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source: cpp/frams/genetics/genman.cpp @ 277

Last change on this file since 277 was 275, checked in by Maciej Komosinski, 10 years ago
Inheritance information during crossing over properly stored as a single genetic operation with a single child (affects phylogenetic analysis window)
Property svn:eol-style set to `native`
File size: 20.4 KB

Line
1	// This file is a part of the Framsticks GDK.
2	// Copyright (C) 1999-2014 Maciej Komosinski and Szymon Ulatowski. See LICENSE.txt for details.
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"
10	#include "common/stl-util.h"
11	#include <frams/errmgr/errmanager.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	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
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	const char *gg = g.getGene();
201	GenoOperators *gf = getOper_f(g.getFormat());
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	{
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;
241	free(g2);
242	if (res == GENOPER_OK)
243	return Geno(sg2, format, geny.getName(), geny.getComment());
244	else
245	return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: validate() for format %c returned invalid value", format));
246	}
247
248	Geno GenMan::Mutate(const Geno& g)
249	{
250	float chg; //how many changes
251	int method; //mutation method
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;
262	while (!ok)
263	{
264	char *gn = strdup(gv.getGene()); //copy for mutation
265	chg = 0;
266	if (gf->mutate(gn, chg, method) == GENOPER_OK)
267	{
268	ErrorHandler eh(ErrorHandler::StoreFirstMessage); //mute testValidity()
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++;
281	free(gn);
282	count++;
283	if (!ok && (count - pcount > 100))
284	{
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");
287	}
288	}
289	mutchg += chg;
290	if (history) saveLink((const char)g.getGene(), "", (const char)gv.getGene(), chg);
291	SString mutinfo;
292	if (extmutinfo == 0) mutinfo = SString::sprintf("%.2f%% mutation of '%s'", 100 * chg, (const char*)g.getName()); else
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 work for parents with differing genetic formats (%c and %c)", format, g2.getFormat()));
303	GenoOperators *gf = getOper_f(format);
304	if (gf == NULL)
305	return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: CrossOver(): no operators found for 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;
331	if (g1n[0] && g2n[0]) if (randomN(2) == 0) g1n[0] = 0; else g2n[0] = 0; //both provided? we want only one
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)g2.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;
369	GenoOperators *gf = getOper_f(format);
370	if (!gf) return GENOPER_NOOPER; else return gf->similarity(g1.getGene(), g2.getGene());
371	}
372
373	uint32_t GenMan::Style(const char *g, int pos)
374	{
375	Geno G(g);
376	if ((pos = G.mapStringToGen(pos)) == -1) return GENSTYLE_COMMENT;
377	GenoOperators *gf = getOper_f(G.getFormat());
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, uint32_t styletab)
383	{
384	Geno G(g);
385	GenoOperators *gf = getOper_f(G.getFormat());
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	uint32_t *styletab = new uint32_t[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	uint32_t 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	{
459	GenoOperators *gf = getOper_f(format);
460	if (!gf) return Geno();
461	string info = "The simplest genotype of format f"; info += format;
462	info += " for operators '"; info += gf->name; info += "'.";
463	return Geno(gf->getSimplest(), format, "Root", info.c_str());
464	}
465
466	void GenMan::p_getsimplest(ExtValue args, ExtValue ret)
467	{
468	int format = args[0].getInt() + 48;
469	if (!getOper_f(format))
470	ret->setEmpty();
471	else
472	*ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(GetSimplest(format)));
473	}
474
475	const char *GenMan::GetOpName(char format)
476	{
477	GenoOperators *gf = getOper_f(format);
478	if (!gf) return "n/a"; else return gf->name.c_str();
479	}
480
481	GenoOperators* GenMan::getOper_f(char format)
482	{
483	int ind = operformats.find(format);
484	if (ind == -1) return NULL;
485	int which_oper_of_format = seloper[ind];
486	for (unsigned int i = 0; i < oper_fx_list.size(); i++)
487	if (oper_fx_list[i]->supported_format == format)
488	if (which_oper_of_format == 0) return oper_fx_list[i]; else which_oper_of_format--;
489	return NULL; //should never happen
490	}
491
492	void GenMan::saveLink(const string parent1, const string parent2, const string child, const float chg)
493	{
494	GenoLink l;
495	l.count = count;
496	l.parent1 = parent1;
497	l.parent2 = parent2;
498	l.child = child;
499	l.chg = chg;
500	l.fit = 0; //temporarily. Will be set when the genotype dies
501	//FMprintf("GenMan","saveLink",0,"#%d: [%d] '%s' + '%s' -> '%s'",GenoLinkList.size(),count,parent1.c_str(),parent2.c_str(),child.c_str());
502	GenoLinkList.push_back(l);
503	}
504
505	void GenMan::onDelGen(void *obj, intptr_t n)
506	{
507	//old code needs update:
508	// ((SpeciesList*)obj)->przyDodaniu(i);
509	/* !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
510	GenMan gm=(GenMan)obj;
511	Genotype gt=(Genotype)(*listaGen)(n); //there is no more "listaGen"
512	string g=(const char*)gt->genotype.getGene();
513	float fit=gt->getFinalFitness();
514	for(int i=0;i<gm->GenoLinkList.size();i++) //find genotype
515	if (gm->GenoLinkList[i].g1==g) {gm->GenoLinkList[i].fit=fit; break;}
516	*/
517	}
518
519	void GenMan::clearStats()
520	{
521	count = 0;
522	valid_m = valid_xo = validated_m = validated_xo = invalid_m = invalid_xo = failed_m = failed_xo = 0;
523	mutchg = xochg = 0;
524	GenoLinkList.clear();
525	}
526
527	void GenMan::p_clearStats(ExtValue args, ExtValue ret) { clearStats(); }
528
529	void GenMan::p_report(ExtValue args, ExtValue ret)
530	{ //should be updated to handle multiple operators for a single format
531	char g, g2;
532	float f1, f2;
533	int m;
534	FramMessage("GenMan", "Report", "The following genetic operators are available:", 0);
535	for (unsigned int i = 0; i < oper_fx_list.size(); i++)
536	{
537	string l;
538	if (oper_fx_list[i]->checkValidity("") != GENOPER_NOOPER) l += " checkValidity";
539	if (oper_fx_list[i]->getSimplest())
540	{
541	g = strdup(oper_fx_list[i]->getSimplest());
542	g2 = strdup(g);
543	if (oper_fx_list[i]->validate(g) != GENOPER_NOOPER) l += " validate";
544	if (oper_fx_list[i]->mutate(g, f1, m) != GENOPER_NOOPER) l += " mutate";
545	if (oper_fx_list[i]->crossOver(g, g2, f1, f2) != GENOPER_NOOPER) l += " crossover";
546	l += " getSimplest";
547	free(g); free(g2);
548	}
549	// if (oper_fx_list[i]->similarity("","")!=GENOPER_NOOPER) l+=" similarity";
550	FMprintf("GenMan", "Report", 0, "format f%c (%s):%s",
551	oper_fx_list[i]->supported_format, oper_fx_list[i]->name.c_str(), l.c_str());
552	}
553	}
554
555	void GenMan::p_validate(ExtValue args, ExtValue ret)
556	{
557	Geno *g = GenoObj::fromObject(args[0]);
558	if (g == NULL)
559	ret->setEmpty();
560	else
561	ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(Validate(g)));
562	}
563
564	void GenMan::p_mutate(ExtValue args, ExtValue ret)
565	{
566	Geno *g = GenoObj::fromObject(args[0]);
567	if (g == NULL)
568	ret->setEmpty();
569	else
570	ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(Mutate(g)));
571	}
572
573	void GenMan::p_crossover(ExtValue args, ExtValue ret)
574	{
575	Geno *g1 = GenoObj::fromObject(args[1]);
576	Geno *g2 = GenoObj::fromObject(args[0]);
577	if (g1 == NULL \|\| g2 == NULL)
578	ret->setEmpty();
579	else
580	ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(CrossOver(g1, *g2)));
581	}

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