source: cpp/frams/genetics/genman.cpp @ 1000

Last change on this file since 1000 was 988, checked in by Maciej Komosinski, 5 years ago

Building a Model from Geno now fails when Model.shape is incompatible with Geno.format; renamed enum constants for genetic formats: xxx_FORMAT => FORMAT_xxx
  • Property svn:eol-style set to native
File size: 25.9 KB
Line 
1// This file is a part of Framsticks SDK.  http://www.framsticks.com/
2// Copyright (C) 1999-2020  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/util-string.h"
11#include <common/loggers/loggers.h>
12
13
14#define GENMAN_REPEAT_FAILED 100 //how many times GenMan tries to repeat a mutation or crossover when the operator does not return acceptable genotype
15#define STRINGIFY_1(x) #x
16#define STRINGIFY(x) STRINGIFY_1(x) //this second-level macro allows the parameter to be a macro itself and to stringify its value, not its name
17#define GENMAN_REPEAT_FAILED_STR STRINGIFY(GENMAN_REPEAT_FAILED)
18
19
20#ifdef USE_GENMAN_f0
21#include "f0/f0_oper.h"
22#endif
23#ifdef USE_GENMAN_f0s
24#include "f0s/f0s_oper.h"
25#endif
26#ifdef USE_GENMAN_f0FUZZY
27#include "f0/f0Fuzzy_oper.h"
28#endif
29#ifdef USE_GENMAN_f1
30#include "f1/f1_oper.h"
31#endif
32#ifdef USE_GENMAN_f2
33#include "f2/f2_oper.h"
34#endif
35#ifdef USE_GENMAN_f2
36#include "f3/f3_oper.h"
37#endif
38#ifdef USE_GENMAN_f4
39#include "f4/f4_oper.h"
40#endif
41#ifdef USE_GENMAN_f5
42#include "f5/f5_oper.h"
43#endif
44#ifdef USE_GENMAN_f6
45#include "f6/f6_oper.h"
46#endif
47#ifdef USE_GENMAN_f7
48#include "f7/f7_oper.h"
49#endif
50#ifdef USE_GENMAN_f8
51#include "f8/f8_oper.h"
52#endif
53#ifdef USE_GENMAN_f9
54#include "f9/f9_oper.h"
55#endif
56#ifdef USE_GENMAN_fF
57#include "fF/fF_oper.h"
58#endif
59#ifdef USE_GENMAN_fn
60#include "fn/fn_oper.h"
61#endif
62#ifdef USE_GENMAN_fT
63#include "fT/fTest_oper.h"
64#endif
65#ifdef USE_GENMAN_fB
66#include "fB/fB_oper.h"
67#endif
68#ifdef USE_GENMAN_fH
69#include "fH/fH_oper.h"
70#endif
71#ifdef USE_GENMAN_fL
72#include "fL/fL_oper.h"
73#endif
74#ifdef USE_GENMAN_fS
75#include "fS/fS_oper.h"
76#endif
77
78using namespace std; //string, vector
79
80//old code needs update:
81//#include "gengroups.h"
82//extern GenGroup *listaGen;
83//   GENGROUP(0)->l_del.add(sim->GM.onDelGen,&sim->GM); //before delete
84//   GENGROUP(0)->l_del.remove(sim->GM.onDelGen,&sim->GM); //before delete
85
86
87#define FIELDSTRUCT GenMan
88
89static ParamEntry GMparam_tab[] =
90{
91        { "Genetics", 1, 11, "GenMan", },
92        { "gen_hist", 0, PARAM_DONTSAVE, "Remember history of genetic operations", "d 0 1 0", FIELD(history), "Required for phylogenetic analysis", },
93        { "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)", },
94        { "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.", },
95        { "operReport", 0, PARAM_DONTSAVE, "Operators report", "p()", PROCEDURE(p_report), "Show available genetic operators", },
96        { "toHTML", 0, PARAM_DONTSAVE, "HTMLize a genotype", "p s(s)", PROCEDURE(p_htmlize), "returns genotype expressed as colored HTML", },
97        { "toHTMLshort", 0, PARAM_DONTSAVE, "HTMLize a genotype, shorten if needed", "p s(s)", PROCEDURE(p_htmlizeshort), "returns genotype (abbreviated if needed) in colored HTML format", },
98        { "toLaTeX", 0, PARAM_DONTSAVE, "LaTeXize a genotype", "p s(s)", PROCEDURE(p_latexize), "returns genotype in colored LaTeX format", },
99        { "validate", 0, PARAM_DONTSAVE | PARAM_USERHIDDEN, "Validate", "p oGeno(oGeno)", PROCEDURE(p_validate), "returns validated (if possible) Geno object from supplied Geno", },
100        { "mutate", 0, PARAM_DONTSAVE | PARAM_USERHIDDEN, "Mutate", "p oGeno(oGeno)", PROCEDURE(p_mutate), "returns mutated Geno object from supplied Geno", },
101        { "crossOver", 0, PARAM_DONTSAVE | PARAM_USERHIDDEN, "Crossover", "p oGeno(oGeno,oGeno)", PROCEDURE(p_crossover), "returns crossed over genotype", },
102        { "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.", },
103        { 0, },
104};
105
106static ParamEntry GMstats_tab[] =
107{
108        { "Genetics", 1, 12, "GenManStats", "Statistics for genetic operations." },
109        { "gen_count", 0, PARAM_READONLY, "Number of genetic operations so far", "d", FIELD(count), "", },
110        { "gen_mvalid", 0, PARAM_READONLY, "Mutations valid", "d", FIELD(valid_m), "", },
111        { "gen_mvalidated", 0, PARAM_READONLY, "Mutations validated", "d", FIELD(validated_m), "", },
112        { "gen_minvalid", 0, PARAM_READONLY, "Mutations invalid", "d", FIELD(invalid_m), "couldn't be repaired", },
113        { "gen_mfailed", 0, PARAM_READONLY, "Mutations failed", "d", FIELD(failed_m), "couldn't be performed", },
114        { "gen_xovalid", 0, PARAM_READONLY, "Crossovers valid", "d", FIELD(valid_xo), "", },
115        { "gen_xovalidated", 0, PARAM_READONLY, "Crossovers validated", "d", FIELD(validated_xo), "", },
116        { "gen_xoinvalid", 0, PARAM_READONLY, "Crossovers invalid", "d", FIELD(invalid_xo), "couldn't be repaired", },
117        { "gen_xofailed", 0, PARAM_READONLY, "Crossovers failed", "d", FIELD(failed_xo), "couldn't be performed", },
118        { "gen_mutimpr", 0, PARAM_READONLY, "Mutations total effect", "f", FIELD(mutchg), "total cumulative mutation change", },
119        { "gen_xoimpr", 0, PARAM_READONLY, "Crossovers total effect", "f", FIELD(xochg), "total cumulative crossover change", },
120        { "clrstats", 0, PARAM_DONTSAVE, "Clear stats and history", "p()", PROCEDURE(p_clearStats), "", },
121        { 0, },
122};
123
124#undef FIELDSTRUCT
125
126GenMan::GenMan() : localpar(GMparam_tab, this), localstats(GMstats_tab, this),
127seloperpar("GenOperators", "Genetics: Active operators"),
128neuronsparam("Genetics: Neurons to add", "neuronsAdd", "neuadd_"),
129par("GenMan", "Manages various genetic operations, using appropriate operators for the argument genotype format.")
130{
131        history = 0;
132        hilite = 1;
133        clearStats();
134
135#ifdef USE_GENMAN_f0
136        oper_fx_list.push_back(new Geno_f0);
137#endif
138#ifdef USE_GENMAN_f0s
139        oper_fx_list.push_back(new Geno_f0s);
140#endif
141#ifdef USE_GENMAN_f0FUZZY
142        oper_fx_list.push_back(new Geno_f0Fuzzy);
143#endif
144#ifdef USE_GENMAN_f1
145        oper_fx_list.push_back(new Geno_f1);
146#endif
147#ifdef USE_GENMAN_f2
148        oper_fx_list.push_back(new Geno_f2);
149#endif
150#ifdef USE_GENMAN_f3
151        oper_fx_list.push_back(new Geno_f3);
152#endif
153#ifdef USE_GENMAN_f4
154        oper_fx_list.push_back(new Geno_f4);
155#endif
156#ifdef USE_GENMAN_f5
157        oper_fx_list.push_back(new Geno_f5);
158#endif
159#ifdef USE_GENMAN_f6
160        oper_fx_list.push_back(new Geno_f6);
161#endif
162#ifdef USE_GENMAN_f7
163        oper_fx_list.push_back(new Geno_f7);
164#endif
165#ifdef USE_GENMAN_f8
166        oper_fx_list.push_back(new Geno_f8);
167#endif
168#ifdef USE_GENMAN_f9
169        oper_fx_list.push_back(new GenoOper_f9);
170#endif
171#ifdef USE_GENMAN_fF
172        oper_fx_list.push_back(new GenoOper_fF);
173#endif
174#ifdef USE_GENMAN_fn
175        oper_fx_list.push_back(new GenoOper_fn);
176#endif
177#ifdef USE_GENMAN_fT
178        oper_fx_list.push_back(new GenoOper_fTest);
179#endif
180#ifdef USE_GENMAN_fB
181        oper_fx_list.push_back(new Geno_fB);
182#endif
183#ifdef USE_GENMAN_fH
184        oper_fx_list.push_back(new Geno_fH);
185#endif
186#ifdef USE_GENMAN_fL
187        oper_fx_list.push_back(new Geno_fL);
188#endif
189#ifdef USE_GENMAN_fS
190        oper_fx_list.push_back(new GenoOper_fS);
191#endif
192
193        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
194        int selopercount = 0;
195        for (unsigned int i = 0; i < oper_fx_list.size(); i++)
196        {
197                if (findOperFormatIndex(oper_fx_list[i]->supported_format) != -1) continue;
198                string type = string("~") + oper_fx_list[i]->name;
199                int dup = 0;
200                for (unsigned int j = i + 1; j < oper_fx_list.size(); j++)
201                        if (oper_fx_list[i]->supported_format == oper_fx_list[j]->supported_format)
202                        {
203                                type += "~";
204                                type += oper_fx_list[j]->name;
205                                dup++;
206                        }
207                type = ssprintf("d 0 %d ", dup) + type;
208                string id = ssprintf("genoper_f%s", oper_fx_list[i]->supported_format.c_str());
209                string name = ssprintf("Operators for f%s", oper_fx_list[i]->supported_format.c_str());
210                seloper[selopercount] = 0;
211                operformats += &oper_fx_list[i]->supported_format;
212                //printf("%x %s %s %s\n",&seloper[selopercount],(const char*)id,(const char*)type,(const char*)name);
213                seloperpar.addProperty(&seloper[selopercount++], id.c_str(), type.c_str(), name.c_str(), "", PARAM_READONLY * (dup == 0));
214        }
215
216        par += &localpar;
217        par += &seloperpar;
218        par += &neuronsparam;
219        for (unsigned int i = 0; i < oper_fx_list.size(); i++)
220                if (oper_fx_list[i]->par.getParamTab()) par += &oper_fx_list[i]->par;
221
222        setDefaults(); //use Param to initialize all values of fields in the paramtab of this object and genetic operators on oper_fx_list
223}
224
225GenMan::~GenMan()
226{
227        for (unsigned int i = 0; i < oper_fx_list.size(); i++) delete oper_fx_list[i];
228        delete[] seloper;
229}
230
231int GenMan::findOperFormatIndex(const SString& format)
232{
233        for (int i = 0; i < operformats.size(); i++)
234                if (*operformats(i) == format)
235                        return i;
236        return -1;
237}
238
239void GenMan::setDefaults()
240{
241        for (unsigned int i = 0; i < oper_fx_list.size(); i++)
242        {
243                oper_fx_list[i]->par.setDefault();
244                oper_fx_list[i]->setDefaults();
245        }
246        localpar.setDefault();
247        //...and we do not reset others that are linked to 'par',
248        //because there quite a few of them, and not every of them defines defaults for each of its parameters.
249}
250
251int GenMan::testValidity(Geno &g, bool &canvalidate)
252{
253        SString ggs = g.getGenes();
254        const char *gg = ggs.c_str();
255        GenoOperators *gf = getOper_f(g.getFormat());
256        int check1;
257        if (!gf) { canvalidate = false; return GENOPER_NOOPER; }
258        else check1 = gf->checkValidity(gg, g.getName().c_str());
259        if (!canvalidate) return check1; //just checking
260        if (check1 == GENOPER_OK) { canvalidate = false; return check1; }
261        char *g2 = strdup(gg);
262        if (gf->validate(g2, g.getName().c_str()) == GENOPER_NOOPER) { free(g2); canvalidate = false; return check1; }
263        if (check1 == GENOPER_NOOPER) //disaster: cannot check because there is no check operator
264        {
265                g.setGenesAssumingSameFormat(g2); free(g2); canvalidate = false; return GENOPER_NOOPER;
266        }
267        int check2 = gf->checkValidity(g2, "validated");
268        if (check2 == GENOPER_OK) g.setGenesAssumingSameFormat(g2);
269        free(g2);
270        if (check2 == GENOPER_OK) return check1;
271        canvalidate = false;
272        return check1; //could not validate.
273}
274
275int GenMan::testGenoValidity(Geno& g)
276{
277        bool fix = false;
278        switch (testValidity(g, fix))
279        {
280        case GENOPER_OK: return 1;
281        case GENOPER_NOOPER: return -1;
282        default: return 0;
283        }
284}
285
286Geno GenMan::validate(const Geno& geny)
287{
288        SString format = geny.getFormat();
289        GenoOperators *gf = getOper_f(format);
290        if (gf == NULL)
291                return Geno("", Geno::FORMAT_INVALID, "", SString::sprintf("GENOPER_NOOPER: Validate(): don't know how to handle genetic format %s", format.c_str()));
292        char *g2 = strdup(geny.getGenes().c_str()); //copy for validation
293        int res = gf->validate(g2, geny.getName().c_str());
294        SString sg2 = g2;
295        free(g2);
296        if (res == GENOPER_OK)
297                return Geno(sg2, format, geny.getName(), geny.getComment());
298        else
299                return Geno("", Geno::FORMAT_INVALID, "", SString::sprintf("GENOPER_NOOPER: validate() for format %s returned invalid value", format.c_str()));
300}
301
302Geno GenMan::mutate(const Geno& g)
303{
304        float chg; //how many changes
305        int method; //mutation method
306        SString format = g.getFormat();
307        GenoOperators *gf = getOper_f(format);
308        if (gf == NULL)
309                return Geno("", Geno::FORMAT_INVALID, "", SString::sprintf("GENOPER_NOOPER: Mutate(): don't know how to handle genetic format %s", format.c_str()));
310        Geno gv = g;
311        bool canvalidate = true;
312        if (testValidity(gv, canvalidate) > 0 && canvalidate == false)
313                return Geno("", Geno::FORMAT_INVALID, "", "GENOPER_OPFAIL: Mutate(): cannot validate invalid source genotype");
314        bool ok = false;
315        int pcount = count;
316        while (!ok)
317        {
318                char *gn = strdup(gv.getGenes().c_str()); //copy for mutation
319                chg = 0;
320                if (gf->mutate(gn, chg, method) == GENOPER_OK)
321                {
322                        LoggerToMemory eh(LoggerBase::Enable | LoggerToMemory::StoreFirstMessage); //mute testValidity()
323                        Geno G(gn, gv.getFormat(), "", "");
324                        canvalidate = true;
325                        int res = testValidity(G, canvalidate);
326                        if (res == GENOPER_OK && canvalidate == false) { valid_m++; ok = true; }
327                        else
328                                if (res > 0 && canvalidate == false) invalid_m++; else
329                                {
330                                        validated_m++; ok = true;
331                                }
332                        if (ok) gv = G;
333                }
334                else failed_m++;
335                free(gn);
336                count++;
337                if (!ok && (count - pcount > GENMAN_REPEAT_FAILED))
338                {
339                        logPrintf("GenMan", "Mutate", LOG_WARN, "Tried " GENMAN_REPEAT_FAILED_STR "x and failed: %s", g.getGenes().c_str());
340                        return Geno("", -1, "", "GENOPER_OPFAIL: Mutate() tried " GENMAN_REPEAT_FAILED_STR "x and failed");
341                }
342        }
343        mutchg += chg;
344        if (history) saveLink(g.getGenes().c_str(), "", gv.getGenes().c_str(), chg);
345        SString mutinfo;
346        if (extmutinfo == 0) mutinfo = SString::sprintf("%.2f%% mutation of '%s'", 100 * chg, g.getName().c_str()); else
347                if (extmutinfo == 1) mutinfo = SString::sprintf("%.2f%% mutation(%d) of '%s'", 100 * chg, method, g.getName().c_str()); else
348                        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());
349        gv.setComment(mutinfo);
350        return gv;
351}
352
353Geno GenMan::crossOver(const Geno& g1, const Geno& g2)
354{
355        SString format = g1.getFormat();
356        if (format != g2.getFormat()) return Geno("", Geno::FORMAT_INVALID, "", SString::sprintf("GENOPER_NOOPER: CrossOver(): does not work for parents with differing genetic formats (%s and %s)", format.c_str(), g2.getFormat().c_str()));
357        GenoOperators *gf = getOper_f(format);
358        if (gf == NULL)
359                return Geno("", Geno::FORMAT_INVALID, "", SString::sprintf("GENOPER_NOOPER: CrossOver(): no operators found for genetic format %s", format.c_str()));
360        Geno g1v = g1, g2v = g2;
361
362        {
363                LoggerToMemory eh(LoggerBase::Enable | LoggerToMemory::StoreFirstMessage); //mute testValidity()
364                bool canvalidate = true;
365                if (testValidity(g1v, canvalidate) > 0 && canvalidate == false)
366                        return Geno("", Geno::FORMAT_INVALID, "", "GENOPER_OPFAIL: CrossOver(): cannot validate invalid source genotype #1");
367                canvalidate = true;
368                if (testValidity(g2v, canvalidate) > 0 && canvalidate == false)
369                        return Geno("", Geno::FORMAT_INVALID, "", "GENOPER_OPFAIL: CrossOver(): cannot validate invalid source genotype #2");
370        }
371
372        float chg;
373        bool ok = false;
374        int pcount = count;
375
376        while (!ok)
377        {
378                float chg1, chg2;
379                char *g1n = strdup(g1.getGenes().c_str()); //copy for crossover
380                char *g2n = strdup(g2.getGenes().c_str()); //copy for crossover
381                chg1 = chg2 = 0;
382                if (gf->crossOver(g1n, g2n, chg1, chg2) == GENOPER_OK)
383                {
384                        char *gn;
385                        if (g1n[0] && g2n[0]) if (rndUint(2) == 0) g1n[0] = 0; else g2n[0] = 0; //both provided? we want only one
386                        if (g1n[0]) { gn = g1n; chg = chg1; }
387                        else { gn = g2n; chg = chg2; }
388                        LoggerToMemory eh(LoggerBase::Enable | LoggerToMemory::StoreFirstMessage); //mute testValidity()
389                        Geno G(gn, g1v.getFormat(), "", "");
390                        bool canvalidate = true;
391                        int res = testValidity(G, canvalidate);
392                        if (res == GENOPER_OK && canvalidate == false) { valid_xo++; ok = true; }
393                        else
394                                if (res > 0 && canvalidate == false) invalid_xo++; else
395                                {
396                                        validated_xo++; ok = true;
397                                }
398                        if (ok) g1v = G;
399                }
400                else failed_xo++;
401                free(g1n);
402                free(g2n);
403                count++;
404                if (!ok && (count - pcount > GENMAN_REPEAT_FAILED))
405                {
406                        logPrintf("GenMan", "CrossOver", LOG_WARN, "Tried " GENMAN_REPEAT_FAILED_STR "x and failed: %s and %s", g1.getGenes().c_str(), g2.getGenes().c_str());
407                        return Geno("", Geno::FORMAT_INVALID, "", "GENOPER_OPFAIL: CrossOver() tried " GENMAN_REPEAT_FAILED_STR "x and failed");
408                }
409        }
410        // result in g1v
411        xochg += chg;
412        if (history) saveLink(g1.getGenes().c_str(), g2.getGenes().c_str(), g1v.getGenes().c_str(), chg);
413        SString xoinfo = SString::sprintf("Crossing over of '%s' (%.2f%%) and '%s' (%.2f%%)",
414                g1.getName().c_str(), 100 * chg, g2.getName().c_str(), 100 * (1 - chg));
415        g1v.setComment(xoinfo);
416        return g1v;
417}
418
419float GenMan::similarity(const Geno& g1, const Geno& g2)
420{
421        SString format = g1.getFormat();
422        if (format != g2.getFormat()) return GENOPER_NOOPER;
423        GenoOperators *gf = getOper_f(format);
424        if (!gf) return GENOPER_NOOPER; else return gf->similarity(g1.getGenes().c_str(), g2.getGenes().c_str());
425}
426
427uint32_t GenMan::getStyle(const char *g, const Geno *G, int pos)
428{
429        SString format = G->getFormat();
430        if (format == Geno::FORMAT_INVALID)
431                return GENSTYLE_RGBS(64, 64, 64, 0); // gray & "valid" (unknown format so we don't know what is valid and what is not)
432        if ((pos = G->mapStringToGen(pos)) == -1) return GENSTYLE_COMMENT;
433        GenoOperators *gf = getOper_f(format);
434        if (!gf) return GENSTYLE_CS(0, 0); //black & valid
435        else return gf->style(G->getGenes().c_str(), pos);
436}
437
438uint32_t GenMan::getStyle(const char *g, int pos)
439{
440        Geno G(g);
441        return getStyle(g, &G, pos);
442}
443
444void GenMan::getFullStyle(const char *g, const Geno *G, uint32_t *styletab)
445{
446        SString format = G->getFormat();
447        if (format == Geno::FORMAT_INVALID)
448        {
449                for (unsigned int pos = 0; pos < strlen(g); pos++)
450                        styletab[pos] = GENSTYLE_RGBS(64, 64, 64, 0); // gray & "valid" (unknown format so we don't know what is valid and what is not)
451                return;
452        }
453        GenoOperators *gf = getOper_f(format);
454        SString geny = G->getGenes();
455        for (unsigned int pos = 0; pos < strlen(g); pos++)
456        {
457                int posmapped = G->mapStringToGen(pos);
458                if (posmapped == -1) styletab[pos] = GENSTYLE_COMMENT;
459                else if (!gf) styletab[pos] = GENSTYLE_CS(0, 0); //black & valid
460                else styletab[pos] = gf->style(geny.c_str(), posmapped);
461                //logPrintf("GenMan", "getFullStyle", LOG_INFO, "%d  char='%c' (%d)  format=0x%08x", pos, g[pos], g[pos], styletab[pos]);
462        }
463}
464
465void GenMan::getFullStyle(const char *g, uint32_t *styletab)
466{
467        Geno G(g);
468        getFullStyle(g, &G, styletab);
469}
470
471string GenMan::HTMLize(const char *g) { return HTMLize(g, false); }
472
473string GenMan::HTMLizeShort(const char *g) { return HTMLize(g, true); }
474
475string GenMan::HTMLize(const char *g, bool shorten)
476{
477        char buf[50];
478        int len = strlen(g);
479        int chars = 0, lines = 0;
480        bool shortened = false;
481        uint32_t *styletab = new uint32_t[len];
482        getFullStyle(g, styletab);
483        string html = "\n<div style=\"background:white;padding:0.2em;font-family:arial,helvetica,sans-serif;font-size:90%\">";
484        uint32_t prevstyle, prevcolor, style = 0, color = 0;
485        for (int i = 0; i < len; i++)
486        {
487                if (shorten && ((lines == 0 && chars > 160) || (lines > 5 || chars > 300))) { shortened = true; break; }
488                if (g[i] == '\r') continue;
489                if (g[i] == '\n') { html += "<br>\n"; lines++; continue; }
490                chars++;
491                prevstyle = style;
492                prevcolor = color;
493                style = GENGETSTYLE(styletab[i]);
494                color = GENGETCOLOR(styletab[i]);
495                if ((i != 0 && (color != prevcolor))) html += "</font>";
496                if ((style & GENSTYLE_INVALID) != (prevstyle & GENSTYLE_INVALID))
497                {
498                        html += "<"; if (!(style & GENSTYLE_INVALID)) html += "/"; html += "u>";
499                }
500                if ((style & GENSTYLE_BOLD) != (prevstyle & GENSTYLE_BOLD))
501                {
502                        html += "<"; if (!(style & GENSTYLE_BOLD)) html += "/"; html += "b>";
503                }
504                if ((style & GENSTYLE_ITALIC) != (prevstyle & GENSTYLE_ITALIC))
505                {
506                        html += "<"; if (!(style & GENSTYLE_ITALIC)) html += "/"; html += "i>";
507                }
508                if ((i == 0 || (color != prevcolor)))
509                {
510                        sprintf(buf, "<font color=#%02x%02x%02x>", GENGET_R(color), GENGET_G(color), GENGET_B(color)); html += buf;
511                }
512                if (g[i] == '<') html += "&lt;"; else if (g[i] == '>') html += "&gt;"; else html += g[i];
513                if ((i % 3) == 0 && g[i] == ' ') html += "\n"; //for readability, insert some newlines into html...
514        }
515        delete[] styletab;
516        html += "</u></b></i></font>";
517        if (shortened) html += " [etc...]";
518        html += "</div>\n";
519        return html;
520}
521
522void GenMan::p_htmlize(ExtValue *args, ExtValue *ret)
523{
524        ret->setString(HTMLize(args->getString().c_str()).c_str());
525}
526
527void GenMan::p_htmlizeshort(ExtValue *args, ExtValue *ret)
528{
529        ret->setString(HTMLizeShort(args->getString().c_str()).c_str());
530}
531
532string GenMan::LaTeXize(const char *g)
533{
534        char buf[50];
535        int len = strlen(g);
536        int chars = 0, lines = 0; //currently not used
537        uint32_t *styletab = new uint32_t[len];
538        getFullStyle(g, styletab);
539        string latex = "\\usepackage{xcolor}\n% Using \\texttt{} may be beneficial for some genetic encodings, but then you may lose bold/italic.\n\\noindent \\sloppy";
540        uint32_t prevstyle, prevcolor, style = 0, color = 0;
541        for (int i = 0; i < len; i++)
542        {
543                if (g[i] == '\r') continue;
544                if (g[i] == '\n') { latex += "\\\\\n"; lines++; continue; }
545                chars++;
546                prevstyle = style;
547                prevcolor = color;
548                style = GENGETSTYLE(styletab[i]);
549                color = GENGETCOLOR(styletab[i]);
550
551                // Unfortunately, LaTeX (as opposed to HTML) uses the same closing tags "}" for color, bold, italic, underline - so they cannot intersect.
552                // Therefore we have to "turn off" everything on every change of style or color, and then "turn on" (to avoid problems with e.g. red-bold-blue-unbold or bold-italic-unbold-unitalic).
553                // This could be optimized by a more complex logic and tracking which color/style section starts and ends within another section.
554
555                if (((style & GENSTYLE_INVALID) != (prevstyle & GENSTYLE_INVALID))
556                        ||
557                        ((style & GENSTYLE_BOLD) != (prevstyle & GENSTYLE_BOLD))
558                        ||
559                        ((style & GENSTYLE_ITALIC) != (prevstyle & GENSTYLE_ITALIC))
560                        ||
561                        ((i == 0 || (color != prevcolor))))
562                {
563                        if (prevstyle & GENSTYLE_INVALID) latex += "}";
564                        if (prevstyle & GENSTYLE_BOLD) latex += "}";
565                        if (prevstyle & GENSTYLE_ITALIC) latex += "}";
566                        if (i != 0) latex += "}"; //for color
567                        if (style & GENSTYLE_INVALID) latex += "\\underline{";
568                        if (style & GENSTYLE_BOLD) latex += "\\textbf{";
569                        if (style & GENSTYLE_ITALIC) latex += "\\textit{";
570                        sprintf(buf, "\\textcolor[rgb]{%.2g,%.2g,%.2g}{", GENGET_R(color) / 255.0, GENGET_G(color) / 255.0, GENGET_B(color) / 255.0); latex += buf;
571                }
572                if (g[i] == '<') latex += "$<$"; else if (g[i] == '>') latex += "$>$"; else
573                        if (g[i] == '-') latex += "$-$"; else if (g[i] == '|') latex += "$|$"; else
574                                if (g[i] == '$') latex += "\\$"; else if (g[i] == '%') latex += "\\%"; else latex += g[i];
575                if ((i % 3) == 0 && g[i] == ' ') latex += "\n"; //for readability, insert some newlines into latex...
576                if (i % 10 == 0) latex += "{\\hskip 0pt}"; // https://tex.stackexchange.com/questions/33526/automatic-line-breaking-of-long-lines-of-text
577        }
578        delete[] styletab;
579        latex += "}"; //for color (it was used at least once)
580        if (style & GENSTYLE_INVALID) latex += "}";
581        if (style & GENSTYLE_BOLD) latex += "}";
582        if (style & GENSTYLE_ITALIC) latex += "}";
583        latex += "\n";
584        return latex;
585}
586
587void GenMan::p_latexize(ExtValue *args, ExtValue *ret)
588{
589        ret->setString(LaTeXize(args->getString().c_str()).c_str());
590}
591
592Geno GenMan::getSimplest(const SString& format)
593{
594        GenoOperators *gf = getOper_f(format);
595        if (!gf) return Geno();
596        string info = "The simplest genotype of format f"; info += format.c_str();
597        info += " for operators '"; info += gf->name; info += "'.";
598        return Geno(gf->getSimplest(), format, "Root", info.c_str());
599}
600
601void GenMan::p_getsimplest(ExtValue *args, ExtValue *ret)
602{
603        SString format = GenoObj::formatFromExtValue(args[0]);
604        if (!getOper_f(format))
605                ret->setEmpty();
606        else
607                *ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(getSimplest(format)));
608}
609
610const char *GenMan::getOpName(const SString& format)
611{
612        GenoOperators *gf = getOper_f(format);
613        if (!gf) return "n/a"; else return gf->name.c_str();
614}
615
616GenoOperators* GenMan::getOper_f(const SString& format)
617{
618        int ind = findOperFormatIndex(format);
619        if (ind == -1) return NULL;
620        int which_oper_of_format = seloper[ind];
621        for (unsigned int i = 0; i < oper_fx_list.size(); i++)
622                if (oper_fx_list[i]->supported_format == format)
623                        if (which_oper_of_format == 0) return oper_fx_list[i]; else which_oper_of_format--;
624        return NULL; //should never happen
625}
626
627void GenMan::saveLink(const string parent1, const string parent2, const string child, const float chg)
628{
629        GenoLink l;
630        l.count = count;
631        l.parent1 = parent1;
632        l.parent2 = parent2;
633        l.child = child;
634        l.chg = chg;
635        l.fit = 0; //temporarily. Will be set when the genotype dies
636        //logPrintf("GenMan","saveLink",0,"#%d: [%d] '%s' + '%s' -> '%s'",GenoLinkList.size(),count,parent1.c_str(),parent2.c_str(),child.c_str());
637        GenoLinkList.push_back(l);
638}
639
640void GenMan::onDelGen(void *obj, intptr_t n)
641{
642        //old code needs update:
643        //   ((SpeciesList*)obj)->przyDodaniu(i);
644        /* !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
645           GenMan *gm=(GenMan*)obj;
646           Genotype *gt=(Genotype*)(*listaGen)(n); //there is no more "listaGen"
647           string g=(const char*)gt->genotype.getGene();
648           float fit=gt->getFinalFitness();
649           for(int i=0;i<gm->GenoLinkList.size();i++) //find genotype
650           if (gm->GenoLinkList[i].g1==g) {gm->GenoLinkList[i].fit=fit; break;}
651           */
652}
653
654void GenMan::clearStats()
655{
656        count = 0;
657        valid_m = valid_xo = validated_m = validated_xo = invalid_m = invalid_xo = failed_m = failed_xo = 0;
658        mutchg = xochg = 0;
659        GenoLinkList.clear();
660}
661
662void GenMan::p_clearStats(ExtValue *args, ExtValue *ret) { clearStats(); }
663
664void GenMan::p_report(ExtValue *args, ExtValue *ret)
665{                      //should be updated to handle multiple operators for a single format
666        char *g, *g2;
667        float f1, f2;
668        int m;
669        logMessage("GenMan", "Report", 0, "The following genetic operators are available:");
670        for (unsigned int i = 0; i < oper_fx_list.size(); i++)
671        {
672                string l;
673                if (oper_fx_list[i]->checkValidity("", "") != GENOPER_NOOPER) l += " checkValidity";
674                if (oper_fx_list[i]->getSimplest())
675                {
676                        g = strdup(oper_fx_list[i]->getSimplest());
677                        g2 = strdup(g);
678                        if (oper_fx_list[i]->validate(g, "") != GENOPER_NOOPER) l += " validate";
679                        if (oper_fx_list[i]->mutate(g, f1, m) != GENOPER_NOOPER) l += " mutate";
680                        if (oper_fx_list[i]->crossOver(g, g2, f1, f2) != GENOPER_NOOPER) l += " crossover";
681                        l += " getSimplest";
682                        free(g); free(g2);
683                }
684                //      if (oper_fx_list[i]->similarity("","")!=GENOPER_NOOPER) l+=" similarity";
685                logPrintf("GenMan", "Report", LOG_INFO, "format f%s (%s):%s",
686                        oper_fx_list[i]->supported_format.c_str(), oper_fx_list[i]->name.c_str(), l.c_str());
687        }
688}
689
690void GenMan::p_validate(ExtValue *args, ExtValue *ret)
691{
692        Geno *g = GenoObj::fromObject(args[0]);
693        if (g == NULL)
694                ret->setEmpty();
695        else
696                *ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(validate(*g)));
697}
698
699void GenMan::p_mutate(ExtValue *args, ExtValue *ret)
700{
701        Geno *g = GenoObj::fromObject(args[0]);
702        if (g == NULL)
703                ret->setEmpty();
704        else
705                *ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(mutate(*g)));
706}
707
708void GenMan::p_crossover(ExtValue *args, ExtValue *ret)
709{
710        Geno *g1 = GenoObj::fromObject(args[1]);
711        Geno *g2 = GenoObj::fromObject(args[0]);
712        if (g1 == NULL || g2 == NULL)
713                ret->setEmpty();
714        else
715                *ret = GenoObj::makeDynamicObjectAndDecRef(new Geno(crossOver(*g1, *g2)));
716}
717
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