Changeset 955 for cpp/frams/genetics

Timestamp:

06/25/20 00:34:29 (4 years ago)

Author:

Maciej Komosinski

Message:

Genetic format ID becomes a string (no longer limited to a single character)

Location:

cpp/frams/genetics

Files:

• f4/f4_general.cpp (modified) (1 diff)
• genman.cpp (modified) (25 diffs)
• genman.h (modified) (2 diffs)
• geno.cpp (modified) (17 diffs)
• geno.h (modified) (9 diffs)
• genoconv.cpp (modified) (9 diffs)
• genoconv.h (modified) (5 diffs)
• genooperators.cpp (modified) (1 diff)
• genooperators.h (modified) (2 diffs)

cpp/frams/genetics/f4/f4_general.cpp

@@ -1304 +1304 @@
         unsigned int len;
         // build in a SString, with initial size
-        SString out(strlen(buf) + 2000);
-        out = "";
+        SString out;
+        out.reserve(int(strlen(buf)) + 2000);
 
         sprint(out);

cpp/frams/genetics/genman.cpp

@@ -1 +1 @@
 // This file is a part of Framsticks SDK.  http://www.framsticks.com/
-// Copyright (C) 1999-2018  Maciej Komosinski and Szymon Ulatowski.
+// Copyright (C) 1999-2020  Maciej Komosinski and Szymon Ulatowski.
 // See LICENSE.txt for details.
 
@@ -68 +68 @@
 #ifdef USE_GENMAN_fL
 #include "fL/fL_oper.h"
+#endif
+#ifdef USE_GENMAN_fS
+#include "fS/fS_oper.h"
 #endif
 
@@ -177 +180 @@
         oper_fx_list.push_back(new Geno_fL);
 #endif
+#ifdef USE_GENMAN_fS
+        oper_fx_list.push_back(new GenoOper_fS);
+#endif
 
         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
@@ -182 +188 @@
         for (unsigned int i = 0; i < oper_fx_list.size(); i++)
         {
-                if (operformats.find(oper_fx_list[i]->supported_format) != -1) continue;
+                if (findOperFormatIndex(oper_fx_list[i]->supported_format) != -1) continue;
                 string type = string("~") + oper_fx_list[i]->name;
                 int dup = 0;
@@ -188 +194 @@
                         if (oper_fx_list[i]->supported_format == oper_fx_list[j]->supported_format)
                         {
-                        type += "~";
-                        type += oper_fx_list[j]->name;
-                        dup++;
+                                type += "~";
+                                type += oper_fx_list[j]->name;
+                                dup++;
                         }
                 type = ssprintf("d 0 %d ", dup) + type;
-                string id = ssprintf("genoper_f%c", oper_fx_list[i]->supported_format);
-                string name = ssprintf("Operators for f%c", oper_fx_list[i]->supported_format);
+                string id = ssprintf("genoper_f%s", oper_fx_list[i]->supported_format.c_str());
+                string name = ssprintf("Operators for f%s", oper_fx_list[i]->supported_format.c_str());
                 seloper[selopercount] = 0;
-                operformats += oper_fx_list[i]->supported_format;
+                operformats += &oper_fx_list[i]->supported_format;
                 //printf("%x %s %s %s\n",&seloper[selopercount],(const char*)id,(const char*)type,(const char*)name);
-                seloperpar.addProperty(&seloper[selopercount++], id.c_str(), type.c_str(), name.c_str(), "", PARAM_READONLY*(dup == 0));
+                seloperpar.addProperty(&seloper[selopercount++], id.c_str(), type.c_str(), name.c_str(), "", PARAM_READONLY * (dup == 0));
         }
 
@@ -214 +220 @@
         for (unsigned int i = 0; i < oper_fx_list.size(); i++) delete oper_fx_list[i];
         delete[] seloper;
+}
+
+int GenMan::findOperFormatIndex(const SString& format)
+{
+        for (int i = 0; i < operformats.size(); i++)
+                if (*operformats(i) == format)
+                        return i;
+        return -1;
 }
 
@@ -265 +279 @@
 Geno GenMan::validate(const Geno& geny)
 {
-        char format = geny.getFormat();
+        SString format = geny.getFormat();
         GenoOperators *gf = getOper_f(format);
         if (gf == NULL)
-                return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: Validate(): don't know how to handle genetic format %c", format));
+                return Geno("", Geno::INVALID_FORMAT, "", SString::sprintf("GENOPER_NOOPER: Validate(): don't know how to handle genetic format %s", format.c_str()));
         char *g2 = strdup(geny.getGenes().c_str()); //copy for validation
         int res = gf->validate(g2, geny.getName().c_str());
@@ -276 +290 @@
                 return Geno(sg2, format, geny.getName(), geny.getComment());
         else
-                return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: validate() for format %c returned invalid value", format));
+                return Geno("", Geno::INVALID_FORMAT, "", SString::sprintf("GENOPER_NOOPER: validate() for format %s returned invalid value", format.c_str()));
 }
 
@@ -283 +297 @@
         float chg; //how many changes
         int method; //mutation method
-        char format = g.getFormat();
+        SString format = g.getFormat();
         GenoOperators *gf = getOper_f(format);
         if (gf == NULL)
-                return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: Mutate(): don't know how to handle genetic format %c", format));
+                return Geno("", Geno::INVALID_FORMAT, "", SString::sprintf("GENOPER_NOOPER: Mutate(): don't know how to handle genetic format %s", format.c_str()));
         Geno gv = g;
         bool canvalidate = true;
         if (testValidity(gv, canvalidate) > 0 && canvalidate == false)
-                return Geno("", -1, "", "GENOPER_OPFAIL: Mutate(): cannot validate invalid source genotype");
+                return Geno("", Geno::INVALID_FORMAT, "", "GENOPER_OPFAIL: Mutate(): cannot validate invalid source genotype");
         bool ok = false;
         int pcount = count;
@@ -307 +321 @@
                                 if (res > 0 && canvalidate == false) invalid_m++; else
                                 {
-                                validated_m++; ok = true;
+                                        validated_m++; ok = true;
                                 }
                         if (ok) gv = G;
@@ -316 +330 @@
                 if (!ok && (count - pcount > GENMAN_REPEAT_FAILED))
                 {
-                        logPrintf("GenMan", "Mutate", 2, "Tried " GENMAN_REPEAT_FAILED_STR "x and failed: %s", g.getGenes().c_str());
+                        logPrintf("GenMan", "Mutate", LOG_WARN, "Tried " GENMAN_REPEAT_FAILED_STR "x and failed: %s", g.getGenes().c_str());
                         return Geno("", -1, "", "GENOPER_OPFAIL: Mutate() tried " GENMAN_REPEAT_FAILED_STR "x and failed");
                 }
@@ -332 +346 @@
 Geno GenMan::crossOver(const Geno& g1, const Geno& g2)
 {
-        char format = g1.getFormat();
-        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()));
+        SString format = g1.getFormat();
+        if (format != g2.getFormat()) return Geno("", Geno::INVALID_FORMAT, "", SString::sprintf("GENOPER_NOOPER: CrossOver(): does not work for parents with differing genetic formats (%s and %s)", format.c_str(), g2.getFormat().c_str()));
         GenoOperators *gf = getOper_f(format);
         if (gf == NULL)
-                return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: CrossOver(): no operators found for genetic format %c", format));
+                return Geno("", Geno::INVALID_FORMAT, "", SString::sprintf("GENOPER_NOOPER: CrossOver(): no operators found for genetic format %s", format.c_str()));
         Geno g1v = g1, g2v = g2;
 
@@ -343 +357 @@
                 bool canvalidate = true;
                 if (testValidity(g1v, canvalidate) > 0 && canvalidate == false)
-                        return Geno("", -1, "", "GENOPER_OPFAIL: CrossOver(): cannot validate invalid source genotype #1");
+                        return Geno("", Geno::INVALID_FORMAT, "", "GENOPER_OPFAIL: CrossOver(): cannot validate invalid source genotype #1");
                 canvalidate = true;
                 if (testValidity(g2v, canvalidate) > 0 && canvalidate == false)
-                        return Geno("", -1, "", "GENOPER_OPFAIL: CrossOver(): cannot validate invalid source genotype #2");
+                        return Geno("", Geno::INVALID_FORMAT, "", "GENOPER_OPFAIL: CrossOver(): cannot validate invalid source genotype #2");
         }
 
@@ -373 +387 @@
                                 if (res > 0 && canvalidate == false) invalid_xo++; else
                                 {
-                                validated_xo++; ok = true;
+                                        validated_xo++; ok = true;
                                 }
                         if (ok) g1v = G;
@@ -383 +397 @@
                 if (!ok && (count - pcount > GENMAN_REPEAT_FAILED))
                 {
-                        logPrintf("GenMan", "CrossOver", 2, "Tried " GENMAN_REPEAT_FAILED_STR "x and failed: %s and %s", g1.getGenes().c_str(), g2.getGenes().c_str());
-                        return Geno("", -1, "", "GENOPER_OPFAIL: CrossOver() tried " GENMAN_REPEAT_FAILED_STR "x and failed");
+                        logPrintf("GenMan", "CrossOver", LOG_WARN, "Tried " GENMAN_REPEAT_FAILED_STR "x and failed: %s and %s", g1.getGenes().c_str(), g2.getGenes().c_str());
+                        return Geno("", Geno::INVALID_FORMAT, "", "GENOPER_OPFAIL: CrossOver() tried " GENMAN_REPEAT_FAILED_STR "x and failed");
                 }
         }
@@ -398 +412 @@
 float GenMan::similarity(const Geno& g1, const Geno& g2)
 {
-        char format = g1.getFormat();
+        SString format = g1.getFormat();
         if (format != g2.getFormat()) return GENOPER_NOOPER;
         GenoOperators *gf = getOper_f(format);
@@ -406 +420 @@
 uint32_t GenMan::getStyle(const char *g, const Geno *G, int pos)
 {
-        char format = G->getFormat();
+        SString format = G->getFormat();
         if (format == Geno::INVALID_FORMAT)
                 return GENSTYLE_RGBS(64, 64, 64, 0); // gray & "valid" (unknown format so we don't know what is valid and what is not)
@@ -423 +437 @@
 void GenMan::getFullStyle(const char *g, const Geno *G, uint32_t *styletab)
 {
-        char format = G->getFormat();
+        SString format = G->getFormat();
         if (format == Geno::INVALID_FORMAT)
         {
@@ -438 +452 @@
                 else if (!gf) styletab[pos] = GENSTYLE_CS(0, 0); //black & valid
                 else styletab[pos] = gf->style(geny.c_str(), posmapped);
-                //logPrintf("GenMan", "getFullStyle", 0, "%d  char='%c' (%d)  format=0x%08x", pos, g[pos], g[pos], styletab[pos]);
+                //logPrintf("GenMan", "getFullStyle", LOG_INFO, "%d  char='%c' (%d)  format=0x%08x", pos, g[pos], g[pos], styletab[pos]);
         }
 }
@@ -473 +487 @@
                 color = GENGETCOLOR(styletab[i]);
                 if ((i != 0 && (color != prevcolor))) html += "</font>";
-                if ((style&GENSTYLE_INVALID) != (prevstyle&GENSTYLE_INVALID))
-                {
-                        html += "<"; if (!(style&GENSTYLE_INVALID)) html += "/"; html += "u>";
-                }
-                if ((style&GENSTYLE_BOLD) != (prevstyle&GENSTYLE_BOLD))
-                {
-                        html += "<"; if (!(style&GENSTYLE_BOLD)) html += "/"; html += "b>";
-                }
-                if ((style&GENSTYLE_ITALIC) != (prevstyle&GENSTYLE_ITALIC))
-                {
-                        html += "<"; if (!(style&GENSTYLE_ITALIC)) html += "/"; html += "i>";
+                if ((style & GENSTYLE_INVALID) != (prevstyle & GENSTYLE_INVALID))
+                {
+                        html += "<"; if (!(style & GENSTYLE_INVALID)) html += "/"; html += "u>";
+                }
+                if ((style & GENSTYLE_BOLD) != (prevstyle & GENSTYLE_BOLD))
+                {
+                        html += "<"; if (!(style & GENSTYLE_BOLD)) html += "/"; html += "b>";
+                }
+                if ((style & GENSTYLE_ITALIC) != (prevstyle & GENSTYLE_ITALIC))
+                {
+                        html += "<"; if (!(style & GENSTYLE_ITALIC)) html += "/"; html += "i>";
                 }
                 if ((i == 0 || (color != prevcolor)))
@@ -509 +523 @@
 }
 
-Geno GenMan::getSimplest(char format)
+Geno GenMan::getSimplest(const SString& format)
 {
         GenoOperators *gf = getOper_f(format);
         if (!gf) return Geno();
-        string info = "The simplest genotype of format f"; info += format;
+        string info = "The simplest genotype of format f"; info += format.c_str();
         info += " for operators '"; info += gf->name; info += "'.";
         return Geno(gf->getSimplest(), format, "Root", info.c_str());
@@ -520 +534 @@
 void GenMan::p_getsimplest(ExtValue *args, ExtValue *ret)
 {
-        int format = GenoObj::formatFromExtValue(args[0]);
+        SString format = GenoObj::formatFromExtValue(args[0]);
         if (!getOper_f(format))
                 ret->setEmpty();
@@ -527 +541 @@
 }
 
-const char *GenMan::getOpName(char format)
+const char *GenMan::getOpName(const SString& format)
 {
         GenoOperators *gf = getOper_f(format);
@@ -533 +547 @@
 }
 
-GenoOperators* GenMan::getOper_f(char format)
-{
-        int ind = operformats.find(format);
+GenoOperators* GenMan::getOper_f(const SString& format)
+{
+        int ind = findOperFormatIndex(format);
         if (ind == -1) return NULL;
         int which_oper_of_format = seloper[ind];
@@ -602 +616 @@
                 }
                 //      if (oper_fx_list[i]->similarity("","")!=GENOPER_NOOPER) l+=" similarity";
-                logPrintf("GenMan", "Report", 0, "format f%c (%s):%s",
-                        oper_fx_list[i]->supported_format, oper_fx_list[i]->name.c_str(), l.c_str());
+                logPrintf("GenMan", "Report", LOG_INFO, "format f%s (%s):%s",
+                        oper_fx_list[i]->supported_format.c_str(), oper_fx_list[i]->name.c_str(), l.c_str());
         }
 }

cpp/frams/genetics/genman.h

@@ -52 +52 @@
         string HTMLize(const char *g); //returns colored genotype in HTML.
         string HTMLizeShort(const char *g); //returns colored genotype (abbreviated if needed) in HTML.
-        Geno getSimplest(char format); ///<returns pointer to the simplest genotype of \e format or empty Geno()
-        const char *getOpName(char format); ///<returns pointer to the active operator set for \e format
+        Geno getSimplest(const SString& format); ///<returns pointer to the simplest genotype of \e format or empty Geno()
+        const char *getOpName(const SString& format); ///<returns pointer to the active operator set for \e format
         const vector<GenoOperators*>& GetOperators() const { return oper_fx_list; } ///<returns the list of available genetic operators
 private:
         vector<GenoOperators*> oper_fx_list;
         void saveLink(const string parent1, const string parent2, const string child, const float chg);
-        GenoOperators* getOper_f(char format);
+        GenoOperators* getOper_f(const SString& format);
         string HTMLize(const char *g, bool shorten);
+        int findOperFormatIndex(const SString& format);
 public:
         vector<GenoLink> GenoLinkList;
@@ -68 +69 @@
         int valid_m, valid_xo, validated_m, validated_xo, invalid_m, invalid_xo, failed_m, failed_xo;
         double mutchg, xochg;
-        SListTempl<char> operformats; //the list of supported_format, in the same order as in seloperpar
+        SListTempl<SString*> operformats; //the list of supported_format, in the same order as in seloperpar (raw SString* taken from oper_fx_list, not owned by operformats)
         int* seloper; //fields for seloperpar
         Param localpar, localstats;

cpp/frams/genetics/geno.cpp

@@ -1 +1 @@
 // This file is a part of Framsticks SDK.  http://www.framsticks.com/
-// Copyright (C) 1999-2018  Maciej Komosinski and Szymon Ulatowski.
+// Copyright (C) 1999-2020  Maciej Komosinski and Szymon Ulatowski.
 // See LICENSE.txt for details.
 
@@ -24 +24 @@
 }
 
-void Geno::init(const SString& genstring, char genformat, const SString& genname, const SString& comment)
+const SString Geno::INVALID_FORMAT = "invalid";
+const SString Geno::UNKNOWN_FORMAT = "";
+
+void Geno::init(const SString& genstring, const SString& genformat, const SString& genname, const SString& comment)
 {
         refcount = 1;
@@ -35 +38 @@
 }
 
-void Geno::setGenesAndFormat(const SString& genstring, char genformat)
+static SString trimAndValidateFormat(const SString& input) //the new requirement for genotype format name: no whitespace
+{
+        SString format = trim(input);
+        if (format.len() == 0 || strContainsOneOf(format.c_str(), " \r\n\t"))
+                return Geno::INVALID_FORMAT;
+        return format;
+}
+
+void Geno::setGenesAndFormat(const SString& genstring, const SString& in_genformat)
 {
         mapinshift = 0;
         mapoutshift = 0;
         SString gencopy(genstring);
-        if (genformat == -1)
+        SString genformat = in_genformat;
+        if (genformat == UNKNOWN_FORMAT)
         { // unknown format
-                genformat = '1';
+                genformat = "1";
                 if (genstring.charAt(0) == '/')
                 {
@@ -49 +61 @@
                         {
                         case '/':
-                                genformat = genstring.charAt(2);
                                 if ((end = genstring.indexOf('\n')) >= 0)
                                 {
+                                        genformat = trimAndValidateFormat(genstring.substr(2, end - 2));
                                         mapinshift = end + 1;
                                         gencopy = genstring.substr(end + 1);
                                         if ((end > 0) && (genstring[end - 1] == '\r')) end--;
                                         error_end = end;
-                                        if (end != 3) genformat = INVALID_FORMAT;
                                 }
                                 else
                                 {
-                                        if (genstring.len() != 3) genformat = INVALID_FORMAT;
-                                        gencopy = 0;
+                                        genformat = trimAndValidateFormat(genstring.substr(2));
+                                        gencopy = "";
                                         mapinshift = genstring.len();
                                 }
                                 break;
                         case '*':
-                                genformat = genstring.charAt(2);
                                 if ((end = genstring.indexOf("*/")) >= 0)
                                 {
+                                        genformat = trimAndValidateFormat(genstring.substr(2, end - 2));
                                         error_end = end + 2;
-                                        if (end != 3) genformat = INVALID_FORMAT;
                                         gencopy = genstring.substr(end + 2);
                                         mapinshift = end + 2;
@@ -76 +86 @@
                                 else
                                 {
-                                        if (genstring.len() != 5) genformat = INVALID_FORMAT;
-                                        gencopy = 0;
+                                        genformat = trimAndValidateFormat(genstring.substr(2));
+                                        gencopy = "";
                                         mapinshift = genstring.len();
                                 }
                                 break;
                         }
-                        if (!isalnum(genformat)) genformat = INVALID_FORMAT;
                         if (genformat == INVALID_FORMAT)
                         {
                                 SString cut;
-                                if (error_end<0) error_end = genstring.len();
+                                if (error_end < 0) error_end = genstring.len();
                                 static const int MAX_ERROR = 20;
-                                if (error_end>MAX_ERROR)
+                                if (error_end > MAX_ERROR)
                                         cut = genstring.substr(0, MAX_ERROR) + "...";
                                 else
@@ -113 +122 @@
 }
 
+Geno::Geno(const char *genstring, const char* genformat, const char *genname, const char *comment)
+{
+        init(SString(genstring), SString(genformat), SString(genname), SString(comment));
+}
+
 Geno::Geno(const char *genstring, char genformat, const char *genname, const char *comment)
 {
-        init(SString(genstring), genformat, SString(genname), SString(comment));
-}
-
-Geno::Geno(const SString& genstring, char genformat, const SString& genname, const SString& comment)
+        SString genformat_string;
+        if (genformat > 0)
+                genformat_string = SString(&genformat, 1);
+        init(genstring, genformat_string, genname, comment);
+}
+
+Geno::Geno(const SString& genstring, const SString& genformat, const SString& genname, const SString& comment)
 {
         init(genstring, genformat, genname, comment);
@@ -148 +165 @@
 Geno::Geno(const SString& src)
 {
-        init(src, -1, SString::empty(), SString::empty());
+        init(src, UNKNOWN_FORMAT, SString::empty(), SString::empty());
 }
 
@@ -161 +178 @@
 {
         freeF0();
-        init(g, -1, SString::empty(), SString::empty());
+        init(g, UNKNOWN_FORMAT, SString::empty(), SString::empty());
 }
 
@@ -177 +194 @@
 {
         SString out;
-        if (format != '1')
+        if (format != "1")
         {
                 if (multiline)
@@ -183 +200 @@
                 else
                         out += "/*";
-                if (format == 0)
-                        out += "invalid";
-                else
-                        out += format;
+                out += format;
                 if (multiline)
                         out += "\n";
@@ -213 +227 @@
 SString Geno::getGenes(void) const { return gen; }
 SString Geno::getName(void) const { return name; }
-char Geno::getFormat(void) const { return format; }
+SString Geno::getFormat(void) const { return format; }
 SString Geno::getComment(void) const { return txt; }
 
 int ModelGenoValidator::testGenoValidity(Geno& g)
 {
-        if (g.getFormat() == '0')
+        if (g.getFormat() == "0")
         {
                 Model mod(g);
@@ -226 +240 @@
         {
                 bool converter_missing;
-                Geno f0geno = g.getConverted('0', NULL, false, &converter_missing);
+                Geno f0geno = g.getConverted("0", NULL, false, &converter_missing);
                 if (converter_missing)
                         return -1;//no result
@@ -243 +257 @@
 #ifdef WARN_VALIDATION_INCONSISTENCY
                 vector<int> results;
-                int first_result=-1;
+                int first_result = -1;
                 FOREACH(GenoValidator*, v, (*vals))
                 {
-                        int r=v->testGenoValidity(*this);
-                        if (first_result<0) first_result=r;
+                        int r = v->testGenoValidity(*this);
+                        if (first_result < 0) first_result = r;
                         results.push_back(r);
                 }
-                int N=vals->size();
-                for(int i=1;i<N;i++)
-                        if (results[i]!=results[0])
+                int N = vals->size();
+                for (int i = 1; i < N; i++)
+                        if (results[i] != results[0])
                         {
-                        SString txt="Inconsistent validation results";
-                        for(int i=0;i<N;i++)
-                                txt+=SString::sprintf(" %d",results[i]);
-                        txt+=" for genotype '";
-                        txt+=getGene();
-                        txt+="'";
-                        logPrintf("Geno","validate",LOG_WARN,txt.c_str());
-                        break;
+                                SString txt = "Inconsistent validation results";
+                                for (int i = 0; i < N; i++)
+                                        txt += SString::sprintf(" %d", results[i]);
+                                txt += " for genotype '";
+                                txt += getGene();
+                                txt += "'";
+                                logPrintf("Geno", "validate", LOG_WARN, txt.c_str());
+                                break;
                         }
-                isvalid=first_result;
-                if (isvalid>=0)
+                isvalid = first_result;
+                if (isvalid >= 0)
                         return;
 #else
@@ -273 +287 @@
         }
         isvalid = 0;
-        logPrintf("Geno", "validate", LOG_WARN, "Wrong configuration? No genotype validators defined for genetic format 'f%c'.", format);
+        logPrintf("Geno", "validate", LOG_WARN, "Wrong configuration? No genotype validators defined for genetic format 'f%s'.", format.c_str());
 }
 
@@ -295 +309 @@
 }
 
-Geno Geno::getConverted(char otherformat, MultiMap *m, bool using_checkpoints, bool *converter_missing)
+Geno Geno::getConverted(SString otherformat, MultiMap *m, bool using_checkpoints, bool *converter_missing)
 {
         if (otherformat == getFormat()) { if (converter_missing) *converter_missing = false; return *this; }
@@ -302 +316 @@
         if (converters)
         {
-                if ((otherformat == '0') && (!m) && (!using_checkpoints))
+                if ((otherformat == "0") && (!m) && (!using_checkpoints))
                 {
                         if (!f0gen)
@@ -317 +331 @@
 #endif
         if (converter_missing) *converter_missing = true;
-        return (otherformat == getFormat()) ? *this : Geno(0, 0, 0, "GenConvManager not available");
+        return (otherformat == getFormat()) ? *this : Geno("", "", "", "GenConvManager not available");
 }
 

cpp/frams/genetics/geno.h

@@ -1 +1 @@
 // This file is a part of Framsticks SDK.  http://www.framsticks.com/
-// Copyright (C) 1999-2018  Maciej Komosinski and Szymon Ulatowski.
+// Copyright (C) 1999-2020  Maciej Komosinski and Szymon Ulatowski.
 // See LICENSE.txt for details.
 
@@ -34 +34 @@
         SString gen;
         SString name;
-        char format;
+        SString format;
         SString txt;
         int isvalid; ///< <0 -> unknown   >=0 -> value for "isValid"
@@ -44 +44 @@
         int multiline;
 
-        void init(const SString& genstring, char genformat, const SString& genname, const SString& comment);
+        void init(const SString& genstring, const SString& genformat, const SString& genname, const SString& comment);
         void validate(void);
 
@@ -55 +55 @@
 
 public:
-        static const char INVALID_FORMAT = '!';
+        static const SString INVALID_FORMAT;
+        static const SString UNKNOWN_FORMAT;
         typedef SListTempl<GenoValidator*> Validators;
 
@@ -62 +63 @@
         /// @param genformat genotype format
         /// @param comment information about genotype (for genetic operators and "history")
-        Geno(const char *genstring = 0, char genformat = -1, const char *genname = 0, const char *comment = 0);
+        Geno(const char *genstring = 0, const char* genformat = 0, const char *genname = 0, const char *comment = 0);
+
+        Geno(const char *genstring, char genformat, const char *genname = 0, const char *comment = 0); //old style Geno, accepts char genoformat
 
         /// create a genotype object from primitives
@@ -69 +72 @@
         /// @param name genotype name, new name will generated if needed
         /// @param comment information about genotype (for genetic operators and "history")
-        Geno(const SString& genstring, char genformat, const SString& genname, const SString& comment);
+        Geno(const SString& genstring, const SString& genformat, const SString& genname, const SString& comment);
 
         /// create object from full string, containing optional format and comment information
@@ -89 +92 @@
         void setString(const SString& genewithcomments);
 
-        /** @param genformat=-1 -> detect genotype format from genstring comment (like the constructor does), else specify the valid format in genformat and pure genes in genstring. */
-        void setGenesAndFormat(const SString& genstring, char genformat = -1);
+        /** @param genformat="" -> detect genotype format from genstring comment (like the constructor does), else specify the valid format in genformat and pure genes in genstring. */
+        void setGenesAndFormat(const SString& genstring, const SString& genformat = UNKNOWN_FORMAT);
         /** g must be pure genes, without format. For the standard behavior use setGenesAndFormat() */
         void setGenesAssumingSameFormat(const SString& g);
@@ -97 +100 @@
         SString getName(void) const;
         void setName(const SString&);
-        char getFormat(void) const;
+        SString getFormat(void) const;
 
         SString getComment(void) const;
@@ -107 +110 @@
         /// make converted version of the genotype.
         /// @param converter_missing optional output parameter (ignored when NULL). Receives true if the conversion fails because of the lack of appropriate converter(s) (the returned Geno is always invalid in this case). Receives false if the genotype was converted by a converter or a converter chain (the returned Geno can be valid or invalid, depending on the converter's decision).
-        Geno getConverted(char otherformat, MultiMap *m = 0, bool using_checkpoints = false, bool *converter_missing = NULL);
+        Geno getConverted(SString otherformat, MultiMap *m = 0, bool using_checkpoints = false, bool *converter_missing = NULL);
 
         /// @return -1 = before first char in the string

cpp/frams/genetics/genoconv.cpp

@@ -1 +1 @@
 // This file is a part of Framsticks SDK.  http://www.framsticks.com/
-// Copyright (C) 1999-2018  Maciej Komosinski and Szymon Ulatowski.
+// Copyright (C) 1999-2020  Maciej Komosinski and Szymon Ulatowski.
 // See LICENSE.txt for details.
 
@@ -57 +57 @@
                 pe->flags = 0;
                 std::string descr = "f";
-                descr += gk->in_format;
+                descr += gk->in_format.c_str();
                 descr += " --> f";
-                descr += gk->out_format;
+                descr += gk->out_format.c_str();
                 descr += "  :  ";
                 descr += gk->name;
@@ -101 +101 @@
 }
 
-GenoConverter *GenoConvManager::findConverters(SListTempl<GenoConverter*>* result, char in, char out, int enabled, char* name)
+GenoConverter *GenoConvManager::findConverters(SListTempl<GenoConverter*>* result, const SString& in, const SString& out, int enabled, char* name)
 {
         GenoConverter *gk, *retval = 0;
@@ -107 +107 @@
         for (; gk = (GenoConverter*)converters(i); i++)
         {
-                if ((in != -1) && (in != gk->in_format)) continue;
-                if ((out != -1) && (out != gk->out_format)) continue;
+                if ((in != Geno::UNKNOWN_FORMAT) && (in != gk->in_format)) continue;
+                if ((out != Geno::UNKNOWN_FORMAT) && (out != gk->out_format)) continue;
                 if ((enabled != -1) && (enabled != gk->enabled)) continue;
                 if ((name) && (strcmp(name, gk->name))) continue;
@@ -123 +123 @@
 /// (can be NULL if you don't need this information)
 
-char *GenoConvManager::getPath(char in, char out, char *path, int maxlen, int *mapavailable)
+GenoConverter **GenoConvManager::getPath(const SString& in, const SString& out, GenoConverter **path, int maxlen, int *mapavailable)
 {
         if (!maxlen) return 0;
@@ -132 +132 @@
                 if ((gk->enabled) && (gk->in_format == in))
                 {
-                        *path = (char)i;
+                        *path = gk;
                         if (gk->out_format == out)
                         {
@@ -142 +142 @@
                         {
                                 int mapavail;
-                                char *ret = getPath(gk->out_format, out, path + 1, maxlen - 1, &mapavail);
+                                GenoConverter **ret = getPath(gk->out_format, out, path + 1, maxlen - 1, &mapavail);
                                 if (ret)
                                 {
@@ -155 +155 @@
 }
 
-char *GenoConvManager::getFormatPath(char in, char out, char *path, int maxlen, int *mapavailable)
-{
-        char *ret = getPath(in, out, path, maxlen, mapavailable);
-        if (ret)
-        {
-                for (char*t = path; t <= ret; t++)
-                        *t = ((GenoConverter*)converters(*t))->out_format;
-        }
-        return ret;
-}
-
-Geno GenoConvManager::convert(Geno &in, char format, MultiMap *map, bool using_checkpoints, bool *converter_missing)
+Geno GenoConvManager::convert(Geno &in, SString format, MultiMap *map, bool using_checkpoints, bool *converter_missing)
 {
         if (in.getFormat() == format) { if (converter_missing) *converter_missing = false; return in; }
-        char path[10];
+        GenoConverter *path[10];
         int dep;
-        char *ret;
-        if (in.isInvalid()) { if (converter_missing) *converter_missing = false; return Geno("", 0, "", "invalid genotype cannot be converted"); }
+        GenoConverter **ret;
+        if (in.isInvalid()) { if (converter_missing) *converter_missing = false; return Geno("", Geno::INVALID_FORMAT, "", "invalid genotype cannot be converted"); }
         int mapavail;
         for (dep = 1; dep < (int)sizeof(path); dep++) //iterative deepening
                 if (ret = getPath(in.getFormat(), format, path, dep, &mapavail)) break;
-        if (!ret) { if (converter_missing) *converter_missing = true; return Geno("", 0, "", "converter not found"); }
+        if (!ret) { if (converter_missing) *converter_missing = true; return Geno("", Geno::INVALID_FORMAT, "", "converter not found"); }
         if (converter_missing) *converter_missing = false;
         if (!map) mapavail = 0;
-        char *t = path;
+        GenoConverter **t = path;
         SString tmp;
         tmp = in.getGenes();
@@ -186 +175 @@
         for (; t <= ret; t++)
         {
-                GenoConverter *gk = (GenoConverter*)converters(*t);
+                GenoConverter *gk = *t;
                 tmp = gk->convert(tmp, mapavail ? &tmpmap : 0, using_checkpoints);
                 if (!tmp.len())
                 {
-                        string t = ssprintf("f%c->f%c conversion failed (%s)", gk->in_format, gk->out_format, gk->name);
-                        return Geno(0, 0, 0, t.c_str());
+                        string t = ssprintf("f%s->f%s conversion failed (%s)", gk->in_format.c_str(), gk->out_format.c_str(), gk->name);
+                        return Geno("", Geno::INVALID_FORMAT, "", t.c_str());
                 }
                 if (mapavail)

cpp/frams/genetics/genoconv.h

@@ -1 +1 @@
 // This file is a part of Framsticks SDK.  http://www.framsticks.com/
-// Copyright (C) 1999-2018  Maciej Komosinski and Szymon Ulatowski.
+// Copyright (C) 1999-2020  Maciej Komosinski and Szymon Ulatowski.
 // See LICENSE.txt for details.
 
@@ -43 +43 @@
 public:
         const char *name;       //< converter name (short)
-        char in_format,         //< input format, eg. '1'
-                out_format;     //< output format, eg. '0'
+        SString in_format,      //< input format, eg. "1"
+                out_format;     //< output format, eg. "0"
         paInt enabled;  //< don't touch this! (used by configuration module)
         paInt mapsupport; //< set to 1 if your converter supports genotype mapping
@@ -56 +56 @@
         virtual ~GenoConverter() {}
         /// Don't forget to set public fields in your constructor
-        GenoConverter() :name(""), in_format(-1), out_format('0'), enabled(1), mapsupport(0) {}
+        GenoConverter() :name(""), in_format(Geno::UNKNOWN_FORMAT), out_format("0"), enabled(1), mapsupport(0) {}
 };
 
@@ -77 +77 @@
         /// make a genotype in other format. genotype will be invalid
         /// if GenoConvManager cannot convert it.
-        Geno convert(Geno &in, char format, MultiMap *map = 0, bool using_checkpoints = false, bool *converter_missing = NULL);
+        Geno convert(Geno &in, SString format, MultiMap *map = 0, bool using_checkpoints = false, bool *converter_missing = NULL);
         /// register GenoConverter, the added object will be automatically deleted when GenoConvManager is destructed (call removeConverter() if this is not desirable)
         void addConverter(GenoConverter *conv);
@@ -83 +83 @@
         void removeConverter(GenoConverter *conv);
 
-        char *getPath(char in, char out, char *path, int maxlen, int *mapavailable = 0);
-        char *getFormatPath(char in, char out, char *path, int maxlen, int *mapavailable = 0);
+        GenoConverter **getPath(const SString& in, const SString& out, GenoConverter **path, int maxlen, int *mapavailable = 0);
         /// returns the list of converters meeting the specified criteria
         /// pass result=0 if you only need one result (by return value)
         /// default criteria values mean "don't care", pass anything else to narrow your search
-        GenoConverter *findConverters(SListTempl<GenoConverter*>* result = 0, char in = -1, char out = -1, int enabled = -1, char* name = 0);
+        GenoConverter *findConverters(SListTempl<GenoConverter*>* result = 0, const SString& in = Geno::UNKNOWN_FORMAT, const SString& out = Geno::UNKNOWN_FORMAT, int enabled = -1, char* name = 0);
 };
 

cpp/frams/genetics/genooperators.cpp

@@ -76 +76 @@
 }
 
-int GenoOperators::selectRandomProperty(Neuro *n)
+int GenoOperators::selectRandomNeuProperty(Neuro *n)
 {
         int neuext = n->extraProperties().getPropCount(),

cpp/frams/genetics/genooperators.h

@@ -81 +81 @@
 public:
         Param par;
-        char supported_format; ///<genotype format which is supported by this class ('6' for GenoOper_f6, 'F' for GenoOper_fF, etc.). Must be initialized in constructor
-        string name; ///<name of this set of genetic operators
+        SString supported_format; ///<genotype format which is supported by this class ("6" for GenoOper_f6, "Latent" for GenoOper_fLatent, etc.). Must be initialized in constructor.
+        string name; ///<short human-friendly name of this genetic representation/set of genetic operators
         const char **mutation_method_names; ///<array of names for mutation methods. If initialized (by new const char*[]), must have entries for each method index returned by mutate(geno,chg,METHOD).  If initialized, it is automatically freed by this destructor.
-        GenoOperators() : par(empty_paramtab) { supported_format = 'x'; name = "Default"; mutation_method_names = NULL; setDefaults(); }
+        GenoOperators() : par(empty_paramtab) { supported_format = "x"; name = "Default"; mutation_method_names = NULL; setDefaults(); }
 
         /**Used to perform initializations of Param parameters that are not handled by the Param itself
@@ -182 +182 @@
         static int roulette(const double *probtab, const int count);    ///<returns random index according to probabilities in the \e probtab table or -1 if all probs are zero. \e count is the number of elements in \e probtab.
         static bool getMinMaxDef(ParamInterface *p, int propindex, double &mn, double &mx, double &def); ///<perhaps a more useful (higher-level) way to obtain min/max/def info for integer and double properties. Returns true if min/max/def was really available (otherwise it is just invented).
-        static int selectRandomProperty(Neuro* n); ///<selects random property (either 0-based extraproperty of Neuro or 100-based property of its NeuroClass). -1 if Neuro has no properties.
+        static int selectRandomNeuProperty(Neuro* n); ///<selects random property (either 0-based extraproperty of Neuro or 100-based property of its NeuroClass). -1 if Neuro has no properties.
         static double mutateNeuProperty(double current, Neuro *n, int propindex); ///<returns value \e current mutated for the property \e propindex of NeuroClass \e nc or for extraproperty (\e propindex - 100) of Neuro. Neuro is used as read-only. Give \e propindex == -1 to mutate connection weight (\e nc is then ignored).
         static bool mutatePropertyNaive(ParamInterface &p, int propindex); ///<creep-mutate selected property. Returns true when success. mutateProperty() should be used instead of this function.