]	199	//printf("%x %s %s %s\n",&seloper[selopercount],(const char)id,(const char)type,(const char*)name);
[200]	200	seloperpar.addProperty(&seloper[selopercount++], id.c_str(), type.c_str(), name.c_str(), "", PARAM_READONLY*(dup == 0));
[138]	201	}
	202
	203	par += &localpar;
	204	par += &seloperpar;
	205	par += &neuronsparam;
[145]	206	for (unsigned int i = 0; i < oper_fx_list.size(); i++)
	207	if (oper_fx_list[i]->par.getParamTab()) par += &oper_fx_list[i]->par;
[715]	208
	209	setDefaults(); //use Param to initialize all values of fields in the paramtab of this object and genetic operators on oper_fx_list
[138]	210	}
	211
	212	GenMan::~GenMan()
	213	{
[145]	214	for (unsigned int i = 0; i < oper_fx_list.size(); i++) delete oper_fx_list[i];
[138]	215	delete[] seloper;
	216	}
	217
	218	void GenMan::setDefaults()
	219	{
[145]	220	for (unsigned int i = 0; i < oper_fx_list.size(); i++)
[138]	221	{
[145]	222	oper_fx_list[i]->par.setDefault();
	223	oper_fx_list[i]->setDefaults();
[138]	224	}
	225	localpar.setDefault();
	226	//...and we do not reset others that are linked to 'par',
	227	//because there quite a few of them, and not every of them defines defaults for each of its parameters.
	228	}
	229
	230	int GenMan::testValidity(Geno &g, bool &canvalidate)
	231	{
[761]	232	SString ggs = g.getGenes();
[348]	233	const char *gg = ggs.c_str();
[145]	234	GenoOperators *gf = getOper_f(g.getFormat());
[138]	235	int check1;
	236	if (!gf) { canvalidate = false; return GENOPER_NOOPER; }
[761]	237	else check1 = gf->checkValidity(gg, g.getName().c_str());
[138]	238	if (!canvalidate) return check1; //just checking
	239	if (check1 == GENOPER_OK) { canvalidate = false; return check1; }
	240	char *g2 = strdup(gg);
[761]	241	if (gf->validate(g2, g.getName().c_str()) == GENOPER_NOOPER) { free(g2); canvalidate = false; return check1; }
[138]	242	if (check1 == GENOPER_NOOPER) //disaster: cannot check because there is no check operator
	243	{
[534]	244	g.setGenesAssumingSameFormat(g2); free(g2); canvalidate = false; return GENOPER_NOOPER;
[138]	245	}
[513]	246	int check2 = gf->checkValidity(g2, "validated");
[534]	247	if (check2 == GENOPER_OK) g.setGenesAssumingSameFormat(g2);
[138]	248	free(g2);
	249	if (check2 == GENOPER_OK) return check1;
	250	canvalidate = false;
	251	return check1; //could not validate.
	252	}
	253
	254	int GenMan::testGenoValidity(Geno& g)
	255	{
	256	bool fix = false;
	257	switch (testValidity(g, fix))
	258	{
	259	case GENOPER_OK: return 1;
	260	case GENOPER_NOOPER: return -1;
	261	default: return 0;
	262	}
	263	}
	264
[532]	265	Geno GenMan::validate(const Geno& geny)
[138]	266	{
[168]	267	char format = geny.getFormat();
	268	GenoOperators *gf = getOper_f(format);
	269	if (gf == NULL)
	270	return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: Validate(): don't know how to handle genetic format %c", format));
[534]	271	char *g2 = strdup(geny.getGenes().c_str()); //copy for validation
[513]	272	int res = gf->validate(g2, geny.getName().c_str());
[168]	273	SString sg2 = g2;
[138]	274	free(g2);
[168]	275	if (res == GENOPER_OK)
	276	return Geno(sg2, format, geny.getName(), geny.getComment());
[138]	277	else
[168]	278	return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: validate() for format %c returned invalid value", format));
[138]	279	}
	280
[532]	281	Geno GenMan::mutate(const Geno& g)
[138]	282	{
	283	float chg; //how many changes
	284	int method; //mutation method
[168]	285	char format = g.getFormat();
	286	GenoOperators *gf = getOper_f(format);
	287	if (gf == NULL)
	288	return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: Mutate(): don't know how to handle genetic format %c", format));
	289	Geno gv = g;
	290	bool canvalidate = true;
	291	if (testValidity(gv, canvalidate) > 0 && canvalidate == false)
	292	return Geno("", -1, "", "GENOPER_OPFAIL: Mutate(): cannot validate invalid source genotype");
	293	bool ok = false;
	294	int pcount = count;
[138]	295	while (!ok)
	296	{
[534]	297	char *gn = strdup(gv.getGenes().c_str()); //copy for mutation
[168]	298	chg = 0;
	299	if (gf->mutate(gn, chg, method) == GENOPER_OK)
[138]	300	{
[375]	301	LoggerToMemory eh(LoggerBase::Enable \| LoggerToMemory::StoreFirstMessage); //mute testValidity()
[168]	302	Geno G(gn, gv.getFormat(), "", "");
	303	canvalidate = true;
	304	int res = testValidity(G, canvalidate);
	305	if (res == GENOPER_OK && canvalidate == false) { valid_m++; ok = true; }
	306	else
	307	if (res > 0 && canvalidate == false) invalid_m++; else
	308	{
[761]	309	validated_m++; ok = true;
[168]	310	}
	311	if (ok) gv = G;
	312	}
	313	else failed_m++;
[138]	314	free(gn);
	315	count++;
[761]	316	if (!ok && (count - pcount > GENMAN_REPEAT_FAILED))
[138]	317	{
[761]	318	logPrintf("GenMan", "Mutate", 2, "Tried " GENMAN_REPEAT_FAILED_STR "x and failed: %s", g.getGenes().c_str());
	319	return Geno("", -1, "", "GENOPER_OPFAIL: Mutate() tried " GENMAN_REPEAT_FAILED_STR "x and failed");
[138]	320	}
	321	}
[168]	322	mutchg += chg;
[534]	323	if (history) saveLink(g.getGenes().c_str(), "", gv.getGenes().c_str(), chg);
[138]	324	SString mutinfo;
[348]	325	if (extmutinfo == 0) mutinfo = SString::sprintf("%.2f%% mutation of '%s'", 100 * chg, g.getName().c_str()); else
	326	if (extmutinfo == 1) mutinfo = SString::sprintf("%.2f%% mutation(%d) of '%s'", 100 * chg, method, g.getName().c_str()); else
	327	mutinfo = SString::sprintf("%.2f%% mutation(%s) of '%s'", 100 * chg, gf->mutation_method_names ? gf->mutation_method_names[method] : "unspecified method name", g.getName().c_str());
[138]	328	gv.setComment(mutinfo);
	329	return gv;
	330	}
	331
[532]	332	Geno GenMan::crossOver(const Geno& g1, const Geno& g2)
[138]	333	{
	334	char format = g1.getFormat();
[257]	335	if (format != g2.getFormat()) return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: CrossOver(): does not work for parents with differing genetic formats (%c and %c)", format, g2.getFormat()));
[145]	336	GenoOperators *gf = getOper_f(format);
[138]	337	if (gf == NULL)
[257]	338	return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: CrossOver(): no operators found for genetic format %c", format));
[138]	339	Geno g1v = g1, g2v = g2;
	340
	341	{
[375]	342	LoggerToMemory eh(LoggerBase::Enable \| LoggerToMemory::StoreFirstMessage); //mute testValidity()
[138]	343	bool canvalidate = true;
	344	if (testValidity(g1v, canvalidate) > 0 && canvalidate == false)
	345	return Geno("", -1, "", "GENOPER_OPFAIL: CrossOver(): cannot validate invalid source genotype #1");
	346	canvalidate = true;
	347	if (testValidity(g2v, canvalidate) > 0 && canvalidate == false)
	348	return Geno("", -1, "", "GENOPER_OPFAIL: CrossOver(): cannot validate invalid source genotype #2");
	349	}
	350
	351	float chg;
	352	bool ok = false;
	353	int pcount = count;
	354
	355	while (!ok)
	356	{
	357	float chg1, chg2;
[534]	358	char *g1n = strdup(g1.getGenes().c_str()); //copy for crossover
	359	char *g2n = strdup(g2.getGenes().c_str()); //copy for crossover
[138]	360	chg1 = chg2 = 0;
	361	if (gf->crossOver(g1n, g2n, chg1, chg2) == GENOPER_OK)
	362	{
	363	char *gn;
[896]	364	if (g1n[0] && g2n[0]) if (rndUint(2) == 0) g1n[0] = 0; else g2n[0] = 0; //both provided? we want only one
[138]	365	if (g1n[0]) { gn = g1n; chg = chg1; }
	366	else { gn = g2n; chg = chg2; }
[375]	367	LoggerToMemory eh(LoggerBase::Enable \| LoggerToMemory::StoreFirstMessage); //mute testValidity()
[138]	368	Geno G(gn, g1v.getFormat(), "", "");
	369	bool canvalidate = true;
	370	int res = testValidity(G, canvalidate);
	371	if (res == GENOPER_OK && canvalidate == false) { valid_xo++; ok = true; }
	372	else
	373	if (res > 0 && canvalidate == false) invalid_xo++; else
	374	{
[761]	375	validated_xo++; ok = true;
[138]	376	}
	377	if (ok) g1v = G;
	378	}
	379	else failed_xo++;
	380	free(g1n);
	381	free(g2n);
	382	count++;
[761]	383	if (!ok && (count - pcount > GENMAN_REPEAT_FAILED))
[138]	384	{
[761]	385	logPrintf("GenMan", "CrossOver", 2, "Tried " GENMAN_REPEAT_FAILED_STR "x and failed: %s and %s", g1.getGenes().c_str(), g2.getGenes().c_str());
	386	return Geno("", -1, "", "GENOPER_OPFAIL: CrossOver() tried " GENMAN_REPEAT_FAILED_STR "x and failed");
[138]	387	}
	388	}
	389	// result in g1v
	390	xochg += chg;
[534]	391	if (history) saveLink(g1.getGenes().c_str(), g2.getGenes().c_str(), g1v.getGenes().c_str(), chg);
[138]	392	SString xoinfo = SString::sprintf("Crossing over of '%s' (%.2f%%) and '%s' (%.2f%%)",
[348]	393	g1.getName().c_str(), 100 * chg, g2.getName().c_str(), 100 * (1 - chg));
[138]	394	g1v.setComment(xoinfo);
	395	return g1v;
	396	}
	397
[532]	398	float GenMan::similarity(const Geno& g1, const Geno& g2)
[138]	399	{
	400	char format = g1.getFormat();
	401	if (format != g2.getFormat()) return GENOPER_NOOPER;
[145]	402	GenoOperators *gf = getOper_f(format);
[534]	403	if (!gf) return GENOPER_NOOPER; else return gf->similarity(g1.getGenes().c_str(), g2.getGenes().c_str());
[138]	404	}
	405
[532]	406	uint32_t GenMan::getStyle(const char g, const Geno G, int pos)
[138]	407	{
[532]	408	char format = G->getFormat();
	409	if (format == Geno::INVALID_FORMAT)
	410	return GENSTYLE_RGBS(64, 64, 64, 0); // gray & "valid" (unknown format so we don't know what is valid and what is not)
	411	if ((pos = G->mapStringToGen(pos)) == -1) return GENSTYLE_COMMENT;
	412	GenoOperators *gf = getOper_f(format);
[138]	413	if (!gf) return GENSTYLE_CS(0, 0); //black & valid
[534]	414	else return gf->style(G->getGenes().c_str(), pos);
[138]	415	}
	416
[532]	417	uint32_t GenMan::getStyle(const char *g, int pos)
[138]	418	{
	419	Geno G(g);
[532]	420	return getStyle(g, &G, pos);
	421	}
	422
	423	void GenMan::getFullStyle(const char g, const Geno G, uint32_t *styletab)
	424	{
	425	char format = G->getFormat();
	426	if (format == Geno::INVALID_FORMAT)
	427	{
	428	for (unsigned int pos = 0; pos < strlen(g); pos++)
	429	styletab[pos] = GENSTYLE_RGBS(64, 64, 64, 0); // gray & "valid" (unknown format so we don't know what is valid and what is not)
	430	return;
	431	}
	432	GenoOperators *gf = getOper_f(format);
[761]	433	SString geny = G->getGenes();
[138]	434	for (unsigned int pos = 0; pos < strlen(g); pos++)
	435	{
[532]	436	int posmapped = G->mapStringToGen(pos);
[138]	437	if (posmapped == -1) styletab[pos] = GENSTYLE_COMMENT;
	438	else if (!gf) styletab[pos] = GENSTYLE_CS(0, 0); //black & valid
[348]	439	else styletab[pos] = gf->style(geny.c_str(), posmapped);
[532]	440	//logPrintf("GenMan", "getFullStyle", 0, "%d char='%c' (%d) format=0x%08x", pos, g[pos], g[pos], styletab[pos]);
[138]	441	}
	442	}
	443
[532]	444	void GenMan::getFullStyle(const char g, uint32_t styletab)
	445	{
	446	Geno G(g);
	447	getFullStyle(g, &G, styletab);
	448	}
	449
[467]	450	string GenMan::HTMLize(const char *g) { return HTMLize(g, false); }
[138]	451
[467]	452	string GenMan::HTMLizeShort(const char *g) { return HTMLize(g, true); }
[138]	453
[467]	454	string GenMan::HTMLize(const char *g, bool shorten)
[138]	455	{
	456	char buf[50];
	457	int len = strlen(g);
	458	int chars = 0, lines = 0;
	459	bool shortened = false;
[247]	460	uint32_t *styletab = new uint32_t[len];
[532]	461	getFullStyle(g, styletab);
[467]	462	string html = "\n<div style=\"background:white;padding:0.2em;font-family:arial,helvetica,sans-serif;font-size:90%\">";
[247]	463	uint32_t prevstyle, prevcolor, style = 0, color = 0;
[761]	464	for (int i = 0; i < len; i++)
[138]	465	{
[761]	466	if (shorten && ((lines == 0 && chars > 160) \|\| (lines > 5 \|\| chars > 300))) { shortened = true; break; }
[138]	467	if (g[i] == '\r') continue;
	468	if (g[i] == '\n') { html += "<br>\n"; lines++; continue; }
	469	chars++;
	470	prevstyle = style;
	471	prevcolor = color;
	472	style = GENGETSTYLE(styletab[i]);
	473	color = GENGETCOLOR(styletab[i]);
	474	if ((i != 0 && (color != prevcolor))) html += "</font>";
	475	if ((style&GENSTYLE_INVALID) != (prevstyle&GENSTYLE_INVALID))
	476	{
	477	html += "<"; if (!(style&GENSTYLE_INVALID)) html += "/"; html += "u>";
	478	}
	479	if ((style&GENSTYLE_BOLD) != (prevstyle&GENSTYLE_BOLD))
	480	{
	481	html += "<"; if (!(style&GENSTYLE_BOLD)) html += "/"; html += "b>";
	482	}
	483	if ((style&GENSTYLE_ITALIC) != (prevstyle&GENSTYLE_ITALIC))
	484	{
	485	html += "<"; if (!(style&GENSTYLE_ITALIC)) html += "/"; html += "i>";
	486	}
	487	if ((i == 0 \|\| (color != prevcolor)))
	488	{
	489	sprintf(buf, "<font color=#%02x%02x%02x>", GENGET_R(color), GENGET_G(color), GENGET_B(color)); html += buf;
	490	}
	491	if (g[i] == '<') html += "<"; else if (g[i] == '>') html += ">"; else html += g[i];
	492	if ((i % 3) == 0 && g[i] == ' ') html += "\n"; //for readability, insert some newlines into html...
	493	}
	494	delete[] styletab;
	495	html += "</u></b></i></font>";
	496	if (shortened) html += " [etc...]";
	497	html += "</div>\n";
	498	return html;
	499	}
	500
	501	void GenMan::p_htmlize(ExtValue args, ExtValue ret)
	502	{
[467]	503	ret->setString(HTMLize(args->getString().c_str()).c_str());
[138]	504	}
	505
	506	void GenMan::p_htmlizeshort(ExtValue args, ExtValue ret)
	507	{
[467]	508	ret->setString(HTMLizeShort(args->getString().c_str()).c_str());
[138]	509	}
	510
[532]	511	Geno GenMan::getSimplest(char format)
[138]	512	{
[145]	513	GenoOperators *gf = getOper_f(format);
[138]	514	if (!gf) return Geno();
[200]	515	string info = "The simplest genotype of format f"; info += format;
[138]	516	info += " for operators '"; info += gf->name; info += "'.";
[200]	517	return Geno(gf->getSimplest(), format, "Root", info.c_str());
[138]	518	}
	519
	520	void GenMan::p_getsimplest(ExtValue args, ExtValue ret)
	521	{
[516]	522	int format = GenoObj::formatFromExtValue(args[0]);
[145]	523	if (!getOper_f(format))
[138]	524	ret->setEmpty();
	525	else
[532]	526	*ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(getSimplest(format)));
[138]	527	}
	528
[532]	529	const char *GenMan::getOpName(char format)
[138]	530	{
[145]	531	GenoOperators *gf = getOper_f(format);
[200]	532	if (!gf) return "n/a"; else return gf->name.c_str();
[138]	533	}
	534
[145]	535	GenoOperators* GenMan::getOper_f(char format)
[138]	536	{
	537	int ind = operformats.find(format);
	538	if (ind == -1) return NULL;
[168]	539	int which_oper_of_format = seloper[ind];
[145]	540	for (unsigned int i = 0; i < oper_fx_list.size(); i++)
	541	if (oper_fx_list[i]->supported_format == format)
[168]	542	if (which_oper_of_format == 0) return oper_fx_list[i]; else which_oper_of_format--;
[138]	543	return NULL; //should never happen
	544	}
	545
[275]	546	void GenMan::saveLink(const string parent1, const string parent2, const string child, const float chg)
[138]	547	{
	548	GenoLink l;
	549	l.count = count;
[275]	550	l.parent1 = parent1;
	551	l.parent2 = parent2;
	552	l.child = child;
[138]	553	l.chg = chg;
	554	l.fit = 0; //temporarily. Will be set when the genotype dies
[375]	555	//logPrintf("GenMan","saveLink",0,"#%d: [%d] '%s' + '%s' -> '%s'",GenoLinkList.size(),count,parent1.c_str(),parent2.c_str(),child.c_str());
[138]	556	GenoLinkList.push_back(l);
	557	}
	558
[247]	559	void GenMan::onDelGen(void *obj, intptr_t n)
[138]	560	{
	561	//old code needs update:
	562	// ((SpeciesList*)obj)->przyDodaniu(i);
	563	/* !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
	564	GenMan gm=(GenMan)obj;
	565	Genotype gt=(Genotype)(*listaGen)(n); //there is no more "listaGen"
	566	string g=(const char*)gt->genotype.getGene();
	567	float fit=gt->getFinalFitness();
	568	for(int i=0;i<gm->GenoLinkList.size();i++) //find genotype
	569	if (gm->GenoLinkList[i].g1==g) {gm->GenoLinkList[i].fit=fit; break;}
	570	*/
	571	}
	572
	573	void GenMan::clearStats()
	574	{
	575	count = 0;
	576	valid_m = valid_xo = validated_m = validated_xo = invalid_m = invalid_xo = failed_m = failed_xo = 0;
	577	mutchg = xochg = 0;
	578	GenoLinkList.clear();
	579	}
	580
	581	void GenMan::p_clearStats(ExtValue args, ExtValue ret) { clearStats(); }
	582
	583	void GenMan::p_report(ExtValue args, ExtValue ret)
	584	{ //should be updated to handle multiple operators for a single format
	585	char g, g2;
[145]	586	float f1, f2;
	587	int m;
[375]	588	logMessage("GenMan", "Report", 0, "The following genetic operators are available:");
[145]	589	for (unsigned int i = 0; i < oper_fx_list.size(); i++)
[138]	590	{
[200]	591	string l;
[761]	592	if (oper_fx_list[i]->checkValidity("", "") != GENOPER_NOOPER) l += " checkValidity";
[145]	593	if (oper_fx_list[i]->getSimplest())
[138]	594	{
[145]	595	g = strdup(oper_fx_list[i]->getSimplest());
[138]	596	g2 = strdup(g);
[761]	597	if (oper_fx_list[i]->validate(g, "") != GENOPER_NOOPER) l += " validate";
[145]	598	if (oper_fx_list[i]->mutate(g, f1, m) != GENOPER_NOOPER) l += " mutate";
	599	if (oper_fx_list[i]->crossOver(g, g2, f1, f2) != GENOPER_NOOPER) l += " crossover";
[138]	600	l += " getSimplest";
	601	free(g); free(g2);
	602	}
[145]	603	// if (oper_fx_list[i]->similarity("","")!=GENOPER_NOOPER) l+=" similarity";
[375]	604	logPrintf("GenMan", "Report", 0, "format f%c (%s):%s",
[200]	605	oper_fx_list[i]->supported_format, oper_fx_list[i]->name.c_str(), l.c_str());
[138]	606	}
	607	}
	608
	609	void GenMan::p_validate(ExtValue args, ExtValue ret)
	610	{
	611	Geno *g = GenoObj::fromObject(args[0]);
	612	if (g == NULL)
	613	ret->setEmpty();
	614	else
[532]	615	ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(validate(g)));
[138]	616	}
	617
	618	void GenMan::p_mutate(ExtValue args, ExtValue ret)
	619	{
	620	Geno *g = GenoObj::fromObject(args[0]);
	621	if (g == NULL)
	622	ret->setEmpty();
	623	else
[532]	624	ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(mutate(g)));
[138]	625	}
	626
	627	void GenMan::p_crossover(ExtValue args, ExtValue ret)
	628	{
	629	Geno *g1 = GenoObj::fromObject(args[1]);
	630	Geno *g2 = GenoObj::fromObject(args[0]);
	631	if (g1 == NULL \|\| g2 == NULL)
	632	ret->setEmpty();
	633	else
[532]	634	ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(crossOver(g1, *g2)));
[138]	635	}
[532]	636

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