genomeFile.cpp

   1 /*
   2  *  genomeFile.cpp
   3  *  openc2e
   4  *
   5  *  Created by Alyssa Milburn on Sat 13 Nov 2004.
   6  *  Copyright (c) 2004-2006 Alyssa Milburn. All rights reserved.
   7  *
   8  *  This library is free software; you can redistribute it and/or
   9  *  modify it under the terms of the GNU Lesser General Public
  10  *  License as published by the Free Software Foundation; either
  11  *  version 2 of the License, or (at your option) any later version.
  12  *
  13  *  This library is distributed in the hope that it will be useful,
  14  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
  15  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  16  *  Lesser General Public License for more details.
  17  *
  18  */
  19 #include "genome.h"
  20 #include "streamutils.h"
  21 #include <typeinfo>
  22 #include <exception>
  23 #include <iostream>
  24
  25 geneNote *genomeFile::findNote(uint8 type, uint8 subtype, uint8 which) {
  26         for (vector<gene *>::iterator x = genes.begin(); x != genes.end(); x++) {
  27                 gene *t = *x;
  28                         if ((uint8)t->type() == type)
  29                                 if ((uint8)t->subtype() == subtype)
  30                                         if ((uint8)t->note.which == which)
  31                                                 return &t->note;
  32
  33         if (typeid(*t) == typeid(organGene))
  34                 for (vector<gene *>::iterator y = ((organGene *)t)->genes.begin(); y != ((organGene *)t)->genes.end(); y++) {
  35                         gene *s = *y;
  36                                 if ((uint8)s->type() == type)
  37                                 if ((uint8)s->subtype() == subtype)
  38                                         if ((uint8)s->note.which == which)
  39                                                 return &s->note;
  40                 }
  41         }
  42
  43         return 0;
  44 }
  45
  46 void genomeFile::readNotes(istream &s) {
  47         if (cversion == 3) {
  48                 uint16 gnover = read16(s);
  49                 uint16 nosvnotes = read16(s);
  50                 std::cout << "we have " << nosvnotes << " notes" << std::endl;
  51
  52                 for (int i = 0; i < nosvnotes; i++) {
  53                         uint16 type = read16(s);
  54                         uint16 subtype = read16(s);
  55                         uint16 which = read16(s);
  56                         uint16 rule = read16(s);
  57
  58                         // TODO: we currently skip all the notes (note that there are 18 and then 1!)
  59                         for (int i = 0; i < 19; i++) {
  60                                 uint16 skip = read16(s);
  61                                 uint8 *dummy = new uint8[skip]; s.read((char *)dummy, skip); delete[] dummy;
  62                         }
  63                         }
  64
  65                 uint16 ver = 0;
  66
  67                 while (ver != 0x02) {
  68                         if (s.fail() || s.eof()) throw genomeException("c3 gno loading broke ... second magic not present");
  69                         ver = read16(s);
  70                 }
  71         }
  72
  73         uint16 noentries = read16(s);
  74
  75         for (int i = 0; i < noentries; i++) {
  76                 uint16 type = read16(s);
  77                 uint16 subtype = read16(s);
  78                 uint32 which = read32(s);
  79
  80                 geneNote *n = findNote(type, subtype, which);
  81
  82                 uint16 buflen = read16(s);
  83                 char *buffer = new char[buflen + 1];
  84                 s.read(buffer, buflen); buffer[buflen] = 0;
  85                 if (n != 0) n->description = buffer;
  86                 buflen = read16(s);
  87                 delete[] buffer; buffer = new char[buflen + 1];
  88                 s.read(buffer, buflen); buffer[buflen] = 0;
  89                 if (n != 0) n->comments = buffer;
  90                 delete[] buffer;
  91         }
  92 }
  93
  94 void genomeFile::writeNotes(ostream &s) const {
  95         // TODO
  96 }
  97
  98 gene *genomeFile::nextGene(istream &s) {
  99         uint8 majic[3];
 100         s.read((char *)majic, 3);
 101         if (strncmp((char *)majic, "gen", 3) != 0) throw genomeException("bad majic for a gene");
 102
 103         s >> majic[0];
 104         if (majic[0] == 'd') return 0;
 105         if (majic[0] != 'e')
 106                 throw genomeException("bad majic at stage2 for a gene");
 107
 108         uint8 type, subtype;
 109         s >> type >> subtype;
 110
 111         gene *g = 0;
 112
 113         // the switch statement of doom... is there a better way to do this?
 114         switch (type) {
 115                 case 0:
 116                         switch (subtype) {
 117                                 case 0:
 118                                         switch (cversion) {
 119                                                 case 1: g = new oldBrainLobeGene(cversion); break;
 120                                                 case 2: g = new oldBrainLobeGene(cversion); break;
 121                                                 case 3: g = new c2eBrainLobeGene(cversion); break;
 122                                                 default: g = 0; break;
 123                                         } break;
 124                                 case 1: g = new organGene(cversion, true); break;
 125                                 case 2: g = new c2eBrainTractGene(cversion); break;
 126                         } break;
 127                 case 1:
 128                         switch (subtype) {
 129                                 case 0: g = new bioReceptorGene(cversion); break;
 130                                 case 1: g = new bioEmitterGene(cversion); break;
 131                                 case 2: g = new bioReactionGene(cversion); break;
 132                                 case 3: g = new bioHalfLivesGene(cversion); break;
 133                                 case 4: g = new bioInitialConcentrationGene(cversion); break;
 134                                 case 5: g = new bioNeuroEmitterGene(cversion); break;
 135                         } break;
 136                 case 2:
 137                         switch (subtype) {
 138                                 case 0: g = new creatureStimulusGene(cversion); break;
 139                                 case 1: g = new creatureGenusGene(cversion); break;
 140                                 case 2: g = new creatureAppearanceGene(cversion); break;
 141                                 case 3: g = new creaturePoseGene(cversion); break;
 142                                 case 4: g = new creatureGaitGene(cversion); break;
 143                                 case 5: g = new creatureInstinctGene(cversion); break;
 144                                 case 6: g = new creaturePigmentGene(cversion); break;
 145                                 case 7: g = new creaturePigmentBleedGene(cversion); break;
 146                                 case 8: g = new creatureFacialExpressionGene(cversion); break;
 147                         } break;
 148                 case 3:
 149                         switch (subtype) {
 150                                 case 0: g = new organGene(cversion, false); break;
 151                         } break;
 152         }
 153
 154         if (g == 0) throw genomeException("genefactory failed");
 155
 156         if (((typeid(*g) == typeid(bioReactionGene))
 157                 || (typeid(*g) == typeid(bioEmitterGene)))
 158                 || (typeid(*g) == typeid(bioReceptorGene))) {
 159                 if (currorgan == 0) {
 160                                 if (cversion == 1) genes.push_back(g); // Creatures 1 doesn't have organs
 161                                 else throw genomeException("reaction/emitter/receptor without an attached organ");
 162                 } else currorgan->genes.push_back(g);
 163         } else {
 164                 genes.push_back(g);
 165                 if (typeid(*g) == typeid(organGene))
 166                         if (!((organGene *)g)->isBrain())
 167                                 currorgan = (organGene *)g;
 168         }
 169
 170         s >> *g;
 171
 172         return g;
 173 }
 174
 175 istream &operator >> (istream &s, genomeFile &f) {
 176         char majic[3]; s.read(majic, 3);
 177         if (strncmp((char *)majic, "gen", 3) == 0) {
 178                 s >> majic[0];
 179                 if (majic[0] == 'e') f.cversion = 1;
 180                 else throw genomeException("bad majic for genome");
 181
 182                 s.seekg(0, std::ios::beg);
 183         } else {
 184                 if (strncmp((char *)majic, "dna", 3) != 0) throw genomeException("bad majic for genome");
 185
 186                 s >> majic[0];
 187                 f.cversion = majic[0] - 48; // 48 = ASCII '0'
 188                 if ((f.cversion < 1) || (f.cversion > 3)) throw genomeException("unsupported genome version in majic");
 189         }
 190
 191         //std::cout << "creaturesGenomeFile: reading genome of version " << (unsigned int)f.cversion << ".\n";
 192         f.currorgan = 0;
 193         while (f.nextGene(s) != 0);
 194         f.currorgan = 0;
 195         //std::cout << "creaturesGenomeFile: read " << (unsigned int)f.genes.size() << " top-level genes.\n";
 196
 197         return s;
 198 }
 199
 200 ostream &operator << (ostream &s, const genomeFile &f) {
 201         s << "dna" << char(f.cversion + 48); // 48 = ASCII '0'
 202
 203         // iterate through genes
 204         for (vector<gene *>::iterator x = ((genomeFile &)f).genes.begin(); x != ((genomeFile &)f).genes.end(); x++)
 205                 s << **x;
 206
 207         s << "gend";
 208
 209         return s;
 210 }
 211
 212 gene *genomeFile::getGene(uint8 type, uint8 subtype, unsigned int seq) {
 213         unsigned int c = 0;
 214         for (vector<gene *>::iterator i = genes.begin(); i != genes.end(); i++) {
 215                 if ((*i)->type() == type)
 216                         if ((*i)->subtype() == subtype) {
 217                                 c++;
 218                                 if (seq == c) return *i;
 219                         }
 220         }
 221
 222         return 0;
 223 }
 224
 225 uint8 geneFlags::operator () () const {
 226         return ((_mutable?1:0) + (dupable?2:0) + (delable?4:0) + (maleonly?8:0) +
 227                 (femaleonly?16:0) + (notexpressed?32:0) + (reserved1?64:0) + (reserved2?128:0));
 228 }
 229
 230 void geneFlags::operator () (uint8 f) {
 231         _mutable = ((f & 1) != 0);
 232         dupable = ((f & 2) != 0);
 233         delable = ((f & 4) != 0);
 234         maleonly = ((f & 8) != 0);
 235         femaleonly = ((f & 16) != 0);
 236         notexpressed = ((f & 32) != 0);
 237         reserved1 = ((f & 64) != 0);
 238         reserved2 = ((f & 128) != 0);
 239 }
 240
 241 ostream &operator << (ostream &s, const gene &g) {
 242         s << "gene" << g.type() << g.subtype();
 243
 244         s << g.note.which << g.header.generation << uint8(g.header.switchontime) << g.header.flags();
 245         if (g.cversion > 1) s << g.header.mutweighting;
 246         if (g.cversion == 3) s << g.header.variant;
 247
 248         g.write(s);
 249
 250         return s;
 251 }
 252
 253 istream &operator >> (istream &s, gene &g) {
 254         uint8 b;
 255         s >> g.note.which >> g.header.generation >> b;
 256         g.header.switchontime = (lifestage)b;
 257         s >> b;
 258         g.header.flags(b);
 259         if (g.cversion > 1) s >> g.header.mutweighting;
 260         if (g.cversion == 3) s >> g.header.variant;
 261
 262         g.read(s);
 263
 264         return s;
 265 }
 266
 267 void bioEmitterGene::write(ostream &s) const {
 268         s << organ << tissue << locus << chemical << threshold << rate << gain;
 269         uint8 flags = (clear?1:0) + (digital?2:0) + (invert?4:0);
 270         s << flags;
 271 }
 272
 273 void bioEmitterGene::read(istream &s) {
 274         s >> organ >> tissue >> locus >> chemical >> threshold >> rate >> gain;
 275         uint8 flags;
 276         s >> flags;
 277         clear = ((flags & 1) != 0);
 278         digital = ((flags & 2) != 0);
 279         invert = ((flags & 4) != 0);
 280 }
 281
 282 void bioHalfLivesGene::write(ostream &s) const {
 283         for (int i = 0; i < 256; i++) {
 284         s << halflives[i];
 285         }
 286 }
 287
 288 void bioHalfLivesGene::read(istream &s) {
 289         for (int i = 0; i < 256; i++) {
 290                 s >> halflives[i];
 291         }
 292 }
 293
 294 void bioInitialConcentrationGene::write(ostream &s) const {
 295         s << chemical << quantity;
 296 }
 297
 298 void bioInitialConcentrationGene::read(istream &s) {
 299         s >> chemical >> quantity;
 300 }
 301
 302 void bioNeuroEmitterGene::write(ostream &s) const {
 303         for (int i = 0; i < 3; i++) {
 304                 s << lobes[i] << neurons[i];
 305         }
 306         s << rate;
 307         for (int i = 0; i < 4; i++) {
 308                 s << chemical[i] << quantity[i];
 309         }
 310 }
 311
 312 void bioNeuroEmitterGene::read(istream &s) {
 313         for (int i = 0; i < 3; i++) {
 314                 s >> lobes[i] >> neurons[i];
 315         }
 316         s >> rate;
 317         for (int i = 0; i < 4; i++) {
 318                 s >> chemical[i] >> quantity[i];
 319         }
 320 }
 321
 322 void bioReactionGene::write(ostream &s) const {
 323         for (int i = 0; i < 4; i++) {
 324                 s << quantity[i];
 325                 s << reactant[i];
 326         }
 327
 328         s << rate;
 329 }
 330
 331 void bioReactionGene::read(istream &s) {
 332         for (int i = 0; i < 4; i++) {
 333                 s >> quantity[i];
 334                 s >> reactant[i];
 335         }
 336
 337         s >> rate;
 338 }
 339
 340 void bioReceptorGene::write(ostream &s) const {
 341         s << organ << tissue << locus << chemical << threshold << nominal << gain;
 342         uint8 flags = (inverted?1:0) + (digital?2:0);
 343         s << flags;
 344 }
 345
 346 void bioReceptorGene::read(istream &s) {
 347         s >> organ >> tissue >> locus >> chemical >> threshold >> nominal >> gain;
 348         uint8 flags;
 349         s >> flags;
 350         inverted = ((flags & 1) != 0);
 351         digital = ((flags & 2) != 0);
 352 }
 353
 354 void c2eBrainLobeGene::write(ostream &s) const {
 355         for (int i = 0; i < 4; i++) s << id[i];
 356
 357         write16(s, updatetime, false);
 358         write16(s, x, false);
 359         write16(s, y, false);
 360
 361         s << width << height;
 362         s << red << green << blue;
 363         s << WTA << tissue << initrulealways;
 364
 365         for (int i = 0; i < 7; i++) s << spare[i];
 366         for (int i = 0; i < 48; i++) s << initialiserule[i];
 367         for (int i = 0; i < 48; i++) s << updaterule[i];
 368 }
 369
 370 void c2eBrainLobeGene::read(istream &s) {
 371         for (int i = 0; i < 4; i++) s >> id[i];
 372
 373         updatetime = read16(s, false);
 374         x = read16(s, false);
 375         y = read16(s, false);
 376
 377         s >> width >> height;
 378         s >> red >> green >> blue;
 379         s >> WTA >> tissue >> initrulealways;
 380
 381         for (int i = 0; i < 7; i++) s >> spare[i];
 382         for (int i = 0; i < 48; i++) s >> initialiserule[i];
 383         for (int i = 0; i < 48; i++) s >> updaterule[i];
 384 }
 385
 386 void c2eBrainTractGene::write(ostream &s) const {
 387         write16(s, updatetime, false);
 388         for (int i = 0; i < 4; i++) s << srclobe[i];
 389         write16(s, srclobe_lowerbound, false);
 390         write16(s, srclobe_upperbound, false);
 391         write16(s, src_noconnections, false);
 392         for (int i = 0; i < 4; i++) s << destlobe[i];
 393         write16(s, destlobe_lowerbound, false);
 394         write16(s, destlobe_upperbound, false);
 395         write16(s, dest_noconnections, false);
 396         s << migrates << norandomconnections << srcvar << destvar << initrulealways;
 397         for (int i = 0; i < 5; i++) s << spare[i];
 398         for (int i = 0; i < 48; i++) s << initialiserule[i];
 399         for (int i = 0; i < 48; i++) s << updaterule[i];
 400 }
 401
 402 void c2eBrainTractGene::read(istream &s) {
 403         updatetime = read16(s, false);
 404         for (int i = 0; i < 4; i++) s >> srclobe[i];
 405         srclobe_lowerbound = read16(s, false);
 406         srclobe_upperbound = read16(s, false);
 407         src_noconnections = read16(s, false);
 408         for (int i = 0; i < 4; i++) s >> destlobe[i];
 409         destlobe_lowerbound = read16(s, false);
 410         destlobe_upperbound = read16(s, false);
 411         dest_noconnections = read16(s, false);
 412         s >> migrates >> norandomconnections >> srcvar >> destvar >> initrulealways;
 413         for (int i = 0; i < 5; i++) s >> spare[i];
 414         for (int i = 0; i < 48; i++) s >> initialiserule[i];
 415         for (int i = 0; i < 48; i++) s >> updaterule[i];
 416 }
 417
 418 void creatureAppearanceGene::write(ostream &s) const {
 419         s << part << variant;
 420         if (cversion > 1) s << species;
 421 }
 422
 423 void creatureAppearanceGene::read(istream &s) {
 424         s >> part >> variant;
 425         if (cversion > 1) s >> species;
 426 }
 427
 428 void creatureFacialExpressionGene::write(ostream &s) const {
 429         write16(s, expressionno);
 430         s << weight;
 431
 432         for (int i = 0; i < 4; i++) {
 433                 s << drives[i] << amounts[i];
 434         }
 435 }
 436
 437 void creatureFacialExpressionGene::read(istream &s) {
 438         expressionno = read16(s);
 439         s >> weight;
 440
 441         for (int i = 0; i < 4; i++) {
 442                 s >> drives[i] >> amounts[i];
 443         }
 444 }
 445
 446 void creatureGaitGene::write(ostream &s) const {
 447         s << drive;
 448
 449         for (int i = 0; i < gaitLength(); i++) {
 450                 s << pose[i];
 451         }
 452 }
 453
 454 void creatureGaitGene::read(istream &s) {
 455         s >> drive;
 456
 457         for (int i = 0; i < gaitLength(); i++) {
 458                 s >> pose[i];
 459         }
 460 }
 461
 462 void creatureGenusGene::write(ostream &s) const {
 463         s << genus;
 464
 465         const char *b;
 466
 467         // TODO: we read past the end of the returned buffer here!
 468         b = mum.c_str();
 469         for (int i = 0; i < ((cversion == 3) ? 32 : 4); i++) s << b[i];
 470         b = dad.c_str();
 471         for (int i = 0; i < ((cversion == 3) ? 32 : 4); i++) s << b[i];
 472 }
 473
 474 void creatureGenusGene::read(istream &s) {
 475         s >> genus;
 476
 477         char buf[33];
 478         unsigned int len = ((cversion == 3) ? 32 : 4);
 479
 480         s.read(buf, len);
 481         buf[len] = 0;
 482         mum = (char *)buf;
 483
 484         s.read(buf, len);
 485         buf[len] = 0;
 486         dad = (char *)buf;
 487 }
 488
 489 void creatureInstinctGene::write(ostream &s) const {
 490         for (int i = 0; i < 3; i++) {
 491                 s << lobes[i] << neurons[i];
 492         }
 493
 494         s << action;
 495         s << drive;
 496         s << level;
 497 }
 498
 499 void creatureInstinctGene::read(istream &s) {
 500         for (int i = 0; i < 3; i++) {
 501                 s >> lobes[i] >> neurons[i];
 502         }
 503
 504         s >> action;
 505         s >> drive;
 506         s >> level;
 507 }
 508
 509 void creaturePigmentGene::write(ostream &s) const {
 510         s << color << amount;
 511 }
 512
 513 void creaturePigmentGene::read(istream &s) {
 514         s >> color >> amount;
 515 }
 516
 517 void creaturePigmentBleedGene::write(ostream &s) const {
 518         s << rotation << swap;
 519 }
 520
 521 void creaturePigmentBleedGene::read(istream &s) {
 522         s >> rotation >> swap;
 523 }
 524
 525 void creaturePoseGene::write(ostream &s) const {
 526         s << poseno;
 527
 528         for (int i = 0; i < poseLength(); i++) {
 529                 s << pose[i];
 530         }
 531 }
 532
 533 void creaturePoseGene::read(istream &s) {
 534         s >> poseno;
 535
 536         for (int i = 0; i < poseLength(); i++) {
 537                 s >> pose[i];
 538         }
 539 }
 540
 541 void creatureStimulusGene::write(ostream &s) const {
 542         s << stim << significance << sensoryneuron << intensity;
 543         uint8 flags = (modulate?1:0) + (addoffset?2:0) + (whenasleep?4:0);
 544         if (silent[0]) flags += 16;
 545         if (silent[1]) flags += 32;
 546         if (silent[2]) flags += 64;
 547         if (silent[3]) flags += 128;
 548         s << flags;
 549
 550         for (int i = 0; i < 4; i++) {
 551                 s << drives[i] << amounts[i];
 552         }
 553 }
 554
 555 void creatureStimulusGene::read(istream &s) {
 556         s >> stim >> significance >> sensoryneuron >> intensity;
 557         uint8 flags;
 558         s >> flags;
 559         modulate = ((flags & 1) != 0);
 560         addoffset = ((flags & 2) != 0);
 561         whenasleep = ((flags & 4) != 0);
 562
 563         for (int i = 0; i < 4; i++) {
 564                 s >> drives[i] >> amounts[i];
 565         }
 566
 567         silent[0] = ((flags & 16) != 0);
 568         silent[1] = ((flags & 32) != 0);
 569         silent[2] = ((flags & 64) != 0);
 570         silent[3] = ((flags & 128) != 0);
 571 }
 572
 573 void oldBrainLobeGene::write(ostream &s) const {
 574         s << x << y << width << height << perceptflag << nominalthreshold << leakagerate << reststate << inputgain;
 575         s.write((char *)staterule, (cversion == 1) ? 8 : 12);
 576         s << flags;
 577
 578         s << dendrite1 << dendrite2;
 579 }
 580
 581 void oldBrainLobeGene::read(istream &s) {
 582         s >> x >> y >> width >> height >> perceptflag >> nominalthreshold >> leakagerate >> reststate >> inputgain;
 583         s.read((char *)staterule, (cversion == 1) ? 8 : 12);
 584         s >> flags;
 585
 586         s >> dendrite1 >> dendrite2;
 587 }
 588
 589 void organGene::write(ostream &s) const {
 590         s << clockrate << damagerate << lifeforce << biotickstart << atpdamagecoefficient;
 591
 592         // iterate through children
 593         for (vector<gene *>::iterator x = ((organGene *)this)->genes.begin(); x != ((organGene *)this)->genes.end(); x++)
 594                 s << **x;
 595 }
 596
 597 void organGene::read(istream &s) {
 598         s >> clockrate >> damagerate >> lifeforce >> biotickstart >> atpdamagecoefficient;
 599 }
 600
 601 ostream &operator << (ostream &s, const oldDendriteInfo &i) {
 602         s << i.srclobe << i.min << i.max << i.spread << i.fanout << i.minLTW << i.maxLTW;
 603         s << i.minstr << i.maxstr << i.migrateflag << i.relaxsuscept << i.relaxSTW << i.LTWgainrate;
 604
 605         s << i.strgain;
 606         s.write((char *)i.strgainrule, (i.cversion == 1) ? 8 : 12);
 607         s << i.strloss;
 608         s.write((char *)i.strlossrule, (i.cversion == 1) ? 8 : 12);
 609         s.write((char *)i.susceptrule, (i.cversion == 1) ? 8 : 12);
 610         s.write((char *)i.relaxrule, (i.cversion == 1) ? 8 : 12);
 611
 612         if (i.cversion == 2) {
 613                 s.write((char *)i.backproprule, 12);
 614                 s.write((char *)i.forproprule, 12);
 615         }
 616
 617         return s;
 618 }
 619
 620 istream &operator >> (istream &s, oldDendriteInfo &i) {
 621         s >> i.srclobe >> i.min >> i.max >> i.spread >> i.fanout >> i.minLTW >> i.maxLTW;
 622         s >> i.minstr >> i.maxstr >> i.migrateflag >> i.relaxsuscept >> i.relaxSTW >> i.LTWgainrate;
 623
 624         s >> i.strgain;
 625         s.read((char *)i.strgainrule, (i.cversion == 1) ? 8 : 12);
 626         s >> i.strloss;
 627         s.read((char *)i.strlossrule, (i.cversion == 1) ? 8 : 12);
 628         s.read((char *)i.susceptrule, (i.cversion == 1) ? 8 : 12);
 629         s.read((char *)i.relaxrule, (i.cversion == 1) ? 8 : 12);
 630
 631         if (i.cversion == 2) {
 632                 s.read((char *)i.backproprule, 12);
 633                 s.read((char *)i.forproprule, 12);
 634         }
 635
 636         return s;
 637 }
 638
 639 /* vim: set noet: */