source: cpp/frams/genetics/genman.cpp @ 744

Last change on this file since 744 was 715, checked in by Maciej Komosinski, 7 years ago

GenMan?'s constructor now calls its setDefaults() to initialize all values of fields in its paramtab and genetic operators on its oper_fx_list
  • Property svn:eol-style set to native
File size: 21.5 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_fT
51#include "fT/oper_fTest.h"
52#endif
53
54using 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
65static 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(s format)", PROCEDURE(p_getsimplest), "returns the simplest genotype for a given encoding (format). \"0\" means f0, \"4\" means f4, etc.", },
78        { 0, },
79};
80
81static 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
101GenMan::GenMan() : localpar(GMparam_tab, this), localstats(GMstats_tab, this),
102seloperpar("GenOperators", "Genetics: Active operators"),
103neuronsparam("Genetics: Neurons to add", "neuronsAdd", "neuadd_"),
104par("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        setDefaults(); //use Param to initialize all values of fields in the paramtab of this object and genetic operators on oper_fx_list
180}
181
182GenMan::~GenMan()
183{
184        for (unsigned int i = 0; i < oper_fx_list.size(); i++) delete oper_fx_list[i];
185        delete[] seloper;
186}
187
188void GenMan::setDefaults()
189{
190        for (unsigned int i = 0; i < oper_fx_list.size(); i++)
191        {
192                oper_fx_list[i]->par.setDefault();
193                oper_fx_list[i]->setDefaults();
194        }
195        localpar.setDefault();
196        //...and we do not reset others that are linked to 'par',
197        //because there quite a few of them, and not every of them defines defaults for each of its parameters.
198}
199
200int GenMan::testValidity(Geno &g, bool &canvalidate)
201{
202        SString ggs=g.getGenes();
203        const char *gg = ggs.c_str();
204        GenoOperators *gf = getOper_f(g.getFormat());
205        int check1;
206        if (!gf) { canvalidate = false; return GENOPER_NOOPER; }
207        else check1 = gf->checkValidity(gg,g.getName().c_str());
208        if (!canvalidate) return check1; //just checking
209        if (check1 == GENOPER_OK) { canvalidate = false; return check1; }
210        char *g2 = strdup(gg);
211        if (gf->validate(g2,g.getName().c_str()) == GENOPER_NOOPER) { free(g2); canvalidate = false; return check1; }
212        if (check1 == GENOPER_NOOPER) //disaster: cannot check because there is no check operator
213        {
214                g.setGenesAssumingSameFormat(g2); free(g2); canvalidate = false; return GENOPER_NOOPER;
215        }
216        int check2 = gf->checkValidity(g2, "validated");
217        if (check2 == GENOPER_OK) g.setGenesAssumingSameFormat(g2);
218        free(g2);
219        if (check2 == GENOPER_OK) return check1;
220        canvalidate = false;
221        return check1; //could not validate.
222}
223
224int GenMan::testGenoValidity(Geno& g)
225{
226        bool fix = false;
227        switch (testValidity(g, fix))
228        {
229        case GENOPER_OK: return 1;
230        case GENOPER_NOOPER: return -1;
231        default: return 0;
232        }
233}
234
235Geno GenMan::validate(const Geno& geny)
236{
237        char format = geny.getFormat();
238        GenoOperators *gf = getOper_f(format);
239        if (gf == NULL)
240                return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: Validate(): don't know how to handle genetic format %c", format));
241        char *g2 = strdup(geny.getGenes().c_str()); //copy for validation
242        int res = gf->validate(g2, geny.getName().c_str());
243        SString sg2 = g2;
244        free(g2);
245        if (res == GENOPER_OK)
246                return Geno(sg2, format, geny.getName(), geny.getComment());
247        else
248                return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: validate() for format %c returned invalid value", format));
249}
250
251Geno GenMan::mutate(const Geno& g)
252{
253        float chg; //how many changes
254        int method; //mutation method
255        char format = g.getFormat();
256        GenoOperators *gf = getOper_f(format);
257        if (gf == NULL)
258                return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: Mutate(): don't know how to handle genetic format %c", format));
259        Geno gv = g;
260        bool canvalidate = true;
261        if (testValidity(gv, canvalidate) > 0 && canvalidate == false)
262                return Geno("", -1, "", "GENOPER_OPFAIL: Mutate(): cannot validate invalid source genotype");
263        bool ok = false;
264        int pcount = count;
265        while (!ok)
266        {
267                char *gn = strdup(gv.getGenes().c_str()); //copy for mutation
268                chg = 0;
269                if (gf->mutate(gn, chg, method) == GENOPER_OK)
270                {
271                        LoggerToMemory eh(LoggerBase::Enable | LoggerToMemory::StoreFirstMessage); //mute testValidity()
272                        Geno G(gn, gv.getFormat(), "", "");
273                        canvalidate = true;
274                        int res = testValidity(G, canvalidate);
275                        if (res == GENOPER_OK && canvalidate == false) { valid_m++; ok = true; }
276                        else
277                                if (res > 0 && canvalidate == false) invalid_m++; else
278                                {
279                                        validated_m++; ok = true;
280                                }
281                        if (ok) gv = G;
282                }
283                else failed_m++;
284                free(gn);
285                count++;
286                if (!ok && (count - pcount > 100))
287                {
288                        logPrintf("GenMan", "Mutate", 2, "Tried 100x and failed: %s", g.getGenes().c_str());
289                        return Geno("", -1, "", "GENOPER_OPFAIL: Mutate() tried 100x and failed");
290                }
291        }
292        mutchg += chg;
293        if (history) saveLink(g.getGenes().c_str(), "", gv.getGenes().c_str(), chg);
294        SString mutinfo;
295        if (extmutinfo == 0) mutinfo = SString::sprintf("%.2f%% mutation of '%s'", 100 * chg, g.getName().c_str()); else
296                if (extmutinfo == 1) mutinfo = SString::sprintf("%.2f%% mutation(%d) of '%s'", 100 * chg, method, g.getName().c_str()); else
297                        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());
298        gv.setComment(mutinfo);
299        return gv;
300}
301
302Geno GenMan::crossOver(const Geno& g1, const Geno& g2)
303{
304        char format = g1.getFormat();
305        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()));
306        GenoOperators *gf = getOper_f(format);
307        if (gf == NULL)
308                return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: CrossOver(): no operators found for genetic format %c", format));
309        Geno g1v = g1, g2v = g2;
310
311        {
312                LoggerToMemory eh(LoggerBase::Enable | LoggerToMemory::StoreFirstMessage); //mute testValidity()
313                bool canvalidate = true;
314                if (testValidity(g1v, canvalidate) > 0 && canvalidate == false)
315                        return Geno("", -1, "", "GENOPER_OPFAIL: CrossOver(): cannot validate invalid source genotype #1");
316                canvalidate = true;
317                if (testValidity(g2v, canvalidate) > 0 && canvalidate == false)
318                        return Geno("", -1, "", "GENOPER_OPFAIL: CrossOver(): cannot validate invalid source genotype #2");
319        }
320
321        float chg;
322        bool ok = false;
323        int pcount = count;
324
325        while (!ok)
326        {
327                float chg1, chg2;
328                char *g1n = strdup(g1.getGenes().c_str()); //copy for crossover
329                char *g2n = strdup(g2.getGenes().c_str()); //copy for crossover
330                chg1 = chg2 = 0;
331                if (gf->crossOver(g1n, g2n, chg1, chg2) == GENOPER_OK)
332                {
333                        char *gn;
334                        if (g1n[0] && g2n[0]) if (randomN(2) == 0) g1n[0] = 0; else g2n[0] = 0; //both provided? we want only one
335                        if (g1n[0]) { gn = g1n; chg = chg1; }
336                        else { gn = g2n; chg = chg2; }
337                        LoggerToMemory eh(LoggerBase::Enable | LoggerToMemory::StoreFirstMessage); //mute testValidity()
338                        Geno G(gn, g1v.getFormat(), "", "");
339                        bool canvalidate = true;
340                        int res = testValidity(G, canvalidate);
341                        if (res == GENOPER_OK && canvalidate == false) { valid_xo++; ok = true; }
342                        else
343                                if (res > 0 && canvalidate == false) invalid_xo++; else
344                                {
345                                        validated_xo++; ok = true;
346                                }
347                        if (ok) g1v = G;
348                }
349                else failed_xo++;
350                free(g1n);
351                free(g2n);
352                count++;
353                if (!ok && (count - pcount > 100))
354                {
355                        logPrintf("GenMan", "CrossOver", 2, "Tried 100x and failed: %s and %s", g1.getGenes().c_str(), g2.getGenes().c_str());
356                        return Geno("", -1, "", "GENOPER_OPFAIL: CrossOver() tried 100x and failed");
357                }
358        }
359        // result in g1v
360        xochg += chg;
361        if (history) saveLink(g1.getGenes().c_str(), g2.getGenes().c_str(), g1v.getGenes().c_str(), chg);
362        SString xoinfo = SString::sprintf("Crossing over of '%s' (%.2f%%) and '%s' (%.2f%%)",
363                g1.getName().c_str(), 100 * chg, g2.getName().c_str(), 100 * (1 - chg));
364        g1v.setComment(xoinfo);
365        return g1v;
366}
367
368float GenMan::similarity(const Geno& g1, const Geno& g2)
369{
370        char format = g1.getFormat();
371        if (format != g2.getFormat()) return GENOPER_NOOPER;
372        GenoOperators *gf = getOper_f(format);
373        if (!gf) return GENOPER_NOOPER; else return gf->similarity(g1.getGenes().c_str(), g2.getGenes().c_str());
374}
375
376uint32_t GenMan::getStyle(const char *g, const Geno *G, int pos)
377{
378        char format = G->getFormat();
379        if (format == Geno::INVALID_FORMAT)
380                return GENSTYLE_RGBS(64, 64, 64, 0); // gray & "valid" (unknown format so we don't know what is valid and what is not)
381        if ((pos = G->mapStringToGen(pos)) == -1) return GENSTYLE_COMMENT;
382        GenoOperators *gf = getOper_f(format);
383        if (!gf) return GENSTYLE_CS(0, 0); //black & valid
384        else return gf->style(G->getGenes().c_str(), pos);
385}
386
387uint32_t GenMan::getStyle(const char *g, int pos)
388{
389        Geno G(g);
390        return getStyle(g, &G, pos);
391}
392
393void GenMan::getFullStyle(const char *g, const Geno *G, uint32_t *styletab)
394{
395        char format = G->getFormat();
396        if (format == Geno::INVALID_FORMAT)
397        {
398                for (unsigned int pos = 0; pos < strlen(g); pos++)
399                        styletab[pos] = GENSTYLE_RGBS(64, 64, 64, 0); // gray & "valid" (unknown format so we don't know what is valid and what is not)
400                return;
401        }
402        GenoOperators *gf = getOper_f(format);
403        SString geny=G->getGenes();
404        for (unsigned int pos = 0; pos < strlen(g); pos++)
405        {
406                int posmapped = G->mapStringToGen(pos);
407                if (posmapped == -1) styletab[pos] = GENSTYLE_COMMENT;
408                else if (!gf) styletab[pos] = GENSTYLE_CS(0, 0); //black & valid
409                else styletab[pos] = gf->style(geny.c_str(), posmapped);
410                //logPrintf("GenMan", "getFullStyle", 0, "%d  char='%c' (%d)  format=0x%08x", pos, g[pos], g[pos], styletab[pos]);
411        }
412}
413
414void GenMan::getFullStyle(const char *g, uint32_t *styletab)
415{
416        Geno G(g);
417        getFullStyle(g, &G, styletab);
418}
419
420string GenMan::HTMLize(const char *g) { return HTMLize(g, false); }
421
422string GenMan::HTMLizeShort(const char *g) { return HTMLize(g, true); }
423
424string GenMan::HTMLize(const char *g, bool shorten)
425{
426        char buf[50];
427        int len = strlen(g);
428        int chars = 0, lines = 0;
429        bool shortened = false;
430        uint32_t *styletab = new uint32_t[len];
431        getFullStyle(g, styletab);
432        string html = "\n<div style=\"background:white;padding:0.2em;font-family:arial,helvetica,sans-serif;font-size:90%\">";
433        uint32_t prevstyle, prevcolor, style = 0, color = 0;
434        for (int i = 0; i<len; i++)
435        {
436                if (shorten && ((lines == 0 && chars>160) || (lines > 5 || chars > 300))) { shortened = true; break; }
437                if (g[i] == '\r') continue;
438                if (g[i] == '\n') { html += "<br>\n"; lines++; continue; }
439                chars++;
440                prevstyle = style;
441                prevcolor = color;
442                style = GENGETSTYLE(styletab[i]);
443                color = GENGETCOLOR(styletab[i]);
444                if ((i != 0 && (color != prevcolor))) html += "</font>";
445                if ((style&GENSTYLE_INVALID) != (prevstyle&GENSTYLE_INVALID))
446                {
447                        html += "<"; if (!(style&GENSTYLE_INVALID)) html += "/"; html += "u>";
448                }
449                if ((style&GENSTYLE_BOLD) != (prevstyle&GENSTYLE_BOLD))
450                {
451                        html += "<"; if (!(style&GENSTYLE_BOLD)) html += "/"; html += "b>";
452                }
453                if ((style&GENSTYLE_ITALIC) != (prevstyle&GENSTYLE_ITALIC))
454                {
455                        html += "<"; if (!(style&GENSTYLE_ITALIC)) html += "/"; html += "i>";
456                }
457                if ((i == 0 || (color != prevcolor)))
458                {
459                        sprintf(buf, "<font color=#%02x%02x%02x>", GENGET_R(color), GENGET_G(color), GENGET_B(color)); html += buf;
460                }
461                if (g[i] == '<') html += "&lt;"; else if (g[i] == '>') html += "&gt;"; else html += g[i];
462                if ((i % 3) == 0 && g[i] == ' ') html += "\n"; //for readability, insert some newlines into html...
463        }
464        delete[] styletab;
465        html += "</u></b></i></font>";
466        if (shortened) html += " [etc...]";
467        html += "</div>\n";
468        return html;
469}
470
471void GenMan::p_htmlize(ExtValue *args, ExtValue *ret)
472{
473        ret->setString(HTMLize(args->getString().c_str()).c_str());
474}
475
476void GenMan::p_htmlizeshort(ExtValue *args, ExtValue *ret)
477{
478        ret->setString(HTMLizeShort(args->getString().c_str()).c_str());
479}
480
481Geno GenMan::getSimplest(char format)
482{
483        GenoOperators *gf = getOper_f(format);
484        if (!gf) return Geno();
485        string info = "The simplest genotype of format f"; info += format;
486        info += " for operators '"; info += gf->name; info += "'.";
487        return Geno(gf->getSimplest(), format, "Root", info.c_str());
488}
489
490void GenMan::p_getsimplest(ExtValue *args, ExtValue *ret)
491{
492        int format = GenoObj::formatFromExtValue(args[0]);
493        if (!getOper_f(format))
494                ret->setEmpty();
495        else
496                *ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(getSimplest(format)));
497}
498
499const char *GenMan::getOpName(char format)
500{
501        GenoOperators *gf = getOper_f(format);
502        if (!gf) return "n/a"; else return gf->name.c_str();
503}
504
505GenoOperators* GenMan::getOper_f(char format)
506{
507        int ind = operformats.find(format);
508        if (ind == -1) return NULL;
509        int which_oper_of_format = seloper[ind];
510        for (unsigned int i = 0; i < oper_fx_list.size(); i++)
511                if (oper_fx_list[i]->supported_format == format)
512                        if (which_oper_of_format == 0) return oper_fx_list[i]; else which_oper_of_format--;
513        return NULL; //should never happen
514}
515
516void GenMan::saveLink(const string parent1, const string parent2, const string child, const float chg)
517{
518        GenoLink l;
519        l.count = count;
520        l.parent1 = parent1;
521        l.parent2 = parent2;
522        l.child = child;
523        l.chg = chg;
524        l.fit = 0; //temporarily. Will be set when the genotype dies
525        //logPrintf("GenMan","saveLink",0,"#%d: [%d] '%s' + '%s' -> '%s'",GenoLinkList.size(),count,parent1.c_str(),parent2.c_str(),child.c_str());
526        GenoLinkList.push_back(l);
527}
528
529void GenMan::onDelGen(void *obj, intptr_t n)
530{
531        //old code needs update:
532        //   ((SpeciesList*)obj)->przyDodaniu(i);
533        /* !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
534           GenMan *gm=(GenMan*)obj;
535           Genotype *gt=(Genotype*)(*listaGen)(n); //there is no more "listaGen"
536           string g=(const char*)gt->genotype.getGene();
537           float fit=gt->getFinalFitness();
538           for(int i=0;i<gm->GenoLinkList.size();i++) //find genotype
539           if (gm->GenoLinkList[i].g1==g) {gm->GenoLinkList[i].fit=fit; break;}
540           */
541}
542
543void GenMan::clearStats()
544{
545        count = 0;
546        valid_m = valid_xo = validated_m = validated_xo = invalid_m = invalid_xo = failed_m = failed_xo = 0;
547        mutchg = xochg = 0;
548        GenoLinkList.clear();
549}
550
551void GenMan::p_clearStats(ExtValue *args, ExtValue *ret) { clearStats(); }
552
553void GenMan::p_report(ExtValue *args, ExtValue *ret)
554{                      //should be updated to handle multiple operators for a single format
555        char *g, *g2;
556        float f1, f2;
557        int m;
558        logMessage("GenMan", "Report", 0, "The following genetic operators are available:");
559        for (unsigned int i = 0; i < oper_fx_list.size(); i++)
560        {
561                string l;
562                if (oper_fx_list[i]->checkValidity("","") != GENOPER_NOOPER) l += " checkValidity";
563                if (oper_fx_list[i]->getSimplest())
564                {
565                        g = strdup(oper_fx_list[i]->getSimplest());
566                        g2 = strdup(g);
567                        if (oper_fx_list[i]->validate(g,"") != GENOPER_NOOPER) l += " validate";
568                        if (oper_fx_list[i]->mutate(g, f1, m) != GENOPER_NOOPER) l += " mutate";
569                        if (oper_fx_list[i]->crossOver(g, g2, f1, f2) != GENOPER_NOOPER) l += " crossover";
570                        l += " getSimplest";
571                        free(g); free(g2);
572                }
573                //      if (oper_fx_list[i]->similarity("","")!=GENOPER_NOOPER) l+=" similarity";
574                logPrintf("GenMan", "Report", 0, "format f%c (%s):%s",
575                        oper_fx_list[i]->supported_format, oper_fx_list[i]->name.c_str(), l.c_str());
576        }
577}
578
579void GenMan::p_validate(ExtValue *args, ExtValue *ret)
580{
581        Geno *g = GenoObj::fromObject(args[0]);
582        if (g == NULL)
583                ret->setEmpty();
584        else
585                *ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(validate(*g)));
586}
587
588void GenMan::p_mutate(ExtValue *args, ExtValue *ret)
589{
590        Geno *g = GenoObj::fromObject(args[0]);
591        if (g == NULL)
592                ret->setEmpty();
593        else
594                *ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(mutate(*g)));
595}
596
597void GenMan::p_crossover(ExtValue *args, ExtValue *ret)
598{
599        Geno *g1 = GenoObj::fromObject(args[1]);
600        Geno *g2 = GenoObj::fromObject(args[0]);
601        if (g1 == NULL || g2 == NULL)
602                ret->setEmpty();
603        else
604                *ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(crossOver(*g1, *g2)));
605}
606
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