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source: cpp/frams/genetics/genman.cpp @ 219

Last change on this file since 219 was 200, checked in by Maciej Komosinski, 11 years ago
More stl string, less SString
Property svn:eol-style set to `native`
File size: 20.2 KB

Rev	Line
[138]	1	// This file is a part of the Framsticks GDK.
[197]	2	// Copyright (C) 1999-2014 Maciej Komosinski and Szymon Ulatowski. See LICENSE.txt for details.
[138]	3	// Refer to http://www.framsticks.com/ for further information.
	4
	5	#include "genman.h"
	6	#include <frams/vm/classes/genoobj.h>
	7	#include GEN_CONFIG_FILE //configuration of active genetic operators
	8	#include "common/framsg.h"
	9	#include "common/nonstd_math.h"
[200]	10	#include "common/stl-util.h"
[138]	11	#include <frams/errmgr/errmanager.h>
	12
	13
[139]	14	#ifdef USE_GENMAN_f0
[138]	15	#include "f0/oper_f0.h"
	16	#endif
[139]	17	#ifdef USE_GENMAN_f0FUZZY
[138]	18	#include "f0/oper_f0Fuzzy.h"
	19	#endif
[139]	20	#ifdef USE_GENMAN_f1
[138]	21	#include "f1/oper_f1.h"
	22	#endif
[139]	23	#ifdef USE_GENMAN_f2
[138]	24	#include "f2/oper_f2.h"
	25	#endif
[139]	26	#ifdef USE_GENMAN_f2
[138]	27	#include "f3/oper_f3.h"
	28	#endif
[139]	29	#ifdef USE_GENMAN_f4
[138]	30	#include "f4/oper_f4.h"
	31	#endif
[139]	32	#ifdef USE_GENMAN_f5
[138]	33	#include "f5/oper_f5.h"
	34	#endif
[139]	35	#ifdef USE_GENMAN_f6
[138]	36	#include "f6/oper_f6.h"
	37	#endif
[139]	38	#ifdef USE_GENMAN_f7
[138]	39	#include "f7/oper_f7.h"
	40	#endif
[139]	41	#ifdef USE_GENMAN_f8
[138]	42	#include "f8/oper_f8.h"
	43	#endif
[139]	44	#ifdef USE_GENMAN_f9
[138]	45	#include "f9/oper_f9.h"
	46	#endif
[139]	47	#ifdef USE_GENMAN_fF
	48	#include "fF/oper_fF.h"
	49	#endif
[194]	50	#ifdef USE_GENMAN_fT
	51	#include "fT/oper_fTest.h"
	52	#endif
[138]	53
	54	using namespace std; //string, vector
	55
	56	//old code needs update:
	57	//#include "gengroups.h"
	58	//extern GenGroup *listaGen;
	59	// GENGROUP(0)->l_del.add(sim->GM.onDelGen,&sim->GM); //before delete
	60	// GENGROUP(0)->l_del.remove(sim->GM.onDelGen,&sim->GM); //before delete
	61
	62
	63	#define FIELDSTRUCT GenMan
	64
	65	static ParamEntry GMparam_tab[] =
	66	{
	67	{ "Genetics", 1, 10, "GenMan", },
	68	{ "gen_hist", 0, PARAM_DONTSAVE, "Remember history of genetic operations", "d 0 1 0", FIELD(history), "Required for phylogenetic analysis", },
	69	{ "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)", },
	70	{ "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.", },
	71	{ "operReport", 0, PARAM_DONTSAVE, "Operators report", "p()", PROCEDURE(p_report), "Show available genetic operators", },
	72	{ "toHTML", 0, PARAM_DONTSAVE, "HTMLize a genotype", "p s(s)", PROCEDURE(p_htmlize), "returns genotype expressed as colored HTML", },
	73	{ "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", },
	74	{ "validate", 0, PARAM_DONTSAVE + PARAM_USERHIDDEN, "Validate", "p oGeno(oGeno)", PROCEDURE(p_validate), "returns validated (if possible) Geno object from supplied Geno", },
	75	{ "mutate", 0, PARAM_DONTSAVE + PARAM_USERHIDDEN, "Mutate", "p oGeno(oGeno)", PROCEDURE(p_mutate), "returns mutated Geno object from supplied Geno", },
	76	{ "crossOver", 0, PARAM_DONTSAVE + PARAM_USERHIDDEN, "Crossover", "p oGeno(oGeno,oGeno)", PROCEDURE(p_crossover), "returns crossed over genotype", },
	77	{ "getSimplest", 0, PARAM_DONTSAVE + PARAM_USERHIDDEN, "Get simplest genotype", "p oGeno(d format)", PROCEDURE(p_getsimplest), "returns the simplest genotype for a given encoding (format). 0 means f0, 4 means f4, etc.", },
	78	{ 0, },
	79	};
	80
	81	static ParamEntry GMstats_tab[] =
	82	{
	83	{ "Genetics", 1, 12, "GenManStats", "Statistics for genetic operations." },
	84	{ "gen_count", 0, PARAM_READONLY, "Number of genetic operations so far", "d", FIELD(count), "", },
	85	{ "gen_mvalid", 0, PARAM_READONLY, "Mutations valid", "d", FIELD(valid_m), "", },
	86	{ "gen_mvalidated", 0, PARAM_READONLY, "Mutations validated", "d", FIELD(validated_m), "", },
	87	{ "gen_minvalid", 0, PARAM_READONLY, "Mutations invalid", "d", FIELD(invalid_m), "couldn't be repaired", },
	88	{ "gen_mfailed", 0, PARAM_READONLY, "Mutations failed", "d", FIELD(failed_m), "couldn't be performed", },
	89	{ "gen_xovalid", 0, PARAM_READONLY, "Crossovers valid", "d", FIELD(valid_xo), "", },
	90	{ "gen_xovalidated", 0, PARAM_READONLY, "Crossovers validated", "d", FIELD(validated_xo), "", },
	91	{ "gen_xoinvalid", 0, PARAM_READONLY, "Crossovers invalid", "d", FIELD(invalid_xo), "couldn't be repaired", },
	92	{ "gen_xofailed", 0, PARAM_READONLY, "Crossovers failed", "d", FIELD(failed_xo), "couldn't be performed", },
	93	{ "gen_mutimpr", 0, PARAM_READONLY, "Mutations total effect", "f", FIELD(mutchg), "total cumulative mutation change", },
	94	{ "gen_xoimpr", 0, PARAM_READONLY, "Crossovers total effect", "f", FIELD(xochg), "total cumulative crossover change", },
	95	{ "clrstats", 0, PARAM_DONTSAVE, "Clear stats and history", "p()", PROCEDURE(p_clearStats), "", },
	96	{ 0, },
	97	};
	98
	99	#undef FIELDSTRUCT
	100
	101	GenMan::GenMan() : localpar(GMparam_tab, this), localstats(GMstats_tab, this),
	102	seloperpar("GenOperators", "Genetics: Active operators"),
	103	par("GenMan", "Manages various genetic operations, using appropriate operators for the argument genotype format."),
	104	neuronsparam("Genetics: Neurons to add", "neuronsAdd", "neuadd_")
	105	{
	106	history = 0;
	107	hilite = 1;
	108	clearStats();
	109
[139]	110	#ifdef USE_GENMAN_f0
[145]	111	oper_fx_list.push_back(new Geno_f0);
[138]	112	#endif
[139]	113	#ifdef USE_GENMAN_f0FUZZY
[145]	114	oper_fx_list.push_back(new Geno_f0Fuzzy);
[138]	115	#endif
[139]	116	#ifdef USE_GENMAN_f1
[145]	117	oper_fx_list.push_back(new Geno_f1);
[138]	118	#endif
[139]	119	#ifdef USE_GENMAN_f2
[145]	120	oper_fx_list.push_back(new Geno_f2);
[138]	121	#endif
[139]	122	#ifdef USE_GENMAN_f3
[145]	123	oper_fx_list.push_back(new Geno_f3);
[138]	124	#endif
[139]	125	#ifdef USE_GENMAN_f4
[145]	126	oper_fx_list.push_back(new Geno_f4);
[138]	127	#endif
[139]	128	#ifdef USE_GENMAN_f5
[145]	129	oper_fx_list.push_back(new Geno_f5);
[138]	130	#endif
[139]	131	#ifdef USE_GENMAN_f6
[145]	132	oper_fx_list.push_back(new Geno_f6);
[138]	133	#endif
[139]	134	#ifdef USE_GENMAN_f7
[145]	135	oper_fx_list.push_back(new Geno_f7);
[138]	136	#endif
[139]	137	#ifdef USE_GENMAN_f8
[145]	138	oper_fx_list.push_back(new Geno_f8);
[138]	139	#endif
[139]	140	#ifdef USE_GENMAN_f9
[145]	141	oper_fx_list.push_back(new GenoOper_f9);
[138]	142	#endif
[139]	143	#ifdef USE_GENMAN_fF
[145]	144	oper_fx_list.push_back(new GenoOper_fF);
[139]	145	#endif
[194]	146	#ifdef USE_GENMAN_fT
	147	oper_fx_list.push_back(new GenoOper_fTest);
	148	#endif
[138]	149
[145]	150	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]	151	int selopercount = 0;
[145]	152	for (unsigned int i = 0; i < oper_fx_list.size(); i++)
[138]	153	{
[145]	154	if (operformats.find(oper_fx_list[i]->supported_format) != -1) continue;
[200]	155	string type = string("~") + oper_fx_list[i]->name;
[138]	156	int dup = 0;
[145]	157	for (unsigned int j = i + 1; j < oper_fx_list.size(); j++)
	158	if (oper_fx_list[i]->supported_format == oper_fx_list[j]->supported_format)
[138]	159	{
[200]	160	type += "~";
	161	type += oper_fx_list[j]->name;
	162	dup++;
[138]	163	}
[200]	164	type = ssprintf("d 0 %d ", dup) + type;
	165	string id = ssprintf("genoper_f%c", oper_fx_list[i]->supported_format);
	166	string name = ssprintf("Operators for f%c", oper_fx_list[i]->supported_format);
[138]	167	seloper[selopercount] = 0;
[145]	168	operformats += oper_fx_list[i]->supported_format;
[138]	169	//printf("%x %s %s %s\n",&seloper[selopercount],(const char)id,(const char)type,(const char*)name);
[200]	170	seloperpar.addProperty(&seloper[selopercount++], id.c_str(), type.c_str(), name.c_str(), "", PARAM_READONLY*(dup == 0));
[138]	171	}
	172
	173	par += &localpar;
	174	par += &seloperpar;
	175	par += &neuronsparam;
[145]	176	for (unsigned int i = 0; i < oper_fx_list.size(); i++)
	177	if (oper_fx_list[i]->par.getParamTab()) par += &oper_fx_list[i]->par;
[138]	178	}
	179
	180	GenMan::~GenMan()
	181	{
[145]	182	for (unsigned int i = 0; i < oper_fx_list.size(); i++) delete oper_fx_list[i];
[138]	183	delete[] seloper;
	184	}
	185
	186	void GenMan::setDefaults()
	187	{
[145]	188	for (unsigned int i = 0; i < oper_fx_list.size(); i++)
[138]	189	{
[145]	190	oper_fx_list[i]->par.setDefault();
	191	oper_fx_list[i]->setDefaults();
[138]	192	}
	193	localpar.setDefault();
	194	//...and we do not reset others that are linked to 'par',
	195	//because there quite a few of them, and not every of them defines defaults for each of its parameters.
	196	}
	197
	198	int GenMan::testValidity(Geno &g, bool &canvalidate)
	199	{
	200	const char *gg = g.getGene();
[145]	201	GenoOperators *gf = getOper_f(g.getFormat());
[138]	202	int check1;
	203	if (!gf) { canvalidate = false; return GENOPER_NOOPER; }
	204	else check1 = gf->checkValidity(gg);
	205	if (!canvalidate) return check1; //just checking
	206	if (check1 == GENOPER_OK) { canvalidate = false; return check1; }
	207	char *g2 = strdup(gg);
	208	if (gf->validate(g2) == GENOPER_NOOPER) { free(g2); canvalidate = false; return check1; }
	209	if (check1 == GENOPER_NOOPER) //disaster: cannot check because there is no check operator
	210	{
	211	g.setGene(g2); free(g2); canvalidate = false; return GENOPER_NOOPER;
	212	}
	213	int check2 = gf->checkValidity(g2);
	214	if (check2 == GENOPER_OK) g.setGene(g2);
	215	free(g2);
	216	if (check2 == GENOPER_OK) return check1;
	217	canvalidate = false;
	218	return check1; //could not validate.
	219	}
	220
	221	int GenMan::testGenoValidity(Geno& g)
	222	{
	223	bool fix = false;
	224	switch (testValidity(g, fix))
	225	{
	226	case GENOPER_OK: return 1;
	227	case GENOPER_NOOPER: return -1;
	228	default: return 0;
	229	}
	230	}
	231
	232	Geno GenMan::Validate(const Geno& geny)
	233	{
[168]	234	char format = geny.getFormat();
	235	GenoOperators *gf = getOper_f(format);
	236	if (gf == NULL)
	237	return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: Validate(): don't know how to handle genetic format %c", format));
	238	char *g2 = strdup(geny.getGene()); //copy for validation
	239	int res = gf->validate(g2);
	240	SString sg2 = g2;
[138]	241	free(g2);
[168]	242	if (res == GENOPER_OK)
	243	return Geno(sg2, format, geny.getName(), geny.getComment());
[138]	244	else
[168]	245	return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: validate() for format %c returned invalid value", format));
[138]	246	}
	247
	248	Geno GenMan::Mutate(const Geno& g)
	249	{
	250	float chg; //how many changes
	251	int method; //mutation method
[168]	252	char format = g.getFormat();
	253	GenoOperators *gf = getOper_f(format);
	254	if (gf == NULL)
	255	return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: Mutate(): don't know how to handle genetic format %c", format));
	256	Geno gv = g;
	257	bool canvalidate = true;
	258	if (testValidity(gv, canvalidate) > 0 && canvalidate == false)
	259	return Geno("", -1, "", "GENOPER_OPFAIL: Mutate(): cannot validate invalid source genotype");
	260	bool ok = false;
	261	int pcount = count;
[138]	262	while (!ok)
	263	{
[168]	264	char *gn = strdup(gv.getGene()); //copy for mutation
	265	chg = 0;
	266	if (gf->mutate(gn, chg, method) == GENOPER_OK)
[138]	267	{
	268	ErrorHandler eh(ErrorHandler::StoreFirstMessage); //mute testValidity()
[168]	269	Geno G(gn, gv.getFormat(), "", "");
	270	canvalidate = true;
	271	int res = testValidity(G, canvalidate);
	272	if (res == GENOPER_OK && canvalidate == false) { valid_m++; ok = true; }
	273	else
	274	if (res > 0 && canvalidate == false) invalid_m++; else
	275	{
	276	validated_m++; ok = true;
	277	}
	278	if (ok) gv = G;
	279	}
	280	else failed_m++;
[138]	281	free(gn);
	282	count++;
[168]	283	if (!ok && (count - pcount > 100))
[138]	284	{
[168]	285	FMprintf("GenMan", "Mutate", 2, "Tried 100x and failed: %s", (const char*)g.getGene());
	286	return Geno("", -1, "", "GENOPER_OPFAIL: Mutate() tried 100x and failed");
[138]	287	}
	288	}
[168]	289	mutchg += chg;
	290	if (history) saveLink((const char)g.getGene(), (const char)gv.getGene(), chg);
[138]	291	SString mutinfo;
[168]	292	if (extmutinfo == 0) mutinfo = SString::sprintf("%.2f%% mutation of '%s'", 100 * chg, (const char*)g.getName()); else
[138]	293	if (extmutinfo == 1) mutinfo = SString::sprintf("%.2f%% mutation(%d) of '%s'", 100 * chg, method, (const char*)g.getName()); else
	294	mutinfo = SString::sprintf("%.2f%% mutation(%s) of '%s'", 100 * chg, gf->mutation_method_names ? gf->mutation_method_names[method] : "unspecified method name", (const char*)g.getName());
	295	gv.setComment(mutinfo);
	296	return gv;
	297	}
	298
	299	Geno GenMan::CrossOver(const Geno& g1, const Geno& g2)
	300	{
	301	char format = g1.getFormat();
	302	if (format != g2.getFormat()) return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: CrossOver() does not know how to handle parents with differing genetic formats (%c and %c)", format, g2.getFormat()));
[145]	303	GenoOperators *gf = getOper_f(format);
[138]	304	if (gf == NULL)
	305	return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: CrossOver(): don't know how to handle genetic format %c", format));
	306	Geno g1v = g1, g2v = g2;
	307
	308	{
	309	ErrorHandler eh(ErrorHandler::StoreFirstMessage); //mute testValidity()
	310	bool canvalidate = true;
	311	if (testValidity(g1v, canvalidate) > 0 && canvalidate == false)
	312	return Geno("", -1, "", "GENOPER_OPFAIL: CrossOver(): cannot validate invalid source genotype #1");
	313	canvalidate = true;
	314	if (testValidity(g2v, canvalidate) > 0 && canvalidate == false)
	315	return Geno("", -1, "", "GENOPER_OPFAIL: CrossOver(): cannot validate invalid source genotype #2");
	316	}
	317
	318	float chg;
	319	bool ok = false;
	320	int pcount = count;
	321
	322	while (!ok)
	323	{
	324	float chg1, chg2;
	325	char *g1n = strdup(g1.getGene()); //copy for crossover
	326	char *g2n = strdup(g2.getGene()); //copy for crossover
	327	chg1 = chg2 = 0;
	328	if (gf->crossOver(g1n, g2n, chg1, chg2) == GENOPER_OK)
	329	{
	330	char *gn;
[168]	331	if (g1n[0] && g2n[0]) if (randomN(2) == 0) g1n[0] = 0; else g2n[0] = 0; //both provided? we want only one
[138]	332	if (g1n[0]) { gn = g1n; chg = chg1; }
	333	else { gn = g2n; chg = chg2; }
	334	ErrorHandler eh(ErrorHandler::StoreFirstMessage); //mute testValidity()
	335	Geno G(gn, g1v.getFormat(), "", "");
	336	bool canvalidate = true;
	337	int res = testValidity(G, canvalidate);
	338	if (res == GENOPER_OK && canvalidate == false) { valid_xo++; ok = true; }
	339	else
	340	if (res > 0 && canvalidate == false) invalid_xo++; else
	341	{
	342	validated_xo++; ok = true;
	343	}
	344	if (ok) g1v = G;
	345	}
	346	else failed_xo++;
	347	free(g1n);
	348	free(g2n);
	349	count++;
	350	if (!ok && (count - pcount > 100))
	351	{
	352	FMprintf("GenMan", "CrossOver", 2, "Tried 100x and failed: %s and %s", (const char)g1.getGene(), (const char)g2.getGene());
	353	return Geno("", -1, "", "GENOPER_OPFAIL: CrossOver() tried 100x and failed");
	354	}
	355	}
	356	// result in g1v
	357	xochg += chg;
	358	if (history) saveLink((const char)g1.getGene(), (const char)g1v.getGene(), chg);
	359	SString xoinfo = SString::sprintf("Crossing over of '%s' (%.2f%%) and '%s' (%.2f%%)",
	360	(const char)g1.getName(), 100 chg, (const char)g2.getName(), 100 (1 - chg));
	361	g1v.setComment(xoinfo);
	362	return g1v;
	363	}
	364
	365	float GenMan::Similarity(const Geno& g1, const Geno& g2)
	366	{
	367	char format = g1.getFormat();
	368	if (format != g2.getFormat()) return GENOPER_NOOPER;
[145]	369	GenoOperators *gf = getOper_f(format);
[138]	370	if (!gf) return GENOPER_NOOPER; else return gf->similarity(g1.getGene(), g2.getGene());
	371	}
	372
	373	unsigned long GenMan::Style(const char *g, int pos)
	374	{
	375	Geno G(g);
	376	if ((pos = G.mapStringToGen(pos)) == -1) return GENSTYLE_COMMENT;
[145]	377	GenoOperators *gf = getOper_f(G.getFormat());
[138]	378	if (!gf) return GENSTYLE_CS(0, 0); //black & valid
	379	else return gf->style(G.getGene(), pos);
	380	}
	381
	382	void GenMan::GetFullStyle(const char g, unsigned long styletab)
	383	{
	384	Geno G(g);
[145]	385	GenoOperators *gf = getOper_f(G.getFormat());
[138]	386	SString geny = G.getGene();
	387	for (unsigned int pos = 0; pos < strlen(g); pos++)
	388	{
	389	int posmapped = G.mapStringToGen(pos);
	390	if (posmapped == -1) styletab[pos] = GENSTYLE_COMMENT;
	391	else if (!gf) styletab[pos] = GENSTYLE_CS(0, 0); //black & valid
	392	else styletab[pos] = gf->style(geny, posmapped);
	393	}
	394	}
	395
	396	SString GenMan::HTMLize(const char *g) { return HTMLize(g, false); }
	397
	398	SString GenMan::HTMLizeShort(const char *g) { return HTMLize(g, true); }
	399
	400	SString GenMan::HTMLize(const char *g, bool shorten)
	401	{
	402	char buf[50];
	403	int len = strlen(g);
	404	int chars = 0, lines = 0;
	405	bool shortened = false;
	406	unsigned long *styletab = new unsigned long[len];
	407	GetFullStyle(g, styletab);
	408	SString html = "\n<div style=\"background:white;padding:0.2em;font-family:arial,helvetica,sans-serif;font-size:90%\">";
	409	unsigned long prevstyle, prevcolor, style = 0, color = 0;
	410	for (int i = 0; i<len; i++)
	411	{
	412	if (shorten && ((lines == 0 && chars>160) \|\| (lines > 5 \|\| chars > 300))) { shortened = true; break; }
	413	if (g[i] == '\r') continue;
	414	if (g[i] == '\n') { html += "<br>\n"; lines++; continue; }
	415	chars++;
	416	prevstyle = style;
	417	prevcolor = color;
	418	style = GENGETSTYLE(styletab[i]);
	419	color = GENGETCOLOR(styletab[i]);
	420	if ((i != 0 && (color != prevcolor))) html += "</font>";
	421	if ((style&GENSTYLE_INVALID) != (prevstyle&GENSTYLE_INVALID))
	422	{
	423	html += "<"; if (!(style&GENSTYLE_INVALID)) html += "/"; html += "u>";
	424	}
	425	if ((style&GENSTYLE_BOLD) != (prevstyle&GENSTYLE_BOLD))
	426	{
	427	html += "<"; if (!(style&GENSTYLE_BOLD)) html += "/"; html += "b>";
	428	}
	429	if ((style&GENSTYLE_ITALIC) != (prevstyle&GENSTYLE_ITALIC))
	430	{
	431	html += "<"; if (!(style&GENSTYLE_ITALIC)) html += "/"; html += "i>";
	432	}
	433	if ((i == 0 \|\| (color != prevcolor)))
	434	{
	435	sprintf(buf, "<font color=#%02x%02x%02x>", GENGET_R(color), GENGET_G(color), GENGET_B(color)); html += buf;
	436	}
	437	if (g[i] == '<') html += "<"; else if (g[i] == '>') html += ">"; else html += g[i];
	438	if ((i % 3) == 0 && g[i] == ' ') html += "\n"; //for readability, insert some newlines into html...
	439	}
	440	delete[] styletab;
	441	html += "</u></b></i></font>";
	442	if (shortened) html += " [etc...]";
	443	html += "</div>\n";
	444	return html;
	445	}
	446
	447	void GenMan::p_htmlize(ExtValue args, ExtValue ret)
	448	{
	449	ret->setString(HTMLize(args->getString()));
	450	}
	451
	452	void GenMan::p_htmlizeshort(ExtValue args, ExtValue ret)
	453	{
	454	ret->setString(HTMLizeShort(args->getString()));
	455	}
	456
	457	Geno GenMan::GetSimplest(char format)
	458	{
[145]	459	GenoOperators *gf = getOper_f(format);
[138]	460	if (!gf) return Geno();
[200]	461	string info = "The simplest genotype of format f"; info += format;
[138]	462	info += " for operators '"; info += gf->name; info += "'.";
[200]	463	return Geno(gf->getSimplest(), format, "Root", info.c_str());
[138]	464	}
	465
	466	void GenMan::p_getsimplest(ExtValue args, ExtValue ret)
	467	{
	468	int format = args[0].getInt() + 48;
[145]	469	if (!getOper_f(format))
[138]	470	ret->setEmpty();
	471	else
	472	*ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(GetSimplest(format)));
	473	}
	474
	475	const char *GenMan::GetOpName(char format)
	476	{
[145]	477	GenoOperators *gf = getOper_f(format);
[200]	478	if (!gf) return "n/a"; else return gf->name.c_str();
[138]	479	}
	480
[145]	481	GenoOperators* GenMan::getOper_f(char format)
[138]	482	{
	483	int ind = operformats.find(format);
	484	if (ind == -1) return NULL;
[168]	485	int which_oper_of_format = seloper[ind];
[145]	486	for (unsigned int i = 0; i < oper_fx_list.size(); i++)
	487	if (oper_fx_list[i]->supported_format == format)
[168]	488	if (which_oper_of_format == 0) return oper_fx_list[i]; else which_oper_of_format--;
[138]	489	return NULL; //should never happen
	490	}
	491
	492	void GenMan::saveLink(string prz, string pot, float& chg)
	493	{
	494	GenoLink l;
	495	l.count = count;
	496	l.g1 = prz;
	497	l.g2 = pot;
	498	l.chg = chg;
	499	l.fit = 0; //temporarily. Will be set when the genotype dies
	500	GenoLinkList.push_back(l);
	501	}
	502
	503	void GenMan::onDelGen(void *obj, long n)
	504	{
	505	//old code needs update:
	506	// ((SpeciesList*)obj)->przyDodaniu(i);
	507	/* !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
	508	GenMan gm=(GenMan)obj;
	509	Genotype gt=(Genotype)(*listaGen)(n); //there is no more "listaGen"
	510	string g=(const char*)gt->genotype.getGene();
	511	float fit=gt->getFinalFitness();
	512	for(int i=0;i<gm->GenoLinkList.size();i++) //find genotype
	513	if (gm->GenoLinkList[i].g1==g) {gm->GenoLinkList[i].fit=fit; break;}
	514	*/
	515	}
	516
	517	void GenMan::clearStats()
	518	{
	519	count = 0;
	520	valid_m = valid_xo = validated_m = validated_xo = invalid_m = invalid_xo = failed_m = failed_xo = 0;
	521	mutchg = xochg = 0;
	522	GenoLinkList.clear();
	523	}
	524
	525	void GenMan::p_clearStats(ExtValue args, ExtValue ret) { clearStats(); }
	526
	527	void GenMan::p_report(ExtValue args, ExtValue ret)
	528	{ //should be updated to handle multiple operators for a single format
	529	char g, g2;
[145]	530	float f1, f2;
	531	int m;
[138]	532	FramMessage("GenMan", "Report", "The following genetic operators are available:", 0);
[145]	533	for (unsigned int i = 0; i < oper_fx_list.size(); i++)
[138]	534	{
[200]	535	string l;
[145]	536	if (oper_fx_list[i]->checkValidity("") != GENOPER_NOOPER) l += " checkValidity";
	537	if (oper_fx_list[i]->getSimplest())
[138]	538	{
[145]	539	g = strdup(oper_fx_list[i]->getSimplest());
[138]	540	g2 = strdup(g);
[145]	541	if (oper_fx_list[i]->validate(g) != GENOPER_NOOPER) l += " validate";
	542	if (oper_fx_list[i]->mutate(g, f1, m) != GENOPER_NOOPER) l += " mutate";
	543	if (oper_fx_list[i]->crossOver(g, g2, f1, f2) != GENOPER_NOOPER) l += " crossover";
[138]	544	l += " getSimplest";
	545	free(g); free(g2);
	546	}
[145]	547	// if (oper_fx_list[i]->similarity("","")!=GENOPER_NOOPER) l+=" similarity";
[138]	548	FMprintf("GenMan", "Report", 0, "format f%c (%s):%s",
[200]	549	oper_fx_list[i]->supported_format, oper_fx_list[i]->name.c_str(), l.c_str());
[138]	550	}
	551	}
	552
	553	void GenMan::p_validate(ExtValue args, ExtValue ret)
	554	{
	555	Geno *g = GenoObj::fromObject(args[0]);
	556	if (g == NULL)
	557	ret->setEmpty();
	558	else
	559	ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(Validate(g)));
	560	}
	561
	562	void GenMan::p_mutate(ExtValue args, ExtValue ret)
	563	{
	564	Geno *g = GenoObj::fromObject(args[0]);
	565	if (g == NULL)
	566	ret->setEmpty();
	567	else
	568	ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(Mutate(g)));
	569	}
	570
	571	void GenMan::p_crossover(ExtValue args, ExtValue ret)
	572	{
	573	Geno *g1 = GenoObj::fromObject(args[1]);
	574	Geno *g2 = GenoObj::fromObject(args[0]);
	575	if (g1 == NULL \|\| g2 == NULL)
	576	ret->setEmpty();
	577	else
	578	ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(CrossOver(g1, *g2)));
	579	}

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