// This file is a part of Framsticks SDK. http://www.framsticks.com/ // Copyright (C) 1999-2018 Maciej Komosinski and Szymon Ulatowski. // See LICENSE.txt for details. #include #include #include #include "fB_conv.h" #include "fB_general.h" #include "fB_oper.h" #include "../fH/fH_oper.h" #define FIELDSTRUCT Geno_fB static ParamEntry GENOfBparam_tab[] = { { "Genetics: fB", 3, FB_MUT_COUNT + FB_XOVER_COUNT, }, { "Genetics: fB: Mutation", }, { "Genetics: fB: Crossover", }, { "fB_mut_substitution", 1, 0, "Substitution", "f 0 1 0.6", FIELD(mutationprobs[FB_SUBSTITUTION]), "Probability of mutation by changing single random letter in genotype", }, { "fB_mut_insertion", 1, 0, "Insertion", "f 0 1 0.095", FIELD(mutationprobs[FB_INSERTION]), "Probability of mutation by inserting characters in random place of genotype", }, { "fB_mut_nclassins", 1, 0, "Insertion of neuron class definition", "f 0 1 0.005", FIELD(mutationprobs[FB_NCLASSINS]), "Probability of mutation by inserting neuron class definition in random place of genotype", }, { "fB_mut_deletion", 1, 0, "Deletion", "f 0 1 0.1", FIELD(mutationprobs[FB_DELETION]), "Probability of mutation by deleting random characters in genotype", }, { "fB_mut_duplication", 1, 0, "Duplication", "f 0 1 0.0", FIELD(mutationprobs[FB_DUPLICATION]), "Probability of mutation by copying single *gene* of genotype and appending it to the beginning of this genotype", }, { "fB_mut_translocation", 1, 0, "Translocation", "f 0 1 0.15", FIELD(mutationprobs[FB_TRANSLOCATION]), "Probability of mutation by replacing two substrings in genotype", }, { "fB_cross_gene_transfer", 2, 0, "Horizontal gene transfer", "f 0 1 0.0", FIELD(crossoverprobs[FB_GENE_TRANSFER]), "Probability of crossing over by transferring single genes from both parents to beginning of each other", }, { "fB_cross_crossover", 2, 0, "Crossing over", "f 0 1 1.0", FIELD(crossoverprobs[FB_CROSSING_OVER]), "Probability of crossing over by random distribution of genes from both parents to both children", }, { 0, }, }; #undef FIELDSTRUCT Geno_fB::Geno_fB() { par.setParamTab(GENOfBparam_tab); par.select(this); par.setDefault(); supported_format = 'B'; } bool Geno_fB::hasStick(SString genotype) { for (int i = 0; i < fB_GenoHelpers::geneCount(genotype); i++) { int start, end; SString gene = fB_GenoHelpers::getGene(i, genotype, start, end); int endoffset = 0; if (gene.indexOf("zz", 0) != -1) endoffset = 2; if (gene.len() - endoffset < 3) { return true; // genes with length < 3 are always sticks } else if (gene[2] >= 'a' && gene[2] <= 'i') { return true; // gene within this range is stick } } return false; } int Geno_fB::checkValidity(const char *geno, const char *genoname) { // load genotype SString genotype(geno); SString line; int pos = 0; // if there is no genotype to load, then return error if (!genotype.getNextToken(pos, line, '\n')) { return pos + 1; } // extract dimensions int dims = 0; if (!ExtValue::parseInt(line.c_str(), dims, true, false)) { return 1; } // extract next token in order to check if next line starts with "aa" int genstart = genotype.indexOf("aa", 0); if (genstart != pos) { return pos + 1; } // check if rest of characters are lowercase for (int i = genstart; i < genotype.len(); i++) { if (!islower(genotype[i])) { if (genotype[i] == '"') { SString neuclassdef; int nextid = i + 1; if (!genotype.getNextToken(nextid, neuclassdef, '"')) { return i + 1; } Neuro *neu = new Neuro(); neu->setDetails(neuclassdef); bool isclass = neu->getClass() ? true : false; delete neu; if (!isclass) { return i + 1; } i = nextid; } else { return i + 1; } } } if (!hasStick(genotype)) { return 1; } return GENOPER_OK; } int Geno_fB::validate(char *&geno, const char *genoname) { // load genotype SString genotype(geno); SString strdims; int pos = 0; if (!genotype.getNextToken(pos, strdims, '\n')) { return GENOPER_OPFAIL; } // parse dimension int dims = 0; if (!ExtValue::parseInt(strdims.c_str(), dims, true, false)) { return GENOPER_OPFAIL; } SString line; bool fix = false; int genstart = genotype.indexOf("aa", 0); // if there is no "aa" codon in the beginning of a genotype, then add it if (genstart != pos) { genotype = strdims + "\naa" + genotype.substr(pos); fix = true; } for (int i = pos; i < genotype.len(); i++) { // if character is not alphabetic - error if (!isalpha(genotype[i])) { if (genotype[i] == '"') { SString neuclassdef; int nextid = i + 1; if (!genotype.getNextToken(nextid, neuclassdef, '"')) { return i + 1; } Neuro *neu = new Neuro(); neu->setDetails(neuclassdef); bool isclass = neu->getClass() ? true : false; delete neu; if (!isclass) { return i + 1; } i = nextid; } else { return GENOPER_OPFAIL; } } // if character is uppercase, then convert it to lowercase else if (isupper(genotype[i])) { genotype.directWrite()[i] = tolower(genotype[i]); fix = true; } } // if the genotype does not contain any stick - add it if (!hasStick(genotype)) { genotype = SString("aaazz") + genotype; } // if there were any changes - save them if (fix) { free(geno); geno = strdup(genotype.c_str()); } return GENOPER_OK; } SString Geno_fB::detokenizeSequence(std::list tokenlist) { SString res = ""; for (std::list::iterator it = tokenlist.begin(); it != tokenlist.end(); it++) { res += (*it); } return res; } std::list Geno_fB::tokenizeSequence(SString genotype) { std::list res; int i = 0; while (i < genotype.len()) { // if character is not alphabetic - error if (isalpha(genotype[i])) { SString el = ""; el += genotype[i]; res.push_back(el); i++; } else { SString neuclassdef; i++; genotype.getNextToken(i, neuclassdef, '"'); SString ndef = "\""; ndef += neuclassdef; ndef += "\""; res.push_back(ndef); } } return res; } int Geno_fB::mutate(char *&geno, float &chg, int &method) { SString genotype(geno); SString strdims; int pos = 0; genotype.getNextToken(pos, strdims, '\n'); SString line; genotype.getNextToken(pos, line, '\n'); method = roulette(mutationprobs, FB_MUT_COUNT); switch (method) { case FB_SUBSTITUTION: { std::list tokenized = tokenizeSequence(line); int rndid = randomN(tokenized.size()); // select random letter from genotype // increment/decrement character - when overflow happens, this method // uses reflect method std::list::iterator it = tokenized.begin(); std::advance(it, rndid); SString t = (*it); if ((*it).len() == 1) { if (randomN(2) == 0) { if ((*it)[0] == 'a') (*it).directWrite()[0] = 'b'; else (*it).directWrite()[0] = (*it)[0] - 1; } else { if ((*it)[0] == 'z') (*it).directWrite()[0] = 'y'; else (*it).directWrite()[0] = (*it)[0] + 1; } chg = 1.0 / line.len(); } else { // first method needs to extract quotes SString def = (*it); def = def.substr(1, def.len() - 2); Geno_fH::mutateNeuronProperties(def); SString res = "\""; res += def; res += "\""; (*it) = res; chg = (double)def.len() / line.len(); } line = detokenizeSequence(tokenized); break; } case FB_NCLASSINS: { std::list tokenized = tokenizeSequence(line); std::list::iterator it = tokenized.begin(); int rndid = randomN(tokenized.size()); // select random insertion point std::advance(it, rndid); NeuroClass *cls = getRandomNeuroClass(); if (cls) { SString classdef = cls->getName(); Geno_fH::mutateNeuronProperties(classdef); SString res = "\""; res += classdef; res += "\""; tokenized.insert(it, res); chg = (double)classdef.len() / line.len(); line = detokenizeSequence(tokenized); break; } } /* no break */ case FB_INSERTION: { chg = 1.0 / line.len(); std::list tokenized = tokenizeSequence(line); int rndid = randomN(tokenized.size()); // select random insertion point std::list::iterator it = tokenized.begin(); std::advance(it, rndid); SString letter = "a"; letter.directWrite()[0] = 'a' + randomN(26); tokenized.insert(it, letter); line = detokenizeSequence(tokenized); break; } case FB_DELETION: { chg = 1.0 / line.len(); std::list tokenized = tokenizeSequence(line); std::list::iterator it = tokenized.begin(); int rndid = randomN(tokenized.size()); // select random deletion point std::advance(it, rndid); tokenized.erase(it); line = detokenizeSequence(tokenized); break; } case FB_DUPLICATION: { int rndgene = randomN(fB_GenoHelpers::geneCount(line)); int start, end; SString gene = fB_GenoHelpers::getGene(rndgene, line, start, end); if (gene.indexOf("zz", 0) == -1) gene += "zz"; chg = (float)gene.len() / line.len(); line = gene + line; break; } case FB_TRANSLOCATION: { std::list tokenized = tokenizeSequence(line); std::vector cuts(4); for (int i = 0; i < 4; i++) { cuts[i] = randomN(tokenized.size()); } std::sort(cuts.begin(), cuts.end()); std::vector::iterator> iters(4); for (int i = 0; i < 4; i++) { iters[i] = tokenized.begin(); std::advance(iters[i], cuts[i]); } std::list res; res.insert(res.end(), tokenized.begin(), iters[0]); res.insert(res.end(), iters[2], iters[3]); res.insert(res.end(), iters[1], iters[2]); res.insert(res.end(), iters[0], iters[1]); res.insert(res.end(), iters[3], tokenized.end()); // SString first = line.substr(cuts[0], cuts[1] - cuts[0]); // SString second = line.substr(cuts[2], cuts[3] - cuts[2]); // SString result = line.substr(0, cuts[0]) + second + // line.substr(cuts[1], cuts[2] - cuts[1]) + first + line.substr(cuts[3]); line = detokenizeSequence(res); chg = (float)(cuts[3] - cuts[2] + cuts[1] - cuts[0]) / line.len(); break; } } SString result = strdims + "\n" + line; free(geno); geno = strdup(result.c_str()); return GENOPER_OK; } int Geno_fB::crossOver(char *&g1, char *&g2, float& chg1, float& chg2) { SString p1(g1); SString p2(g2); int dims1 = 0, dims2 = 0; int pos = 0; SString strdims; p1.getNextToken(pos, strdims, '\n'); ExtValue::parseInt(strdims.c_str(), dims1, true, false); SString parent1; p1.getNextToken(pos, parent1, '\n'); pos = 0; p2.getNextToken(pos, strdims, '\n'); ExtValue::parseInt(strdims.c_str(), dims2, true, false); if (dims1 != dims2) { return GENOPER_OPFAIL; } SString parent2; p2.getNextToken(pos, parent2, '\n'); SString child1 = ""; SString child2 = ""; switch (roulette(crossoverprobs, FB_XOVER_COUNT)) { case FB_GENE_TRANSFER: { // get random gene from first parent int choice = randomN(fB_GenoHelpers::geneCount(parent1)); int start, end; SString gene = fB_GenoHelpers::getGene(choice, parent1, start, end); // add this gene to the beginning of the second parent genotype child2 = gene + parent2; chg2 = (float)parent2.len() / (float)child2.len(); // do the same for second parent choice = randomN(fB_GenoHelpers::geneCount(parent2)); gene = fB_GenoHelpers::getGene(choice, parent2, start, end); child1 = gene + parent1; chg1 = (float)parent1.len() / (float)child1.len(); break; } // case FB_CROSSING_OVER: // { // // iterate through all genes of the first parent and assign them // // randomly to children // for (int i = 0; i < fB_GenoHelpers::geneCount(parent1); i++) // { // int start, end; // SString gene = fB_GenoHelpers::getGene(i, parent1, start, end); // if (randomN(2) == 0) // { // child1 += gene; // chg1 += 1.0f; // } // else // { // child2 += gene; // } // } // chg1 /= fB_GenoHelpers::geneCount(parent1); // // // do the same with second parent // for (int i = 0; i < fB_GenoHelpers::geneCount(parent2); i++) // { // int start, end; // SString gene = fB_GenoHelpers::getGene(i, parent2, start, end); // if (randomN(2) == 0) // { // child1 += gene; // } // else // { // child2 += gene; // chg2 += 1.0f; // } // } // chg2 /= fB_GenoHelpers::geneCount(parent2); // break; // } case FB_CROSSING_OVER: { // get maximal count of genes from both parents int maxgenecount = max(fB_GenoHelpers::geneCountNoNested(parent1), fB_GenoHelpers::geneCountNoNested(parent2)); // while there are genes in at least one genotype for (int i = 0; i < maxgenecount; i++) { SString to1 = "", to2 = ""; int start = 0, end = 0; // if both parents have genes available, then distribute them if (i < fB_GenoHelpers::geneCountNoNested(parent1) && i < fB_GenoHelpers::geneCountNoNested(parent2)) { if (randomN(2) == 0) { to1 = fB_GenoHelpers::getNonNestedGene(i, parent1, start, end); to2 = fB_GenoHelpers::getNonNestedGene(i, parent2, start, end); chg1 += 1.0f; chg2 += 1.0f; } else { to1 = fB_GenoHelpers::getNonNestedGene(i, parent2, start, end); to2 = fB_GenoHelpers::getNonNestedGene(i, parent1, start, end); } } else if (i < fB_GenoHelpers::geneCountNoNested(parent1)) { if (randomN(2) == 0) { to1 = fB_GenoHelpers::getNonNestedGene(i, parent1, start, end); chg1 += 1.0f; } else { to2 = fB_GenoHelpers::getNonNestedGene(i, parent1, start, end); } } else // if (i < fB_GenoHelpers::geneCountNoNested(parent2)) { if (randomN(2) == 0) { to1 = fB_GenoHelpers::getNonNestedGene(i, parent2, start, end); } else { to2 = fB_GenoHelpers::getNonNestedGene(i, parent2, start, end); chg2 += 1.0f; } } child1 += to1; child2 += to2; } chg1 /= fB_GenoHelpers::geneCountNoNested(parent1); chg2 /= fB_GenoHelpers::geneCountNoNested(parent2); break; } } free(g1); free(g2); if (child1.len() > 0 && child2.len() == 0) { child1 = strdims + "\n" + child1; g1 = strdup(child1.c_str()); g2 = strdup(""); } else if (child2.len() > 0 && child1.len() == 0) { child2 = strdims + "\n" + child2; g1 = strdup(child2.c_str()); g2 = strdup(""); } else { child1 = strdims + "\n" + child1; child2 = strdims + "\n" + child2; g1 = strdup(child1.c_str()); g2 = strdup(child2.c_str()); } return GENOPER_OK; } uint32_t Geno_fB::style(const char *geno, int pos) { char ch = geno[pos]; if (isdigit(ch)) { while (pos > 0) { pos--; if (isdigit(geno[pos]) == 0) { return GENSTYLE_CS(0, GENSTYLE_INVALID); } } return GENSTYLE_RGBS(0, 0, 200, GENSTYLE_BOLD); } if (islower(ch) == 0) { return GENSTYLE_CS(0, GENSTYLE_INVALID); } uint32_t style = GENSTYLE_CS(GENCOLOR_TEXT, GENSTYLE_NONE); if (ch == 'a' && pos > 0 && (geno[pos - 1] == 'a' || geno[pos - 1] == '\n')) { style = GENSTYLE_RGBS(0, 200, 0, GENSTYLE_BOLD); } else if (ch == 'z' && pos > 0 && geno[pos - 1] == 'z') { style = GENSTYLE_RGBS(200, 0, 0, GENSTYLE_BOLD); } return style; }