source: cpp/frams/genetics/genman.cpp @ 757

Last change on this file since 757 was 748, checked in by Maciej Komosinski, 7 years ago

Configured and activated the new "fn" genetic representation
  • Property svn:eol-style set to native
File size: 21.6 KB
Line 
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_fn
51#include "fn/oper_fn.h"
52#endif
53#ifdef USE_GENMAN_fT
54#include "fT/oper_fTest.h"
55#endif
56
57using namespace std; //string, vector
58
59//old code needs update:
60//#include "gengroups.h"
61//extern GenGroup *listaGen;
62//   GENGROUP(0)->l_del.add(sim->GM.onDelGen,&sim->GM); //before delete
63//   GENGROUP(0)->l_del.remove(sim->GM.onDelGen,&sim->GM); //before delete
64
65
66#define FIELDSTRUCT GenMan
67
68static ParamEntry GMparam_tab[] =
69{
70        { "Genetics", 1, 10, "GenMan", },
71        { "gen_hist", 0, PARAM_DONTSAVE, "Remember history of genetic operations", "d 0 1 0", FIELD(history), "Required for phylogenetic analysis", },
72        { "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)", },
73        { "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.", },
74        { "operReport", 0, PARAM_DONTSAVE, "Operators report", "p()", PROCEDURE(p_report), "Show available genetic operators", },
75        { "toHTML", 0, PARAM_DONTSAVE, "HTMLize a genotype", "p s(s)", PROCEDURE(p_htmlize), "returns genotype expressed as colored HTML", },
76        { "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", },
77        { "validate", 0, PARAM_DONTSAVE | PARAM_USERHIDDEN, "Validate", "p oGeno(oGeno)", PROCEDURE(p_validate), "returns validated (if possible) Geno object from supplied Geno", },
78        { "mutate", 0, PARAM_DONTSAVE | PARAM_USERHIDDEN, "Mutate", "p oGeno(oGeno)", PROCEDURE(p_mutate), "returns mutated Geno object from supplied Geno", },
79        { "crossOver", 0, PARAM_DONTSAVE | PARAM_USERHIDDEN, "Crossover", "p oGeno(oGeno,oGeno)", PROCEDURE(p_crossover), "returns crossed over genotype", },
80        { "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.", },
81        { 0, },
82};
83
84static ParamEntry GMstats_tab[] =
85{
86        { "Genetics", 1, 12, "GenManStats", "Statistics for genetic operations." },
87        { "gen_count", 0, PARAM_READONLY, "Number of genetic operations so far", "d", FIELD(count), "", },
88        { "gen_mvalid", 0, PARAM_READONLY, "Mutations valid", "d", FIELD(valid_m), "", },
89        { "gen_mvalidated", 0, PARAM_READONLY, "Mutations validated", "d", FIELD(validated_m), "", },
90        { "gen_minvalid", 0, PARAM_READONLY, "Mutations invalid", "d", FIELD(invalid_m), "couldn't be repaired", },
91        { "gen_mfailed", 0, PARAM_READONLY, "Mutations failed", "d", FIELD(failed_m), "couldn't be performed", },
92        { "gen_xovalid", 0, PARAM_READONLY, "Crossovers valid", "d", FIELD(valid_xo), "", },
93        { "gen_xovalidated", 0, PARAM_READONLY, "Crossovers validated", "d", FIELD(validated_xo), "", },
94        { "gen_xoinvalid", 0, PARAM_READONLY, "Crossovers invalid", "d", FIELD(invalid_xo), "couldn't be repaired", },
95        { "gen_xofailed", 0, PARAM_READONLY, "Crossovers failed", "d", FIELD(failed_xo), "couldn't be performed", },
96        { "gen_mutimpr", 0, PARAM_READONLY, "Mutations total effect", "f", FIELD(mutchg), "total cumulative mutation change", },
97        { "gen_xoimpr", 0, PARAM_READONLY, "Crossovers total effect", "f", FIELD(xochg), "total cumulative crossover change", },
98        { "clrstats", 0, PARAM_DONTSAVE, "Clear stats and history", "p()", PROCEDURE(p_clearStats), "", },
99        { 0, },
100};
101
102#undef FIELDSTRUCT
103
104GenMan::GenMan() : localpar(GMparam_tab, this), localstats(GMstats_tab, this),
105seloperpar("GenOperators", "Genetics: Active operators"),
106neuronsparam("Genetics: Neurons to add", "neuronsAdd", "neuadd_"),
107par("GenMan", "Manages various genetic operations, using appropriate operators for the argument genotype format.")
108{
109        history = 0;
110        hilite = 1;
111        clearStats();
112
113#ifdef USE_GENMAN_f0
114        oper_fx_list.push_back(new Geno_f0);
115#endif
116#ifdef USE_GENMAN_f0FUZZY
117        oper_fx_list.push_back(new Geno_f0Fuzzy);
118#endif
119#ifdef USE_GENMAN_f1
120        oper_fx_list.push_back(new Geno_f1);
121#endif
122#ifdef USE_GENMAN_f2
123        oper_fx_list.push_back(new Geno_f2);
124#endif
125#ifdef USE_GENMAN_f3
126        oper_fx_list.push_back(new Geno_f3);
127#endif
128#ifdef USE_GENMAN_f4
129        oper_fx_list.push_back(new Geno_f4);
130#endif
131#ifdef USE_GENMAN_f5
132        oper_fx_list.push_back(new Geno_f5);
133#endif
134#ifdef USE_GENMAN_f6
135        oper_fx_list.push_back(new Geno_f6);
136#endif
137#ifdef USE_GENMAN_f7
138        oper_fx_list.push_back(new Geno_f7);
139#endif
140#ifdef USE_GENMAN_f8
141        oper_fx_list.push_back(new Geno_f8);
142#endif
143#ifdef USE_GENMAN_f9
144        oper_fx_list.push_back(new GenoOper_f9);
145#endif
146#ifdef USE_GENMAN_fF
147        oper_fx_list.push_back(new GenoOper_fF);
148#endif
149#ifdef USE_GENMAN_fn
150        oper_fx_list.push_back(new GenoOper_fn);
151#endif
152#ifdef USE_GENMAN_fT
153        oper_fx_list.push_back(new GenoOper_fTest);
154#endif
155
156        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
157        int selopercount = 0;
158        for (unsigned int i = 0; i < oper_fx_list.size(); i++)
159        {
160                if (operformats.find(oper_fx_list[i]->supported_format) != -1) continue;
161                string type = string("~") + oper_fx_list[i]->name;
162                int dup = 0;
163                for (unsigned int j = i + 1; j < oper_fx_list.size(); j++)
164                        if (oper_fx_list[i]->supported_format == oper_fx_list[j]->supported_format)
165                        {
166                                type += "~";
167                                type += oper_fx_list[j]->name;
168                                dup++;
169                        }
170                type = ssprintf("d 0 %d ", dup) + type;
171                string id = ssprintf("genoper_f%c", oper_fx_list[i]->supported_format);
172                string name = ssprintf("Operators for f%c", oper_fx_list[i]->supported_format);
173                seloper[selopercount] = 0;
174                operformats += oper_fx_list[i]->supported_format;
175                //printf("%x %s %s %s\n",&seloper[selopercount],(const char*)id,(const char*)type,(const char*)name);
176                seloperpar.addProperty(&seloper[selopercount++], id.c_str(), type.c_str(), name.c_str(), "", PARAM_READONLY*(dup == 0));
177        }
178
179        par += &localpar;
180        par += &seloperpar;
181        par += &neuronsparam;
182        for (unsigned int i = 0; i < oper_fx_list.size(); i++)
183                if (oper_fx_list[i]->par.getParamTab()) par += &oper_fx_list[i]->par;
184
185        setDefaults(); //use Param to initialize all values of fields in the paramtab of this object and genetic operators on oper_fx_list
186}
187
188GenMan::~GenMan()
189{
190        for (unsigned int i = 0; i < oper_fx_list.size(); i++) delete oper_fx_list[i];
191        delete[] seloper;
192}
193
194void GenMan::setDefaults()
195{
196        for (unsigned int i = 0; i < oper_fx_list.size(); i++)
197        {
198                oper_fx_list[i]->par.setDefault();
199                oper_fx_list[i]->setDefaults();
200        }
201        localpar.setDefault();
202        //...and we do not reset others that are linked to 'par',
203        //because there quite a few of them, and not every of them defines defaults for each of its parameters.
204}
205
206int GenMan::testValidity(Geno &g, bool &canvalidate)
207{
208        SString ggs=g.getGenes();
209        const char *gg = ggs.c_str();
210        GenoOperators *gf = getOper_f(g.getFormat());
211        int check1;
212        if (!gf) { canvalidate = false; return GENOPER_NOOPER; }
213        else check1 = gf->checkValidity(gg,g.getName().c_str());
214        if (!canvalidate) return check1; //just checking
215        if (check1 == GENOPER_OK) { canvalidate = false; return check1; }
216        char *g2 = strdup(gg);
217        if (gf->validate(g2,g.getName().c_str()) == GENOPER_NOOPER) { free(g2); canvalidate = false; return check1; }
218        if (check1 == GENOPER_NOOPER) //disaster: cannot check because there is no check operator
219        {
220                g.setGenesAssumingSameFormat(g2); free(g2); canvalidate = false; return GENOPER_NOOPER;
221        }
222        int check2 = gf->checkValidity(g2, "validated");
223        if (check2 == GENOPER_OK) g.setGenesAssumingSameFormat(g2);
224        free(g2);
225        if (check2 == GENOPER_OK) return check1;
226        canvalidate = false;
227        return check1; //could not validate.
228}
229
230int GenMan::testGenoValidity(Geno& g)
231{
232        bool fix = false;
233        switch (testValidity(g, fix))
234        {
235        case GENOPER_OK: return 1;
236        case GENOPER_NOOPER: return -1;
237        default: return 0;
238        }
239}
240
241Geno GenMan::validate(const Geno& geny)
242{
243        char format = geny.getFormat();
244        GenoOperators *gf = getOper_f(format);
245        if (gf == NULL)
246                return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: Validate(): don't know how to handle genetic format %c", format));
247        char *g2 = strdup(geny.getGenes().c_str()); //copy for validation
248        int res = gf->validate(g2, geny.getName().c_str());
249        SString sg2 = g2;
250        free(g2);
251        if (res == GENOPER_OK)
252                return Geno(sg2, format, geny.getName(), geny.getComment());
253        else
254                return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: validate() for format %c returned invalid value", format));
255}
256
257Geno GenMan::mutate(const Geno& g)
258{
259        float chg; //how many changes
260        int method; //mutation method
261        char format = g.getFormat();
262        GenoOperators *gf = getOper_f(format);
263        if (gf == NULL)
264                return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: Mutate(): don't know how to handle genetic format %c", format));
265        Geno gv = g;
266        bool canvalidate = true;
267        if (testValidity(gv, canvalidate) > 0 && canvalidate == false)
268                return Geno("", -1, "", "GENOPER_OPFAIL: Mutate(): cannot validate invalid source genotype");
269        bool ok = false;
270        int pcount = count;
271        while (!ok)
272        {
273                char *gn = strdup(gv.getGenes().c_str()); //copy for mutation
274                chg = 0;
275                if (gf->mutate(gn, chg, method) == GENOPER_OK)
276                {
277                        LoggerToMemory eh(LoggerBase::Enable | LoggerToMemory::StoreFirstMessage); //mute testValidity()
278                        Geno G(gn, gv.getFormat(), "", "");
279                        canvalidate = true;
280                        int res = testValidity(G, canvalidate);
281                        if (res == GENOPER_OK && canvalidate == false) { valid_m++; ok = true; }
282                        else
283                                if (res > 0 && canvalidate == false) invalid_m++; else
284                                {
285                                        validated_m++; ok = true;
286                                }
287                        if (ok) gv = G;
288                }
289                else failed_m++;
290                free(gn);
291                count++;
292                if (!ok && (count - pcount > 100))
293                {
294                        logPrintf("GenMan", "Mutate", 2, "Tried 100x and failed: %s", g.getGenes().c_str());
295                        return Geno("", -1, "", "GENOPER_OPFAIL: Mutate() tried 100x and failed");
296                }
297        }
298        mutchg += chg;
299        if (history) saveLink(g.getGenes().c_str(), "", gv.getGenes().c_str(), chg);
300        SString mutinfo;
301        if (extmutinfo == 0) mutinfo = SString::sprintf("%.2f%% mutation of '%s'", 100 * chg, g.getName().c_str()); else
302                if (extmutinfo == 1) mutinfo = SString::sprintf("%.2f%% mutation(%d) of '%s'", 100 * chg, method, g.getName().c_str()); else
303                        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());
304        gv.setComment(mutinfo);
305        return gv;
306}
307
308Geno GenMan::crossOver(const Geno& g1, const Geno& g2)
309{
310        char format = g1.getFormat();
311        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()));
312        GenoOperators *gf = getOper_f(format);
313        if (gf == NULL)
314                return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: CrossOver(): no operators found for genetic format %c", format));
315        Geno g1v = g1, g2v = g2;
316
317        {
318                LoggerToMemory eh(LoggerBase::Enable | LoggerToMemory::StoreFirstMessage); //mute testValidity()
319                bool canvalidate = true;
320                if (testValidity(g1v, canvalidate) > 0 && canvalidate == false)
321                        return Geno("", -1, "", "GENOPER_OPFAIL: CrossOver(): cannot validate invalid source genotype #1");
322                canvalidate = true;
323                if (testValidity(g2v, canvalidate) > 0 && canvalidate == false)
324                        return Geno("", -1, "", "GENOPER_OPFAIL: CrossOver(): cannot validate invalid source genotype #2");
325        }
326
327        float chg;
328        bool ok = false;
329        int pcount = count;
330
331        while (!ok)
332        {
333                float chg1, chg2;
334                char *g1n = strdup(g1.getGenes().c_str()); //copy for crossover
335                char *g2n = strdup(g2.getGenes().c_str()); //copy for crossover
336                chg1 = chg2 = 0;
337                if (gf->crossOver(g1n, g2n, chg1, chg2) == GENOPER_OK)
338                {
339                        char *gn;
340                        if (g1n[0] && g2n[0]) if (randomN(2) == 0) g1n[0] = 0; else g2n[0] = 0; //both provided? we want only one
341                        if (g1n[0]) { gn = g1n; chg = chg1; }
342                        else { gn = g2n; chg = chg2; }
343                        LoggerToMemory eh(LoggerBase::Enable | LoggerToMemory::StoreFirstMessage); //mute testValidity()
344                        Geno G(gn, g1v.getFormat(), "", "");
345                        bool canvalidate = true;
346                        int res = testValidity(G, canvalidate);
347                        if (res == GENOPER_OK && canvalidate == false) { valid_xo++; ok = true; }
348                        else
349                                if (res > 0 && canvalidate == false) invalid_xo++; else
350                                {
351                                        validated_xo++; ok = true;
352                                }
353                        if (ok) g1v = G;
354                }
355                else failed_xo++;
356                free(g1n);
357                free(g2n);
358                count++;
359                if (!ok && (count - pcount > 100))
360                {
361                        logPrintf("GenMan", "CrossOver", 2, "Tried 100x and failed: %s and %s", g1.getGenes().c_str(), g2.getGenes().c_str());
362                        return Geno("", -1, "", "GENOPER_OPFAIL: CrossOver() tried 100x and failed");
363                }
364        }
365        // result in g1v
366        xochg += chg;
367        if (history) saveLink(g1.getGenes().c_str(), g2.getGenes().c_str(), g1v.getGenes().c_str(), chg);
368        SString xoinfo = SString::sprintf("Crossing over of '%s' (%.2f%%) and '%s' (%.2f%%)",
369                g1.getName().c_str(), 100 * chg, g2.getName().c_str(), 100 * (1 - chg));
370        g1v.setComment(xoinfo);
371        return g1v;
372}
373
374float GenMan::similarity(const Geno& g1, const Geno& g2)
375{
376        char format = g1.getFormat();
377        if (format != g2.getFormat()) return GENOPER_NOOPER;
378        GenoOperators *gf = getOper_f(format);
379        if (!gf) return GENOPER_NOOPER; else return gf->similarity(g1.getGenes().c_str(), g2.getGenes().c_str());
380}
381
382uint32_t GenMan::getStyle(const char *g, const Geno *G, int pos)
383{
384        char format = G->getFormat();
385        if (format == Geno::INVALID_FORMAT)
386                return GENSTYLE_RGBS(64, 64, 64, 0); // gray & "valid" (unknown format so we don't know what is valid and what is not)
387        if ((pos = G->mapStringToGen(pos)) == -1) return GENSTYLE_COMMENT;
388        GenoOperators *gf = getOper_f(format);
389        if (!gf) return GENSTYLE_CS(0, 0); //black & valid
390        else return gf->style(G->getGenes().c_str(), pos);
391}
392
393uint32_t GenMan::getStyle(const char *g, int pos)
394{
395        Geno G(g);
396        return getStyle(g, &G, pos);
397}
398
399void GenMan::getFullStyle(const char *g, const Geno *G, uint32_t *styletab)
400{
401        char format = G->getFormat();
402        if (format == Geno::INVALID_FORMAT)
403        {
404                for (unsigned int pos = 0; pos < strlen(g); pos++)
405                        styletab[pos] = GENSTYLE_RGBS(64, 64, 64, 0); // gray & "valid" (unknown format so we don't know what is valid and what is not)
406                return;
407        }
408        GenoOperators *gf = getOper_f(format);
409        SString geny=G->getGenes();
410        for (unsigned int pos = 0; pos < strlen(g); pos++)
411        {
412                int posmapped = G->mapStringToGen(pos);
413                if (posmapped == -1) styletab[pos] = GENSTYLE_COMMENT;
414                else if (!gf) styletab[pos] = GENSTYLE_CS(0, 0); //black & valid
415                else styletab[pos] = gf->style(geny.c_str(), posmapped);
416                //logPrintf("GenMan", "getFullStyle", 0, "%d  char='%c' (%d)  format=0x%08x", pos, g[pos], g[pos], styletab[pos]);
417        }
418}
419
420void GenMan::getFullStyle(const char *g, uint32_t *styletab)
421{
422        Geno G(g);
423        getFullStyle(g, &G, styletab);
424}
425
426string GenMan::HTMLize(const char *g) { return HTMLize(g, false); }
427
428string GenMan::HTMLizeShort(const char *g) { return HTMLize(g, true); }
429
430string GenMan::HTMLize(const char *g, bool shorten)
431{
432        char buf[50];
433        int len = strlen(g);
434        int chars = 0, lines = 0;
435        bool shortened = false;
436        uint32_t *styletab = new uint32_t[len];
437        getFullStyle(g, styletab);
438        string html = "\n<div style=\"background:white;padding:0.2em;font-family:arial,helvetica,sans-serif;font-size:90%\">";
439        uint32_t prevstyle, prevcolor, style = 0, color = 0;
440        for (int i = 0; i<len; i++)
441        {
442                if (shorten && ((lines == 0 && chars>160) || (lines > 5 || chars > 300))) { shortened = true; break; }
443                if (g[i] == '\r') continue;
444                if (g[i] == '\n') { html += "<br>\n"; lines++; continue; }
445                chars++;
446                prevstyle = style;
447                prevcolor = color;
448                style = GENGETSTYLE(styletab[i]);
449                color = GENGETCOLOR(styletab[i]);
450                if ((i != 0 && (color != prevcolor))) html += "</font>";
451                if ((style&GENSTYLE_INVALID) != (prevstyle&GENSTYLE_INVALID))
452                {
453                        html += "<"; if (!(style&GENSTYLE_INVALID)) html += "/"; html += "u>";
454                }
455                if ((style&GENSTYLE_BOLD) != (prevstyle&GENSTYLE_BOLD))
456                {
457                        html += "<"; if (!(style&GENSTYLE_BOLD)) html += "/"; html += "b>";
458                }
459                if ((style&GENSTYLE_ITALIC) != (prevstyle&GENSTYLE_ITALIC))
460                {
461                        html += "<"; if (!(style&GENSTYLE_ITALIC)) html += "/"; html += "i>";
462                }
463                if ((i == 0 || (color != prevcolor)))
464                {
465                        sprintf(buf, "<font color=#%02x%02x%02x>", GENGET_R(color), GENGET_G(color), GENGET_B(color)); html += buf;
466                }
467                if (g[i] == '<') html += "&lt;"; else if (g[i] == '>') html += "&gt;"; else html += g[i];
468                if ((i % 3) == 0 && g[i] == ' ') html += "\n"; //for readability, insert some newlines into html...
469        }
470        delete[] styletab;
471        html += "</u></b></i></font>";
472        if (shortened) html += " [etc...]";
473        html += "</div>\n";
474        return html;
475}
476
477void GenMan::p_htmlize(ExtValue *args, ExtValue *ret)
478{
479        ret->setString(HTMLize(args->getString().c_str()).c_str());
480}
481
482void GenMan::p_htmlizeshort(ExtValue *args, ExtValue *ret)
483{
484        ret->setString(HTMLizeShort(args->getString().c_str()).c_str());
485}
486
487Geno GenMan::getSimplest(char format)
488{
489        GenoOperators *gf = getOper_f(format);
490        if (!gf) return Geno();
491        string info = "The simplest genotype of format f"; info += format;
492        info += " for operators '"; info += gf->name; info += "'.";
493        return Geno(gf->getSimplest(), format, "Root", info.c_str());
494}
495
496void GenMan::p_getsimplest(ExtValue *args, ExtValue *ret)
497{
498        int format = GenoObj::formatFromExtValue(args[0]);
499        if (!getOper_f(format))
500                ret->setEmpty();
501        else
502                *ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(getSimplest(format)));
503}
504
505const char *GenMan::getOpName(char format)
506{
507        GenoOperators *gf = getOper_f(format);
508        if (!gf) return "n/a"; else return gf->name.c_str();
509}
510
511GenoOperators* GenMan::getOper_f(char format)
512{
513        int ind = operformats.find(format);
514        if (ind == -1) return NULL;
515        int which_oper_of_format = seloper[ind];
516        for (unsigned int i = 0; i < oper_fx_list.size(); i++)
517                if (oper_fx_list[i]->supported_format == format)
518                        if (which_oper_of_format == 0) return oper_fx_list[i]; else which_oper_of_format--;
519        return NULL; //should never happen
520}
521
522void GenMan::saveLink(const string parent1, const string parent2, const string child, const float chg)
523{
524        GenoLink l;
525        l.count = count;
526        l.parent1 = parent1;
527        l.parent2 = parent2;
528        l.child = child;
529        l.chg = chg;
530        l.fit = 0; //temporarily. Will be set when the genotype dies
531        //logPrintf("GenMan","saveLink",0,"#%d: [%d] '%s' + '%s' -> '%s'",GenoLinkList.size(),count,parent1.c_str(),parent2.c_str(),child.c_str());
532        GenoLinkList.push_back(l);
533}
534
535void GenMan::onDelGen(void *obj, intptr_t n)
536{
537        //old code needs update:
538        //   ((SpeciesList*)obj)->przyDodaniu(i);
539        /* !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
540           GenMan *gm=(GenMan*)obj;
541           Genotype *gt=(Genotype*)(*listaGen)(n); //there is no more "listaGen"
542           string g=(const char*)gt->genotype.getGene();
543           float fit=gt->getFinalFitness();
544           for(int i=0;i<gm->GenoLinkList.size();i++) //find genotype
545           if (gm->GenoLinkList[i].g1==g) {gm->GenoLinkList[i].fit=fit; break;}
546           */
547}
548
549void GenMan::clearStats()
550{
551        count = 0;
552        valid_m = valid_xo = validated_m = validated_xo = invalid_m = invalid_xo = failed_m = failed_xo = 0;
553        mutchg = xochg = 0;
554        GenoLinkList.clear();
555}
556
557void GenMan::p_clearStats(ExtValue *args, ExtValue *ret) { clearStats(); }
558
559void GenMan::p_report(ExtValue *args, ExtValue *ret)
560{                      //should be updated to handle multiple operators for a single format
561        char *g, *g2;
562        float f1, f2;
563        int m;
564        logMessage("GenMan", "Report", 0, "The following genetic operators are available:");
565        for (unsigned int i = 0; i < oper_fx_list.size(); i++)
566        {
567                string l;
568                if (oper_fx_list[i]->checkValidity("","") != GENOPER_NOOPER) l += " checkValidity";
569                if (oper_fx_list[i]->getSimplest())
570                {
571                        g = strdup(oper_fx_list[i]->getSimplest());
572                        g2 = strdup(g);
573                        if (oper_fx_list[i]->validate(g,"") != GENOPER_NOOPER) l += " validate";
574                        if (oper_fx_list[i]->mutate(g, f1, m) != GENOPER_NOOPER) l += " mutate";
575                        if (oper_fx_list[i]->crossOver(g, g2, f1, f2) != GENOPER_NOOPER) l += " crossover";
576                        l += " getSimplest";
577                        free(g); free(g2);
578                }
579                //      if (oper_fx_list[i]->similarity("","")!=GENOPER_NOOPER) l+=" similarity";
580                logPrintf("GenMan", "Report", 0, "format f%c (%s):%s",
581                        oper_fx_list[i]->supported_format, oper_fx_list[i]->name.c_str(), l.c_str());
582        }
583}
584
585void GenMan::p_validate(ExtValue *args, ExtValue *ret)
586{
587        Geno *g = GenoObj::fromObject(args[0]);
588        if (g == NULL)
589                ret->setEmpty();
590        else
591                *ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(validate(*g)));
592}
593
594void GenMan::p_mutate(ExtValue *args, ExtValue *ret)
595{
596        Geno *g = GenoObj::fromObject(args[0]);
597        if (g == NULL)
598                ret->setEmpty();
599        else
600                *ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(mutate(*g)));
601}
602
603void GenMan::p_crossover(ExtValue *args, ExtValue *ret)
604{
605        Geno *g1 = GenoObj::fromObject(args[1]);
606        Geno *g2 = GenoObj::fromObject(args[0]);
607        if (g1 == NULL || g2 == NULL)
608                ret->setEmpty();
609        else
610                *ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(crossOver(*g1, *g2)));
611}
612
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