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source: cpp/frams/genetics/genman.cpp @ 413

Last change on this file since 413 was 391, checked in by sz, 10 years ago
Moved frams/loggers to common/loggers
Property svn:eol-style set to `native`
File size: 20.5 KB

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1	// This file is a part of Framsticks SDK. http://www.framsticks.com/
2	// Copyright (C) 1999-2015 Maciej Komosinski and Szymon Ulatowski.
3	// See LICENSE.txt for details.
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/log.h"
9	#include "common/nonstd_math.h"
10	#include "common/stl-util.h"
11	#include <common/loggers/loggers.h>
12
13
14	#ifdef USE_GENMAN_f0
15	#include "f0/oper_f0.h"
16	#endif
17	#ifdef USE_GENMAN_f0FUZZY
18	#include "f0/oper_f0Fuzzy.h"
19	#endif
20	#ifdef USE_GENMAN_f1
21	#include "f1/oper_f1.h"
22	#endif
23	#ifdef USE_GENMAN_f2
24	#include "f2/oper_f2.h"
25	#endif
26	#ifdef USE_GENMAN_f2
27	#include "f3/oper_f3.h"
28	#endif
29	#ifdef USE_GENMAN_f4
30	#include "f4/oper_f4.h"
31	#endif
32	#ifdef USE_GENMAN_f5
33	#include "f5/oper_f5.h"
34	#endif
35	#ifdef USE_GENMAN_f6
36	#include "f6/oper_f6.h"
37	#endif
38	#ifdef USE_GENMAN_f7
39	#include "f7/oper_f7.h"
40	#endif
41	#ifdef USE_GENMAN_f8
42	#include "f8/oper_f8.h"
43	#endif
44	#ifdef USE_GENMAN_f9
45	#include "f9/oper_f9.h"
46	#endif
47	#ifdef USE_GENMAN_fF
48	#include "fF/oper_fF.h"
49	#endif
50	#ifdef USE_GENMAN_fT
51	#include "fT/oper_fTest.h"
52	#endif
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	neuronsparam("Genetics: Neurons to add", "neuronsAdd", "neuadd_"),
104	par("GenMan", "Manages various genetic operations, using appropriate operators for the argument genotype format.")
105	{
106	history = 0;
107	hilite = 1;
108	clearStats();
109
110	#ifdef USE_GENMAN_f0
111	oper_fx_list.push_back(new Geno_f0);
112	#endif
113	#ifdef USE_GENMAN_f0FUZZY
114	oper_fx_list.push_back(new Geno_f0Fuzzy);
115	#endif
116	#ifdef USE_GENMAN_f1
117	oper_fx_list.push_back(new Geno_f1);
118	#endif
119	#ifdef USE_GENMAN_f2
120	oper_fx_list.push_back(new Geno_f2);
121	#endif
122	#ifdef USE_GENMAN_f3
123	oper_fx_list.push_back(new Geno_f3);
124	#endif
125	#ifdef USE_GENMAN_f4
126	oper_fx_list.push_back(new Geno_f4);
127	#endif
128	#ifdef USE_GENMAN_f5
129	oper_fx_list.push_back(new Geno_f5);
130	#endif
131	#ifdef USE_GENMAN_f6
132	oper_fx_list.push_back(new Geno_f6);
133	#endif
134	#ifdef USE_GENMAN_f7
135	oper_fx_list.push_back(new Geno_f7);
136	#endif
137	#ifdef USE_GENMAN_f8
138	oper_fx_list.push_back(new Geno_f8);
139	#endif
140	#ifdef USE_GENMAN_f9
141	oper_fx_list.push_back(new GenoOper_f9);
142	#endif
143	#ifdef USE_GENMAN_fF
144	oper_fx_list.push_back(new GenoOper_fF);
145	#endif
146	#ifdef USE_GENMAN_fT
147	oper_fx_list.push_back(new GenoOper_fTest);
148	#endif
149
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
151	int selopercount = 0;
152	for (unsigned int i = 0; i < oper_fx_list.size(); i++)
153	{
154	if (operformats.find(oper_fx_list[i]->supported_format) != -1) continue;
155	string type = string("~") + oper_fx_list[i]->name;
156	int dup = 0;
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)
159	{
160	type += "~";
161	type += oper_fx_list[j]->name;
162	dup++;
163	}
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);
167	seloper[selopercount] = 0;
168	operformats += oper_fx_list[i]->supported_format;
169	//printf("%x %s %s %s\n",&seloper[selopercount],(const char)id,(const char)type,(const char*)name);
170	seloperpar.addProperty(&seloper[selopercount++], id.c_str(), type.c_str(), name.c_str(), "", PARAM_READONLY*(dup == 0));
171	}
172
173	par += &localpar;
174	par += &seloperpar;
175	par += &neuronsparam;
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;
178	}
179
180	GenMan::~GenMan()
181	{
182	for (unsigned int i = 0; i < oper_fx_list.size(); i++) delete oper_fx_list[i];
183	delete[] seloper;
184	}
185
186	void GenMan::setDefaults()
187	{
188	for (unsigned int i = 0; i < oper_fx_list.size(); i++)
189	{
190	oper_fx_list[i]->par.setDefault();
191	oper_fx_list[i]->setDefaults();
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	SString ggs=g.getGene();
201	const char *gg = ggs.c_str();
202	GenoOperators *gf = getOper_f(g.getFormat());
203	int check1;
204	if (!gf) { canvalidate = false; return GENOPER_NOOPER; }
205	else check1 = gf->checkValidity(gg);
206	if (!canvalidate) return check1; //just checking
207	if (check1 == GENOPER_OK) { canvalidate = false; return check1; }
208	char *g2 = strdup(gg);
209	if (gf->validate(g2) == GENOPER_NOOPER) { free(g2); canvalidate = false; return check1; }
210	if (check1 == GENOPER_NOOPER) //disaster: cannot check because there is no check operator
211	{
212	g.setGene(g2); free(g2); canvalidate = false; return GENOPER_NOOPER;
213	}
214	int check2 = gf->checkValidity(g2);
215	if (check2 == GENOPER_OK) g.setGene(g2);
216	free(g2);
217	if (check2 == GENOPER_OK) return check1;
218	canvalidate = false;
219	return check1; //could not validate.
220	}
221
222	int GenMan::testGenoValidity(Geno& g)
223	{
224	bool fix = false;
225	switch (testValidity(g, fix))
226	{
227	case GENOPER_OK: return 1;
228	case GENOPER_NOOPER: return -1;
229	default: return 0;
230	}
231	}
232
233	Geno GenMan::Validate(const Geno& geny)
234	{
235	char format = geny.getFormat();
236	GenoOperators *gf = getOper_f(format);
237	if (gf == NULL)
238	return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: Validate(): don't know how to handle genetic format %c", format));
239	char *g2 = strdup(geny.getGene().c_str()); //copy for validation
240	int res = gf->validate(g2);
241	SString sg2 = g2;
242	free(g2);
243	if (res == GENOPER_OK)
244	return Geno(sg2, format, geny.getName(), geny.getComment());
245	else
246	return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: validate() for format %c returned invalid value", format));
247	}
248
249	Geno GenMan::Mutate(const Geno& g)
250	{
251	float chg; //how many changes
252	int method; //mutation method
253	char format = g.getFormat();
254	GenoOperators *gf = getOper_f(format);
255	if (gf == NULL)
256	return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: Mutate(): don't know how to handle genetic format %c", format));
257	Geno gv = g;
258	bool canvalidate = true;
259	if (testValidity(gv, canvalidate) > 0 && canvalidate == false)
260	return Geno("", -1, "", "GENOPER_OPFAIL: Mutate(): cannot validate invalid source genotype");
261	bool ok = false;
262	int pcount = count;
263	while (!ok)
264	{
265	char *gn = strdup(gv.getGene().c_str()); //copy for mutation
266	chg = 0;
267	if (gf->mutate(gn, chg, method) == GENOPER_OK)
268	{
269	LoggerToMemory eh(LoggerBase::Enable \| LoggerToMemory::StoreFirstMessage); //mute testValidity()
270	Geno G(gn, gv.getFormat(), "", "");
271	canvalidate = true;
272	int res = testValidity(G, canvalidate);
273	if (res == GENOPER_OK && canvalidate == false) { valid_m++; ok = true; }
274	else
275	if (res > 0 && canvalidate == false) invalid_m++; else
276	{
277	validated_m++; ok = true;
278	}
279	if (ok) gv = G;
280	}
281	else failed_m++;
282	free(gn);
283	count++;
284	if (!ok && (count - pcount > 100))
285	{
286	logPrintf("GenMan", "Mutate", 2, "Tried 100x and failed: %s", g.getGene().c_str());
287	return Geno("", -1, "", "GENOPER_OPFAIL: Mutate() tried 100x and failed");
288	}
289	}
290	mutchg += chg;
291	if (history) saveLink(g.getGene().c_str(), "", gv.getGene().c_str(), chg);
292	SString mutinfo;
293	if (extmutinfo == 0) mutinfo = SString::sprintf("%.2f%% mutation of '%s'", 100 * chg, g.getName().c_str()); else
294	if (extmutinfo == 1) mutinfo = SString::sprintf("%.2f%% mutation(%d) of '%s'", 100 * chg, method, g.getName().c_str()); else
295	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());
296	gv.setComment(mutinfo);
297	return gv;
298	}
299
300	Geno GenMan::CrossOver(const Geno& g1, const Geno& g2)
301	{
302	char format = g1.getFormat();
303	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()));
304	GenoOperators *gf = getOper_f(format);
305	if (gf == NULL)
306	return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: CrossOver(): no operators found for genetic format %c", format));
307	Geno g1v = g1, g2v = g2;
308
309	{
310	LoggerToMemory eh(LoggerBase::Enable \| LoggerToMemory::StoreFirstMessage); //mute testValidity()
311	bool canvalidate = true;
312	if (testValidity(g1v, canvalidate) > 0 && canvalidate == false)
313	return Geno("", -1, "", "GENOPER_OPFAIL: CrossOver(): cannot validate invalid source genotype #1");
314	canvalidate = true;
315	if (testValidity(g2v, canvalidate) > 0 && canvalidate == false)
316	return Geno("", -1, "", "GENOPER_OPFAIL: CrossOver(): cannot validate invalid source genotype #2");
317	}
318
319	float chg;
320	bool ok = false;
321	int pcount = count;
322
323	while (!ok)
324	{
325	float chg1, chg2;
326	char *g1n = strdup(g1.getGene().c_str()); //copy for crossover
327	char *g2n = strdup(g2.getGene().c_str()); //copy for crossover
328	chg1 = chg2 = 0;
329	if (gf->crossOver(g1n, g2n, chg1, chg2) == GENOPER_OK)
330	{
331	char *gn;
332	if (g1n[0] && g2n[0]) if (randomN(2) == 0) g1n[0] = 0; else g2n[0] = 0; //both provided? we want only one
333	if (g1n[0]) { gn = g1n; chg = chg1; }
334	else { gn = g2n; chg = chg2; }
335	LoggerToMemory eh(LoggerBase::Enable \| LoggerToMemory::StoreFirstMessage); //mute testValidity()
336	Geno G(gn, g1v.getFormat(), "", "");
337	bool canvalidate = true;
338	int res = testValidity(G, canvalidate);
339	if (res == GENOPER_OK && canvalidate == false) { valid_xo++; ok = true; }
340	else
341	if (res > 0 && canvalidate == false) invalid_xo++; else
342	{
343	validated_xo++; ok = true;
344	}
345	if (ok) g1v = G;
346	}
347	else failed_xo++;
348	free(g1n);
349	free(g2n);
350	count++;
351	if (!ok && (count - pcount > 100))
352	{
353	logPrintf("GenMan", "CrossOver", 2, "Tried 100x and failed: %s and %s", g1.getGene().c_str(), g2.getGene().c_str());
354	return Geno("", -1, "", "GENOPER_OPFAIL: CrossOver() tried 100x and failed");
355	}
356	}
357	// result in g1v
358	xochg += chg;
359	if (history) saveLink(g1.getGene().c_str(), g2.getGene().c_str(), g1v.getGene().c_str(), chg);
360	SString xoinfo = SString::sprintf("Crossing over of '%s' (%.2f%%) and '%s' (%.2f%%)",
361	g1.getName().c_str(), 100 * chg, g2.getName().c_str(), 100 * (1 - chg));
362	g1v.setComment(xoinfo);
363	return g1v;
364	}
365
366	float GenMan::Similarity(const Geno& g1, const Geno& g2)
367	{
368	char format = g1.getFormat();
369	if (format != g2.getFormat()) return GENOPER_NOOPER;
370	GenoOperators *gf = getOper_f(format);
371	if (!gf) return GENOPER_NOOPER; else return gf->similarity(g1.getGene().c_str(), g2.getGene().c_str());
372	}
373
374	uint32_t GenMan::Style(const char *g, int pos)
375	{
376	Geno G(g);
377	if ((pos = G.mapStringToGen(pos)) == -1) return GENSTYLE_COMMENT;
378	GenoOperators *gf = getOper_f(G.getFormat());
379	if (!gf) return GENSTYLE_CS(0, 0); //black & valid
380	else return gf->style(G.getGene().c_str(), pos);
381	}
382
383	void GenMan::GetFullStyle(const char g, uint32_t styletab)
384	{
385	Geno G(g);
386	GenoOperators *gf = getOper_f(G.getFormat());
387	SString geny = G.getGene();
388	for (unsigned int pos = 0; pos < strlen(g); pos++)
389	{
390	int posmapped = G.mapStringToGen(pos);
391	if (posmapped == -1) styletab[pos] = GENSTYLE_COMMENT;
392	else if (!gf) styletab[pos] = GENSTYLE_CS(0, 0); //black & valid
393	else styletab[pos] = gf->style(geny.c_str(), posmapped);
394	}
395	}
396
397	SString GenMan::HTMLize(const char *g) { return HTMLize(g, false); }
398
399	SString GenMan::HTMLizeShort(const char *g) { return HTMLize(g, true); }
400
401	SString GenMan::HTMLize(const char *g, bool shorten)
402	{
403	char buf[50];
404	int len = strlen(g);
405	int chars = 0, lines = 0;
406	bool shortened = false;
407	uint32_t *styletab = new uint32_t[len];
408	GetFullStyle(g, styletab);
409	SString html = "\n<div style=\"background:white;padding:0.2em;font-family:arial,helvetica,sans-serif;font-size:90%\">";
410	uint32_t prevstyle, prevcolor, style = 0, color = 0;
411	for (int i = 0; i<len; i++)
412	{
413	if (shorten && ((lines == 0 && chars>160) \|\| (lines > 5 \|\| chars > 300))) { shortened = true; break; }
414	if (g[i] == '\r') continue;
415	if (g[i] == '\n') { html += "<br>\n"; lines++; continue; }
416	chars++;
417	prevstyle = style;
418	prevcolor = color;
419	style = GENGETSTYLE(styletab[i]);
420	color = GENGETCOLOR(styletab[i]);
421	if ((i != 0 && (color != prevcolor))) html += "</font>";
422	if ((style&GENSTYLE_INVALID) != (prevstyle&GENSTYLE_INVALID))
423	{
424	html += "<"; if (!(style&GENSTYLE_INVALID)) html += "/"; html += "u>";
425	}
426	if ((style&GENSTYLE_BOLD) != (prevstyle&GENSTYLE_BOLD))
427	{
428	html += "<"; if (!(style&GENSTYLE_BOLD)) html += "/"; html += "b>";
429	}
430	if ((style&GENSTYLE_ITALIC) != (prevstyle&GENSTYLE_ITALIC))
431	{
432	html += "<"; if (!(style&GENSTYLE_ITALIC)) html += "/"; html += "i>";
433	}
434	if ((i == 0 \|\| (color != prevcolor)))
435	{
436	sprintf(buf, "<font color=#%02x%02x%02x>", GENGET_R(color), GENGET_G(color), GENGET_B(color)); html += buf;
437	}
438	if (g[i] == '<') html += "<"; else if (g[i] == '>') html += ">"; else html += g[i];
439	if ((i % 3) == 0 && g[i] == ' ') html += "\n"; //for readability, insert some newlines into html...
440	}
441	delete[] styletab;
442	html += "</u></b></i></font>";
443	if (shortened) html += " [etc...]";
444	html += "</div>\n";
445	return html;
446	}
447
448	void GenMan::p_htmlize(ExtValue args, ExtValue ret)
449	{
450	ret->setString(HTMLize(args->getString().c_str()));
451	}
452
453	void GenMan::p_htmlizeshort(ExtValue args, ExtValue ret)
454	{
455	ret->setString(HTMLizeShort(args->getString().c_str()));
456	}
457
458	Geno GenMan::GetSimplest(char format)
459	{
460	GenoOperators *gf = getOper_f(format);
461	if (!gf) return Geno();
462	string info = "The simplest genotype of format f"; info += format;
463	info += " for operators '"; info += gf->name; info += "'.";
464	return Geno(gf->getSimplest(), format, "Root", info.c_str());
465	}
466
467	void GenMan::p_getsimplest(ExtValue args, ExtValue ret)
468	{
469	int format = args[0].getInt() + 48;
470	if (!getOper_f(format))
471	ret->setEmpty();
472	else
473	*ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(GetSimplest(format)));
474	}
475
476	const char *GenMan::GetOpName(char format)
477	{
478	GenoOperators *gf = getOper_f(format);
479	if (!gf) return "n/a"; else return gf->name.c_str();
480	}
481
482	GenoOperators* GenMan::getOper_f(char format)
483	{
484	int ind = operformats.find(format);
485	if (ind == -1) return NULL;
486	int which_oper_of_format = seloper[ind];
487	for (unsigned int i = 0; i < oper_fx_list.size(); i++)
488	if (oper_fx_list[i]->supported_format == format)
489	if (which_oper_of_format == 0) return oper_fx_list[i]; else which_oper_of_format--;
490	return NULL; //should never happen
491	}
492
493	void GenMan::saveLink(const string parent1, const string parent2, const string child, const float chg)
494	{
495	GenoLink l;
496	l.count = count;
497	l.parent1 = parent1;
498	l.parent2 = parent2;
499	l.child = child;
500	l.chg = chg;
501	l.fit = 0; //temporarily. Will be set when the genotype dies
502	//logPrintf("GenMan","saveLink",0,"#%d: [%d] '%s' + '%s' -> '%s'",GenoLinkList.size(),count,parent1.c_str(),parent2.c_str(),child.c_str());
503	GenoLinkList.push_back(l);
504	}
505
506	void GenMan::onDelGen(void *obj, intptr_t n)
507	{
508	//old code needs update:
509	// ((SpeciesList*)obj)->przyDodaniu(i);
510	/* !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
511	GenMan gm=(GenMan)obj;
512	Genotype gt=(Genotype)(*listaGen)(n); //there is no more "listaGen"
513	string g=(const char*)gt->genotype.getGene();
514	float fit=gt->getFinalFitness();
515	for(int i=0;i<gm->GenoLinkList.size();i++) //find genotype
516	if (gm->GenoLinkList[i].g1==g) {gm->GenoLinkList[i].fit=fit; break;}
517	*/
518	}
519
520	void GenMan::clearStats()
521	{
522	count = 0;
523	valid_m = valid_xo = validated_m = validated_xo = invalid_m = invalid_xo = failed_m = failed_xo = 0;
524	mutchg = xochg = 0;
525	GenoLinkList.clear();
526	}
527
528	void GenMan::p_clearStats(ExtValue args, ExtValue ret) { clearStats(); }
529
530	void GenMan::p_report(ExtValue args, ExtValue ret)
531	{ //should be updated to handle multiple operators for a single format
532	char g, g2;
533	float f1, f2;
534	int m;
535	logMessage("GenMan", "Report", 0, "The following genetic operators are available:");
536	for (unsigned int i = 0; i < oper_fx_list.size(); i++)
537	{
538	string l;
539	if (oper_fx_list[i]->checkValidity("") != GENOPER_NOOPER) l += " checkValidity";
540	if (oper_fx_list[i]->getSimplest())
541	{
542	g = strdup(oper_fx_list[i]->getSimplest());
543	g2 = strdup(g);
544	if (oper_fx_list[i]->validate(g) != GENOPER_NOOPER) l += " validate";
545	if (oper_fx_list[i]->mutate(g, f1, m) != GENOPER_NOOPER) l += " mutate";
546	if (oper_fx_list[i]->crossOver(g, g2, f1, f2) != GENOPER_NOOPER) l += " crossover";
547	l += " getSimplest";
548	free(g); free(g2);
549	}
550	// if (oper_fx_list[i]->similarity("","")!=GENOPER_NOOPER) l+=" similarity";
551	logPrintf("GenMan", "Report", 0, "format f%c (%s):%s",
552	oper_fx_list[i]->supported_format, oper_fx_list[i]->name.c_str(), l.c_str());
553	}
554	}
555
556	void GenMan::p_validate(ExtValue args, ExtValue ret)
557	{
558	Geno *g = GenoObj::fromObject(args[0]);
559	if (g == NULL)
560	ret->setEmpty();
561	else
562	ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(Validate(g)));
563	}
564
565	void GenMan::p_mutate(ExtValue args, ExtValue ret)
566	{
567	Geno *g = GenoObj::fromObject(args[0]);
568	if (g == NULL)
569	ret->setEmpty();
570	else
571	ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(Mutate(g)));
572	}
573
574	void GenMan::p_crossover(ExtValue args, ExtValue ret)
575	{
576	Geno *g1 = GenoObj::fromObject(args[1]);
577	Geno *g2 = GenoObj::fromObject(args[0]);
578	if (g1 == NULL \|\| g2 == NULL)
579	ret->setEmpty();
580	else
581	ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(CrossOver(g1, *g2)));
582	}

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