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source: cpp/frams/genetics/genman.cpp @ 975

Last change on this file since 975 was 966, checked in by Maciej Komosinski, 5 years ago
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File size: 25.8 KB

Rev	Line
[286]	1	// This file is a part of Framsticks SDK. http://www.framsticks.com/
[955]	2	// Copyright (C) 1999-2020 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
[955]	71	#ifdef USE_GENMAN_fS
	72	#include "fS/fS_oper.h"
	73	#endif
[138]	74
	75	using namespace std; //string, vector
	76
	77	//old code needs update:
	78	//#include "gengroups.h"
	79	//extern GenGroup *listaGen;
	80	// GENGROUP(0)->l_del.add(sim->GM.onDelGen,&sim->GM); //before delete
	81	// GENGROUP(0)->l_del.remove(sim->GM.onDelGen,&sim->GM); //before delete
	82
	83
	84	#define FIELDSTRUCT GenMan
	85
	86	static ParamEntry GMparam_tab[] =
	87	{
[965]	88	{ "Genetics", 1, 11, "GenMan", },
[138]	89	{ "gen_hist", 0, PARAM_DONTSAVE, "Remember history of genetic operations", "d 0 1 0", FIELD(history), "Required for phylogenetic analysis", },
	90	{ "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)", },
	91	{ "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.", },
	92	{ "operReport", 0, PARAM_DONTSAVE, "Operators report", "p()", PROCEDURE(p_report), "Show available genetic operators", },
	93	{ "toHTML", 0, PARAM_DONTSAVE, "HTMLize a genotype", "p s(s)", PROCEDURE(p_htmlize), "returns genotype expressed as colored HTML", },
[965]	94	{ "toHTMLshort", 0, PARAM_DONTSAVE, "HTMLize a genotype, shorten if needed", "p s(s)", PROCEDURE(p_htmlizeshort), "returns genotype (abbreviated if needed) in colored HTML format", },
	95	{ "toLaTeX", 0, PARAM_DONTSAVE, "LaTeXize a genotype", "p s(s)", PROCEDURE(p_latexize), "returns genotype in colored LaTeX format", },
[240]	96	{ "validate", 0, PARAM_DONTSAVE \| PARAM_USERHIDDEN, "Validate", "p oGeno(oGeno)", PROCEDURE(p_validate), "returns validated (if possible) Geno object from supplied Geno", },
	97	{ "mutate", 0, PARAM_DONTSAVE \| PARAM_USERHIDDEN, "Mutate", "p oGeno(oGeno)", PROCEDURE(p_mutate), "returns mutated Geno object from supplied Geno", },
	98	{ "crossOver", 0, PARAM_DONTSAVE \| PARAM_USERHIDDEN, "Crossover", "p oGeno(oGeno,oGeno)", PROCEDURE(p_crossover), "returns crossed over genotype", },
[668]	99	{ "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]	100	{ 0, },
	101	};
	102
	103	static ParamEntry GMstats_tab[] =
	104	{
	105	{ "Genetics", 1, 12, "GenManStats", "Statistics for genetic operations." },
	106	{ "gen_count", 0, PARAM_READONLY, "Number of genetic operations so far", "d", FIELD(count), "", },
	107	{ "gen_mvalid", 0, PARAM_READONLY, "Mutations valid", "d", FIELD(valid_m), "", },
	108	{ "gen_mvalidated", 0, PARAM_READONLY, "Mutations validated", "d", FIELD(validated_m), "", },
	109	{ "gen_minvalid", 0, PARAM_READONLY, "Mutations invalid", "d", FIELD(invalid_m), "couldn't be repaired", },
	110	{ "gen_mfailed", 0, PARAM_READONLY, "Mutations failed", "d", FIELD(failed_m), "couldn't be performed", },
	111	{ "gen_xovalid", 0, PARAM_READONLY, "Crossovers valid", "d", FIELD(valid_xo), "", },
	112	{ "gen_xovalidated", 0, PARAM_READONLY, "Crossovers validated", "d", FIELD(validated_xo), "", },
	113	{ "gen_xoinvalid", 0, PARAM_READONLY, "Crossovers invalid", "d", FIELD(invalid_xo), "couldn't be repaired", },
	114	{ "gen_xofailed", 0, PARAM_READONLY, "Crossovers failed", "d", FIELD(failed_xo), "couldn't be performed", },
	115	{ "gen_mutimpr", 0, PARAM_READONLY, "Mutations total effect", "f", FIELD(mutchg), "total cumulative mutation change", },
	116	{ "gen_xoimpr", 0, PARAM_READONLY, "Crossovers total effect", "f", FIELD(xochg), "total cumulative crossover change", },
	117	{ "clrstats", 0, PARAM_DONTSAVE, "Clear stats and history", "p()", PROCEDURE(p_clearStats), "", },
	118	{ 0, },
	119	};
	120
	121	#undef FIELDSTRUCT
	122
	123	GenMan::GenMan() : localpar(GMparam_tab, this), localstats(GMstats_tab, this),
	124	seloperpar("GenOperators", "Genetics: Active operators"),
[319]	125	neuronsparam("Genetics: Neurons to add", "neuronsAdd", "neuadd_"),
	126	par("GenMan", "Manages various genetic operations, using appropriate operators for the argument genotype format.")
[138]	127	{
	128	history = 0;
	129	hilite = 1;
	130	clearStats();
	131
[139]	132	#ifdef USE_GENMAN_f0
[145]	133	oper_fx_list.push_back(new Geno_f0);
[138]	134	#endif
[139]	135	#ifdef USE_GENMAN_f0FUZZY
[145]	136	oper_fx_list.push_back(new Geno_f0Fuzzy);
[138]	137	#endif
[139]	138	#ifdef USE_GENMAN_f1
[145]	139	oper_fx_list.push_back(new Geno_f1);
[138]	140	#endif
[139]	141	#ifdef USE_GENMAN_f2
[145]	142	oper_fx_list.push_back(new Geno_f2);
[138]	143	#endif
[139]	144	#ifdef USE_GENMAN_f3
[145]	145	oper_fx_list.push_back(new Geno_f3);
[138]	146	#endif
[139]	147	#ifdef USE_GENMAN_f4
[145]	148	oper_fx_list.push_back(new Geno_f4);
[138]	149	#endif
[139]	150	#ifdef USE_GENMAN_f5
[145]	151	oper_fx_list.push_back(new Geno_f5);
[138]	152	#endif
[139]	153	#ifdef USE_GENMAN_f6
[145]	154	oper_fx_list.push_back(new Geno_f6);
[138]	155	#endif
[139]	156	#ifdef USE_GENMAN_f7
[145]	157	oper_fx_list.push_back(new Geno_f7);
[138]	158	#endif
[139]	159	#ifdef USE_GENMAN_f8
[145]	160	oper_fx_list.push_back(new Geno_f8);
[138]	161	#endif
[139]	162	#ifdef USE_GENMAN_f9
[145]	163	oper_fx_list.push_back(new GenoOper_f9);
[138]	164	#endif
[139]	165	#ifdef USE_GENMAN_fF
[145]	166	oper_fx_list.push_back(new GenoOper_fF);
[139]	167	#endif
[748]	168	#ifdef USE_GENMAN_fn
	169	oper_fx_list.push_back(new GenoOper_fn);
	170	#endif
[194]	171	#ifdef USE_GENMAN_fT
	172	oper_fx_list.push_back(new GenoOper_fTest);
	173	#endif
[780]	174	#ifdef USE_GENMAN_fB
	175	oper_fx_list.push_back(new Geno_fB);
	176	#endif
	177	#ifdef USE_GENMAN_fH
	178	oper_fx_list.push_back(new Geno_fH);
	179	#endif
	180	#ifdef USE_GENMAN_fL
	181	oper_fx_list.push_back(new Geno_fL);
	182	#endif
[955]	183	#ifdef USE_GENMAN_fS
	184	oper_fx_list.push_back(new GenoOper_fS);
	185	#endif
[138]	186
[145]	187	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]	188	int selopercount = 0;
[145]	189	for (unsigned int i = 0; i < oper_fx_list.size(); i++)
[138]	190	{
[955]	191	if (findOperFormatIndex(oper_fx_list[i]->supported_format) != -1) continue;
[200]	192	string type = string("~") + oper_fx_list[i]->name;
[138]	193	int dup = 0;
[145]	194	for (unsigned int j = i + 1; j < oper_fx_list.size(); j++)
	195	if (oper_fx_list[i]->supported_format == oper_fx_list[j]->supported_format)
[138]	196	{
[955]	197	type += "~";
	198	type += oper_fx_list[j]->name;
	199	dup++;
[138]	200	}
[200]	201	type = ssprintf("d 0 %d ", dup) + type;
[955]	202	string id = ssprintf("genoper_f%s", oper_fx_list[i]->supported_format.c_str());
	203	string name = ssprintf("Operators for f%s", oper_fx_list[i]->supported_format.c_str());
[138]	204	seloper[selopercount] = 0;
[955]	205	operformats += &oper_fx_list[i]->supported_format;
[138]	206	//printf("%x %s %s %s\n",&seloper[selopercount],(const char)id,(const char)type,(const char*)name);
[955]	207	seloperpar.addProperty(&seloper[selopercount++], id.c_str(), type.c_str(), name.c_str(), "", PARAM_READONLY * (dup == 0));
[138]	208	}
	209
	210	par += &localpar;
	211	par += &seloperpar;
	212	par += &neuronsparam;
[145]	213	for (unsigned int i = 0; i < oper_fx_list.size(); i++)
	214	if (oper_fx_list[i]->par.getParamTab()) par += &oper_fx_list[i]->par;
[715]	215
	216	setDefaults(); //use Param to initialize all values of fields in the paramtab of this object and genetic operators on oper_fx_list
[138]	217	}
	218
	219	GenMan::~GenMan()
	220	{
[145]	221	for (unsigned int i = 0; i < oper_fx_list.size(); i++) delete oper_fx_list[i];
[138]	222	delete[] seloper;
	223	}
	224
[955]	225	int GenMan::findOperFormatIndex(const SString& format)
	226	{
	227	for (int i = 0; i < operformats.size(); i++)
	228	if (*operformats(i) == format)
	229	return i;
	230	return -1;
	231	}
	232
[138]	233	void GenMan::setDefaults()
	234	{
[145]	235	for (unsigned int i = 0; i < oper_fx_list.size(); i++)
[138]	236	{
[145]	237	oper_fx_list[i]->par.setDefault();
	238	oper_fx_list[i]->setDefaults();
[138]	239	}
	240	localpar.setDefault();
	241	//...and we do not reset others that are linked to 'par',
	242	//because there quite a few of them, and not every of them defines defaults for each of its parameters.
	243	}
	244
	245	int GenMan::testValidity(Geno &g, bool &canvalidate)
	246	{
[761]	247	SString ggs = g.getGenes();
[348]	248	const char *gg = ggs.c_str();
[145]	249	GenoOperators *gf = getOper_f(g.getFormat());
[138]	250	int check1;
	251	if (!gf) { canvalidate = false; return GENOPER_NOOPER; }
[761]	252	else check1 = gf->checkValidity(gg, g.getName().c_str());
[138]	253	if (!canvalidate) return check1; //just checking
	254	if (check1 == GENOPER_OK) { canvalidate = false; return check1; }
	255	char *g2 = strdup(gg);
[761]	256	if (gf->validate(g2, g.getName().c_str()) == GENOPER_NOOPER) { free(g2); canvalidate = false; return check1; }
[138]	257	if (check1 == GENOPER_NOOPER) //disaster: cannot check because there is no check operator
	258	{
[534]	259	g.setGenesAssumingSameFormat(g2); free(g2); canvalidate = false; return GENOPER_NOOPER;
[138]	260	}
[513]	261	int check2 = gf->checkValidity(g2, "validated");
[534]	262	if (check2 == GENOPER_OK) g.setGenesAssumingSameFormat(g2);
[138]	263	free(g2);
	264	if (check2 == GENOPER_OK) return check1;
	265	canvalidate = false;
	266	return check1; //could not validate.
	267	}
	268
	269	int GenMan::testGenoValidity(Geno& g)
	270	{
	271	bool fix = false;
	272	switch (testValidity(g, fix))
	273	{
	274	case GENOPER_OK: return 1;
	275	case GENOPER_NOOPER: return -1;
	276	default: return 0;
	277	}
	278	}
	279
[532]	280	Geno GenMan::validate(const Geno& geny)
[138]	281	{
[955]	282	SString format = geny.getFormat();
[168]	283	GenoOperators *gf = getOper_f(format);
	284	if (gf == NULL)
[955]	285	return Geno("", Geno::INVALID_FORMAT, "", SString::sprintf("GENOPER_NOOPER: Validate(): don't know how to handle genetic format %s", format.c_str()));
[534]	286	char *g2 = strdup(geny.getGenes().c_str()); //copy for validation
[513]	287	int res = gf->validate(g2, geny.getName().c_str());
[168]	288	SString sg2 = g2;
[138]	289	free(g2);
[168]	290	if (res == GENOPER_OK)
	291	return Geno(sg2, format, geny.getName(), geny.getComment());
[138]	292	else
[955]	293	return Geno("", Geno::INVALID_FORMAT, "", SString::sprintf("GENOPER_NOOPER: validate() for format %s returned invalid value", format.c_str()));
[138]	294	}
	295
[532]	296	Geno GenMan::mutate(const Geno& g)
[138]	297	{
	298	float chg; //how many changes
	299	int method; //mutation method
[955]	300	SString format = g.getFormat();
[168]	301	GenoOperators *gf = getOper_f(format);
	302	if (gf == NULL)
[955]	303	return Geno("", Geno::INVALID_FORMAT, "", SString::sprintf("GENOPER_NOOPER: Mutate(): don't know how to handle genetic format %s", format.c_str()));
[168]	304	Geno gv = g;
	305	bool canvalidate = true;
	306	if (testValidity(gv, canvalidate) > 0 && canvalidate == false)
[955]	307	return Geno("", Geno::INVALID_FORMAT, "", "GENOPER_OPFAIL: Mutate(): cannot validate invalid source genotype");
[168]	308	bool ok = false;
	309	int pcount = count;
[138]	310	while (!ok)
	311	{
[534]	312	char *gn = strdup(gv.getGenes().c_str()); //copy for mutation
[168]	313	chg = 0;
	314	if (gf->mutate(gn, chg, method) == GENOPER_OK)
[138]	315	{
[375]	316	LoggerToMemory eh(LoggerBase::Enable \| LoggerToMemory::StoreFirstMessage); //mute testValidity()
[168]	317	Geno G(gn, gv.getFormat(), "", "");
	318	canvalidate = true;
	319	int res = testValidity(G, canvalidate);
	320	if (res == GENOPER_OK && canvalidate == false) { valid_m++; ok = true; }
	321	else
	322	if (res > 0 && canvalidate == false) invalid_m++; else
	323	{
[955]	324	validated_m++; ok = true;
[168]	325	}
	326	if (ok) gv = G;
	327	}
	328	else failed_m++;
[138]	329	free(gn);
	330	count++;
[761]	331	if (!ok && (count - pcount > GENMAN_REPEAT_FAILED))
[138]	332	{
[955]	333	logPrintf("GenMan", "Mutate", LOG_WARN, "Tried " GENMAN_REPEAT_FAILED_STR "x and failed: %s", g.getGenes().c_str());
[761]	334	return Geno("", -1, "", "GENOPER_OPFAIL: Mutate() tried " GENMAN_REPEAT_FAILED_STR "x and failed");
[138]	335	}
	336	}
[168]	337	mutchg += chg;
[534]	338	if (history) saveLink(g.getGenes().c_str(), "", gv.getGenes().c_str(), chg);
[138]	339	SString mutinfo;
[348]	340	if (extmutinfo == 0) mutinfo = SString::sprintf("%.2f%% mutation of '%s'", 100 * chg, g.getName().c_str()); else
	341	if (extmutinfo == 1) mutinfo = SString::sprintf("%.2f%% mutation(%d) of '%s'", 100 * chg, method, g.getName().c_str()); else
	342	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]	343	gv.setComment(mutinfo);
	344	return gv;
	345	}
	346
[532]	347	Geno GenMan::crossOver(const Geno& g1, const Geno& g2)
[138]	348	{
[955]	349	SString format = g1.getFormat();
	350	if (format != g2.getFormat()) return Geno("", Geno::INVALID_FORMAT, "", SString::sprintf("GENOPER_NOOPER: CrossOver(): does not work for parents with differing genetic formats (%s and %s)", format.c_str(), g2.getFormat().c_str()));
[145]	351	GenoOperators *gf = getOper_f(format);
[138]	352	if (gf == NULL)
[955]	353	return Geno("", Geno::INVALID_FORMAT, "", SString::sprintf("GENOPER_NOOPER: CrossOver(): no operators found for genetic format %s", format.c_str()));
[138]	354	Geno g1v = g1, g2v = g2;
	355
	356	{
[375]	357	LoggerToMemory eh(LoggerBase::Enable \| LoggerToMemory::StoreFirstMessage); //mute testValidity()
[138]	358	bool canvalidate = true;
	359	if (testValidity(g1v, canvalidate) > 0 && canvalidate == false)
[955]	360	return Geno("", Geno::INVALID_FORMAT, "", "GENOPER_OPFAIL: CrossOver(): cannot validate invalid source genotype #1");
[138]	361	canvalidate = true;
	362	if (testValidity(g2v, canvalidate) > 0 && canvalidate == false)
[955]	363	return Geno("", Geno::INVALID_FORMAT, "", "GENOPER_OPFAIL: CrossOver(): cannot validate invalid source genotype #2");
[138]	364	}
	365
	366	float chg;
	367	bool ok = false;
	368	int pcount = count;
	369
	370	while (!ok)
	371	{
	372	float chg1, chg2;
[534]	373	char *g1n = strdup(g1.getGenes().c_str()); //copy for crossover
	374	char *g2n = strdup(g2.getGenes().c_str()); //copy for crossover
[138]	375	chg1 = chg2 = 0;
	376	if (gf->crossOver(g1n, g2n, chg1, chg2) == GENOPER_OK)
	377	{
	378	char *gn;
[896]	379	if (g1n[0] && g2n[0]) if (rndUint(2) == 0) g1n[0] = 0; else g2n[0] = 0; //both provided? we want only one
[138]	380	if (g1n[0]) { gn = g1n; chg = chg1; }
	381	else { gn = g2n; chg = chg2; }
[375]	382	LoggerToMemory eh(LoggerBase::Enable \| LoggerToMemory::StoreFirstMessage); //mute testValidity()
[138]	383	Geno G(gn, g1v.getFormat(), "", "");
	384	bool canvalidate = true;
	385	int res = testValidity(G, canvalidate);
	386	if (res == GENOPER_OK && canvalidate == false) { valid_xo++; ok = true; }
	387	else
	388	if (res > 0 && canvalidate == false) invalid_xo++; else
	389	{
[955]	390	validated_xo++; ok = true;
[138]	391	}
	392	if (ok) g1v = G;
	393	}
	394	else failed_xo++;
	395	free(g1n);
	396	free(g2n);
	397	count++;
[761]	398	if (!ok && (count - pcount > GENMAN_REPEAT_FAILED))
[138]	399	{
[955]	400	logPrintf("GenMan", "CrossOver", LOG_WARN, "Tried " GENMAN_REPEAT_FAILED_STR "x and failed: %s and %s", g1.getGenes().c_str(), g2.getGenes().c_str());
	401	return Geno("", Geno::INVALID_FORMAT, "", "GENOPER_OPFAIL: CrossOver() tried " GENMAN_REPEAT_FAILED_STR "x and failed");
[138]	402	}
	403	}
	404	// result in g1v
	405	xochg += chg;
[534]	406	if (history) saveLink(g1.getGenes().c_str(), g2.getGenes().c_str(), g1v.getGenes().c_str(), chg);
[138]	407	SString xoinfo = SString::sprintf("Crossing over of '%s' (%.2f%%) and '%s' (%.2f%%)",
[348]	408	g1.getName().c_str(), 100 * chg, g2.getName().c_str(), 100 * (1 - chg));
[138]	409	g1v.setComment(xoinfo);
	410	return g1v;
	411	}
	412
[532]	413	float GenMan::similarity(const Geno& g1, const Geno& g2)
[138]	414	{
[955]	415	SString format = g1.getFormat();
[138]	416	if (format != g2.getFormat()) return GENOPER_NOOPER;
[145]	417	GenoOperators *gf = getOper_f(format);
[534]	418	if (!gf) return GENOPER_NOOPER; else return gf->similarity(g1.getGenes().c_str(), g2.getGenes().c_str());
[138]	419	}
	420
[532]	421	uint32_t GenMan::getStyle(const char g, const Geno G, int pos)
[138]	422	{
[955]	423	SString format = G->getFormat();
[532]	424	if (format == Geno::INVALID_FORMAT)
	425	return GENSTYLE_RGBS(64, 64, 64, 0); // gray & "valid" (unknown format so we don't know what is valid and what is not)
	426	if ((pos = G->mapStringToGen(pos)) == -1) return GENSTYLE_COMMENT;
	427	GenoOperators *gf = getOper_f(format);
[138]	428	if (!gf) return GENSTYLE_CS(0, 0); //black & valid
[534]	429	else return gf->style(G->getGenes().c_str(), pos);
[138]	430	}
	431
[532]	432	uint32_t GenMan::getStyle(const char *g, int pos)
[138]	433	{
	434	Geno G(g);
[532]	435	return getStyle(g, &G, pos);
	436	}
	437
	438	void GenMan::getFullStyle(const char g, const Geno G, uint32_t *styletab)
	439	{
[955]	440	SString format = G->getFormat();
[532]	441	if (format == Geno::INVALID_FORMAT)
	442	{
	443	for (unsigned int pos = 0; pos < strlen(g); pos++)
	444	styletab[pos] = GENSTYLE_RGBS(64, 64, 64, 0); // gray & "valid" (unknown format so we don't know what is valid and what is not)
	445	return;
	446	}
	447	GenoOperators *gf = getOper_f(format);
[761]	448	SString geny = G->getGenes();
[138]	449	for (unsigned int pos = 0; pos < strlen(g); pos++)
	450	{
[532]	451	int posmapped = G->mapStringToGen(pos);
[138]	452	if (posmapped == -1) styletab[pos] = GENSTYLE_COMMENT;
	453	else if (!gf) styletab[pos] = GENSTYLE_CS(0, 0); //black & valid
[348]	454	else styletab[pos] = gf->style(geny.c_str(), posmapped);
[955]	455	//logPrintf("GenMan", "getFullStyle", LOG_INFO, "%d char='%c' (%d) format=0x%08x", pos, g[pos], g[pos], styletab[pos]);
[138]	456	}
	457	}
	458
[532]	459	void GenMan::getFullStyle(const char g, uint32_t styletab)
	460	{
	461	Geno G(g);
	462	getFullStyle(g, &G, styletab);
	463	}
	464
[467]	465	string GenMan::HTMLize(const char *g) { return HTMLize(g, false); }
[138]	466
[467]	467	string GenMan::HTMLizeShort(const char *g) { return HTMLize(g, true); }
[138]	468
[467]	469	string GenMan::HTMLize(const char *g, bool shorten)
[138]	470	{
	471	char buf[50];
	472	int len = strlen(g);
	473	int chars = 0, lines = 0;
	474	bool shortened = false;
[247]	475	uint32_t *styletab = new uint32_t[len];
[532]	476	getFullStyle(g, styletab);
[467]	477	string html = "\n<div style=\"background:white;padding:0.2em;font-family:arial,helvetica,sans-serif;font-size:90%\">";
[247]	478	uint32_t prevstyle, prevcolor, style = 0, color = 0;
[761]	479	for (int i = 0; i < len; i++)
[138]	480	{
[761]	481	if (shorten && ((lines == 0 && chars > 160) \|\| (lines > 5 \|\| chars > 300))) { shortened = true; break; }
[138]	482	if (g[i] == '\r') continue;
	483	if (g[i] == '\n') { html += "<br>\n"; lines++; continue; }
	484	chars++;
	485	prevstyle = style;
	486	prevcolor = color;
	487	style = GENGETSTYLE(styletab[i]);
	488	color = GENGETCOLOR(styletab[i]);
	489	if ((i != 0 && (color != prevcolor))) html += "</font>";
[955]	490	if ((style & GENSTYLE_INVALID) != (prevstyle & GENSTYLE_INVALID))
[138]	491	{
[955]	492	html += "<"; if (!(style & GENSTYLE_INVALID)) html += "/"; html += "u>";
[138]	493	}
[955]	494	if ((style & GENSTYLE_BOLD) != (prevstyle & GENSTYLE_BOLD))
[138]	495	{
[955]	496	html += "<"; if (!(style & GENSTYLE_BOLD)) html += "/"; html += "b>";
[138]	497	}
[955]	498	if ((style & GENSTYLE_ITALIC) != (prevstyle & GENSTYLE_ITALIC))
[138]	499	{
[955]	500	html += "<"; if (!(style & GENSTYLE_ITALIC)) html += "/"; html += "i>";
[138]	501	}
	502	if ((i == 0 \|\| (color != prevcolor)))
	503	{
	504	sprintf(buf, "<font color=#%02x%02x%02x>", GENGET_R(color), GENGET_G(color), GENGET_B(color)); html += buf;
	505	}
	506	if (g[i] == '<') html += "<"; else if (g[i] == '>') html += ">"; else html += g[i];
	507	if ((i % 3) == 0 && g[i] == ' ') html += "\n"; //for readability, insert some newlines into html...
	508	}
	509	delete[] styletab;
	510	html += "</u></b></i></font>";
	511	if (shortened) html += " [etc...]";
	512	html += "</div>\n";
	513	return html;
	514	}
	515
	516	void GenMan::p_htmlize(ExtValue args, ExtValue ret)
	517	{
[467]	518	ret->setString(HTMLize(args->getString().c_str()).c_str());
[138]	519	}
	520
	521	void GenMan::p_htmlizeshort(ExtValue args, ExtValue ret)
	522	{
[467]	523	ret->setString(HTMLizeShort(args->getString().c_str()).c_str());
[138]	524	}
	525
[965]	526	string GenMan::LaTeXize(const char *g)
	527	{
	528	char buf[50];
	529	int len = strlen(g);
	530	int chars = 0, lines = 0; //currently not used
	531	uint32_t *styletab = new uint32_t[len];
	532	getFullStyle(g, styletab);
	533	string latex = "\\usepackage{xcolor}\n% Using \\texttt{} may be beneficial for some genetic encodings, but then you may lose bold/italic.\n\\noindent \\sloppy";
	534	uint32_t prevstyle, prevcolor, style = 0, color = 0;
	535	for (int i = 0; i < len; i++)
	536	{
	537	if (g[i] == '\r') continue;
	538	if (g[i] == '\n') { latex += "\\\\\n"; lines++; continue; }
	539	chars++;
	540	prevstyle = style;
	541	prevcolor = color;
	542	style = GENGETSTYLE(styletab[i]);
	543	color = GENGETCOLOR(styletab[i]);
	544
	545	// Unfortunately, LaTeX (as opposed to HTML) uses the same closing tags "}" for color, bold, italic, underline - so they cannot intersect.
	546	// Therefore we have to "turn off" everything on every change of style or color, and then "turn on" (to avoid problems with e.g. red-bold-blue-unbold or bold-italic-unbold-unitalic).
	547	// This could be optimized by a more complex logic and tracking which color/style section starts and ends within another section.
	548
	549	if (((style & GENSTYLE_INVALID) != (prevstyle & GENSTYLE_INVALID))
	550	\|\|
	551	((style & GENSTYLE_BOLD) != (prevstyle & GENSTYLE_BOLD))
	552	\|\|
	553	((style & GENSTYLE_ITALIC) != (prevstyle & GENSTYLE_ITALIC))
	554	\|\|
	555	((i == 0 \|\| (color != prevcolor))))
	556	{
	557	if (prevstyle & GENSTYLE_INVALID) latex += "}";
	558	if (prevstyle & GENSTYLE_BOLD) latex += "}";
	559	if (prevstyle & GENSTYLE_ITALIC) latex += "}";
	560	if (i != 0) latex += "}"; //for color
	561	if (style & GENSTYLE_INVALID) latex += "\\underline{";
	562	if (style & GENSTYLE_BOLD) latex += "\\textbf{";
	563	if (style & GENSTYLE_ITALIC) latex += "\\textit{";
	564	sprintf(buf, "\\textcolor[rgb]{%.2g,%.2g,%.2g}{", GENGET_R(color) / 255.0, GENGET_G(color) / 255.0, GENGET_B(color) / 255.0); latex += buf;
	565	}
	566	if (g[i] == '<') latex += "$<$"; else if (g[i] == '>') latex += "$>$"; else
	567	if (g[i] == '-') latex += "$-$"; else if (g[i] == '\|') latex += "$\|$"; else
	568	if (g[i] == '$') latex += "\\$"; else if (g[i] == '%') latex += "\\%"; else latex += g[i];
	569	if ((i % 3) == 0 && g[i] == ' ') latex += "\n"; //for readability, insert some newlines into latex...
	570	if (i % 10 == 0) latex += "{\\hskip 0pt}"; // https://tex.stackexchange.com/questions/33526/automatic-line-breaking-of-long-lines-of-text
	571	}
	572	delete[] styletab;
	573	latex += "}"; //for color (it was used at least once)
[966]	574	if (style & GENSTYLE_INVALID) latex += "}";
[965]	575	if (style & GENSTYLE_BOLD) latex += "}";
	576	if (style & GENSTYLE_ITALIC) latex += "}";
	577	latex += "\n";
	578	return latex;
	579	}
	580
	581	void GenMan::p_latexize(ExtValue args, ExtValue ret)
	582	{
	583	ret->setString(LaTeXize(args->getString().c_str()).c_str());
	584	}
	585
[955]	586	Geno GenMan::getSimplest(const SString& format)
[138]	587	{
[145]	588	GenoOperators *gf = getOper_f(format);
[138]	589	if (!gf) return Geno();
[955]	590	string info = "The simplest genotype of format f"; info += format.c_str();
[138]	591	info += " for operators '"; info += gf->name; info += "'.";
[200]	592	return Geno(gf->getSimplest(), format, "Root", info.c_str());
[138]	593	}
	594
	595	void GenMan::p_getsimplest(ExtValue args, ExtValue ret)
	596	{
[955]	597	SString format = GenoObj::formatFromExtValue(args[0]);
[145]	598	if (!getOper_f(format))
[138]	599	ret->setEmpty();
	600	else
[532]	601	*ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(getSimplest(format)));
[138]	602	}
	603
[955]	604	const char *GenMan::getOpName(const SString& format)
[138]	605	{
[145]	606	GenoOperators *gf = getOper_f(format);
[200]	607	if (!gf) return "n/a"; else return gf->name.c_str();
[138]	608	}
	609
[955]	610	GenoOperators* GenMan::getOper_f(const SString& format)
[138]	611	{
[955]	612	int ind = findOperFormatIndex(format);
[138]	613	if (ind == -1) return NULL;
[168]	614	int which_oper_of_format = seloper[ind];
[145]	615	for (unsigned int i = 0; i < oper_fx_list.size(); i++)
	616	if (oper_fx_list[i]->supported_format == format)
[168]	617	if (which_oper_of_format == 0) return oper_fx_list[i]; else which_oper_of_format--;
[138]	618	return NULL; //should never happen
	619	}
	620
[275]	621	void GenMan::saveLink(const string parent1, const string parent2, const string child, const float chg)
[138]	622	{
	623	GenoLink l;
	624	l.count = count;
[275]	625	l.parent1 = parent1;
	626	l.parent2 = parent2;
	627	l.child = child;
[138]	628	l.chg = chg;
	629	l.fit = 0; //temporarily. Will be set when the genotype dies
[375]	630	//logPrintf("GenMan","saveLink",0,"#%d: [%d] '%s' + '%s' -> '%s'",GenoLinkList.size(),count,parent1.c_str(),parent2.c_str(),child.c_str());
[138]	631	GenoLinkList.push_back(l);
	632	}
	633
[247]	634	void GenMan::onDelGen(void *obj, intptr_t n)
[138]	635	{
	636	//old code needs update:
	637	// ((SpeciesList*)obj)->przyDodaniu(i);
	638	/* !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
	639	GenMan gm=(GenMan)obj;
	640	Genotype gt=(Genotype)(*listaGen)(n); //there is no more "listaGen"
	641	string g=(const char*)gt->genotype.getGene();
	642	float fit=gt->getFinalFitness();
	643	for(int i=0;i<gm->GenoLinkList.size();i++) //find genotype
	644	if (gm->GenoLinkList[i].g1==g) {gm->GenoLinkList[i].fit=fit; break;}
	645	*/
	646	}
	647
	648	void GenMan::clearStats()
	649	{
	650	count = 0;
	651	valid_m = valid_xo = validated_m = validated_xo = invalid_m = invalid_xo = failed_m = failed_xo = 0;
	652	mutchg = xochg = 0;
	653	GenoLinkList.clear();
	654	}
	655
	656	void GenMan::p_clearStats(ExtValue args, ExtValue ret) { clearStats(); }
	657
	658	void GenMan::p_report(ExtValue args, ExtValue ret)
	659	{ //should be updated to handle multiple operators for a single format
	660	char g, g2;
[145]	661	float f1, f2;
	662	int m;
[375]	663	logMessage("GenMan", "Report", 0, "The following genetic operators are available:");
[145]	664	for (unsigned int i = 0; i < oper_fx_list.size(); i++)
[138]	665	{
[200]	666	string l;
[761]	667	if (oper_fx_list[i]->checkValidity("", "") != GENOPER_NOOPER) l += " checkValidity";
[145]	668	if (oper_fx_list[i]->getSimplest())
[138]	669	{
[145]	670	g = strdup(oper_fx_list[i]->getSimplest());
[138]	671	g2 = strdup(g);
[761]	672	if (oper_fx_list[i]->validate(g, "") != GENOPER_NOOPER) l += " validate";
[145]	673	if (oper_fx_list[i]->mutate(g, f1, m) != GENOPER_NOOPER) l += " mutate";
	674	if (oper_fx_list[i]->crossOver(g, g2, f1, f2) != GENOPER_NOOPER) l += " crossover";
[138]	675	l += " getSimplest";
	676	free(g); free(g2);
	677	}
[145]	678	// if (oper_fx_list[i]->similarity("","")!=GENOPER_NOOPER) l+=" similarity";
[955]	679	logPrintf("GenMan", "Report", LOG_INFO, "format f%s (%s):%s",
	680	oper_fx_list[i]->supported_format.c_str(), oper_fx_list[i]->name.c_str(), l.c_str());
[138]	681	}
	682	}
	683
	684	void GenMan::p_validate(ExtValue args, ExtValue ret)
	685	{
	686	Geno *g = GenoObj::fromObject(args[0]);
	687	if (g == NULL)
	688	ret->setEmpty();
	689	else
[532]	690	ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(validate(g)));
[138]	691	}
	692
	693	void GenMan::p_mutate(ExtValue args, ExtValue ret)
	694	{
	695	Geno *g = GenoObj::fromObject(args[0]);
	696	if (g == NULL)
	697	ret->setEmpty();
	698	else
[532]	699	ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(mutate(g)));
[138]	700	}
	701
	702	void GenMan::p_crossover(ExtValue args, ExtValue ret)
	703	{
	704	Geno *g1 = GenoObj::fromObject(args[1]);
	705	Geno *g2 = GenoObj::fromObject(args[0]);
	706	if (g1 == NULL \|\| g2 == NULL)
	707	ret->setEmpty();
	708	else
[532]	709	ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(crossOver(g1, *g2)));
[138]	710	}
[532]	711

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