Changeset 348 for cpp/frams/genetics

Timestamp:

04/09/15 23:51:28 (10 years ago)

Author:

Maciej Komosinski

Message:

• explicit c_str() in SString instead of (const char*) cast
• genetic converters and GenMan? are now thread-local which enables multi-threaded simulator separation

Location:

cpp/frams/genetics

Files:

• f1/conv_f1.cpp (modified) (3 diffs)
• f4/f4_general.cpp (modified) (2 diffs)
• f9/oper_f9.cpp (modified) (2 diffs)
• fF/conv_fF.cpp (modified) (1 diff)
• fF/fF_genotype.h (modified) (1 diff)
• fT/oper_fTest.cpp (modified) (1 diff)
• genman.cpp (modified) (11 diffs)
• geno.cpp (modified) (4 diffs)
• geno.h (modified) (1 diff)
• oper_fx.cpp (modified) (1 diff)
• preconfigured.h (modified) (2 diffs)

cpp/frams/genetics/f1/conv_f1.cpp

@@ -102 +102 @@
 SString GenoConv_f1::convert(SString &i,MultiMap *map)
 {
-const char* g=(const char*)i;
+const char* g=i.c_str();
 Builder builder(g,map?1:0);
 builder.model.open();
@@ -403 +403 @@
                                         lastNeuroClassParam();
                                         //special handling: muscle properties (can be overwritten by subsequent property assignments)
-                                        if (!strcmp(cls->getName(),"|"))
+                                        if (!strcmp(cls->getName().c_str(),"|"))
                                                 {
                                                 neuro_cls_param->setDoubleById("p",lastjoint_muscle_power);
                                                 neuro_cls_param->setDoubleById("r",props.bendrange);
                                                 }
-                                        else if (!strcmp(cls->getName(),"@"))
+                                        else if (!strcmp(cls->getName().c_str(),"@"))
                                                 {
                                                 neuro_cls_param->setDoubleById("p",lastjoint_muscle_power);
@@ -485 +485 @@
         SString name(begin,colon-begin);
         SString value(colon+1,end-(colon+1));
-        addClassParam(name,value);
-        }
-}
+        addClassParam(name.c_str(),value.c_str());
+        }
+}

cpp/frams/genetics/f4/f4_general.cpp

@@ -714 +714 @@
         // transform geno from string to nodes
         f4rootnode = new f4_node();
-        res = f4_processrec((const char*)genome, (unsigned)0, f4rootnode);
+        res = f4_processrec(genome.c_str(), (unsigned)0, f4rootnode);
         if ((res < 0) || (1 != f4rootnode->childCount()))
         {
@@ -1197 +1197 @@
                 buf = (char*)realloc(buf, len + 1);
         }
-        strcpy(buf, (const char*)out);
+        strcpy(buf, out.c_str());
 }
 

cpp/frams/genetics/f9/oper_f9.cpp

@@ -42 +42 @@
                 if (strchr(turtle_commands_f9, gene[i])) validated += gene[i];  //validated contains only turtle_commands_f9
         free(gene);
-        gene = strdup(validated); //reallocate
+        gene = strdup(validated.c_str()); //reallocate
         return GENOPER_OK;
 }
@@ -84 +84 @@
                 }
                 free(gene);
-                gene = strdup(newgeno); //reallocate
+                gene = strdup(newgeno.c_str()); //reallocate
         }
 

cpp/frams/genetics/fF/conv_fF.cpp

@@ -39 +39 @@
 {
         fF_growth_params gp;
-        if (!gp.load(in)) //invalid input genotype?
+        if (!gp.load(in.c_str())) //invalid input genotype?
                 return ""; //so we return an invalid f0 genotype
 

cpp/frams/genetics/fF/fF_genotype.h

@@ -43 +43 @@
                 SString tmp;
                 param.save2(tmp, NULL/*object containing default values for comparison*/, false/*add CR*/, false/*force field names*/);
-                return string((const char*)tmp);
+                return string(tmp.c_str());
         }
 };

cpp/frams/genetics/fT/oper_fTest.cpp

@@ -77 +77 @@
                 if (strchr("ATGC", gene[i])) validated += gene[i];  //validated contains only ATGC
         free(gene);
-        gene = strdup(validated); //reallocate
+        gene = strdup(validated.c_str()); //reallocate
         return GENOPER_OK;
 }

cpp/frams/genetics/genman.cpp

@@ -199 +199 @@
 {
         SString ggs=g.getGene();
-        const char *gg = ggs;
+        const char *gg = ggs.c_str();
         GenoOperators *gf = getOper_f(g.getFormat());
         int check1;
@@ -237 +237 @@
         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));
-        char *g2 = strdup(geny.getGene()); //copy for validation
+        char *g2 = strdup(geny.getGene().c_str()); //copy for validation
         int res = gf->validate(g2);
         SString sg2 = g2;
@@ -263 +263 @@
         while (!ok)
         {
-                char *gn = strdup(gv.getGene()); //copy for mutation
+                char *gn = strdup(gv.getGene().c_str()); //copy for mutation
                 chg = 0;
                 if (gf->mutate(gn, chg, method) == GENOPER_OK)
@@ -284 +284 @@
                 if (!ok && (count - pcount > 100))
                 {
-                        FMprintf("GenMan", "Mutate", 2, "Tried 100x and failed: %s", (const char*)g.getGene());
+                        FMprintf("GenMan", "Mutate", 2, "Tried 100x and failed: %s", g.getGene().c_str());
                         return Geno("", -1, "", "GENOPER_OPFAIL: Mutate() tried 100x and failed");
                 }
         }
         mutchg += chg;
-        if (history) saveLink((const char*)g.getGene(), "", (const char*)gv.getGene(), chg);
+        if (history) saveLink(g.getGene().c_str(), "", gv.getGene().c_str(), chg);
         SString mutinfo;
-        if (extmutinfo == 0) mutinfo = SString::sprintf("%.2f%% mutation of '%s'", 100 * chg, (const char*)g.getName()); else
-                if (extmutinfo == 1) mutinfo = SString::sprintf("%.2f%% mutation(%d) of '%s'", 100 * chg, method, (const char*)g.getName()); else
-                        mutinfo = SString::sprintf("%.2f%% mutation(%s) of '%s'", 100 * chg, gf->mutation_method_names ? gf->mutation_method_names[method] : "unspecified method name", (const char*)g.getName());
+        if (extmutinfo == 0) mutinfo = SString::sprintf("%.2f%% mutation of '%s'", 100 * chg, g.getName().c_str()); else
+                if (extmutinfo == 1) mutinfo = SString::sprintf("%.2f%% mutation(%d) of '%s'", 100 * chg, method, g.getName().c_str()); else
+                        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());
         gv.setComment(mutinfo);
         return gv;
@@ -324 +324 @@
         {
                 float chg1, chg2;
-                char *g1n = strdup(g1.getGene()); //copy for crossover
-                char *g2n = strdup(g2.getGene()); //copy for crossover
+                char *g1n = strdup(g1.getGene().c_str()); //copy for crossover
+                char *g2n = strdup(g2.getGene().c_str()); //copy for crossover
                 chg1 = chg2 = 0;
                 if (gf->crossOver(g1n, g2n, chg1, chg2) == GENOPER_OK)
@@ -351 +351 @@
                 if (!ok && (count - pcount > 100))
                 {
-                        FMprintf("GenMan", "CrossOver", 2, "Tried 100x and failed: %s and %s", (const char*)g1.getGene(), (const char*)g2.getGene());
+                        FMprintf("GenMan", "CrossOver", 2, "Tried 100x and failed: %s and %s", g1.getGene().c_str(), g2.getGene().c_str());
                         return Geno("", -1, "", "GENOPER_OPFAIL: CrossOver() tried 100x and failed");
                 }
@@ -357 +357 @@
         // result in g1v
         xochg += chg;
-        if (history) saveLink((const char*)g1.getGene(), (const char*)g2.getGene(), (const char*)g1v.getGene(), chg);
+        if (history) saveLink(g1.getGene().c_str(), g2.getGene().c_str(), g1v.getGene().c_str(), chg);
         SString xoinfo = SString::sprintf("Crossing over of '%s' (%.2f%%) and '%s' (%.2f%%)",
-                (const char*)g1.getName(), 100 * chg, (const char*)g2.getName(), 100 * (1 - chg));
+                g1.getName().c_str(), 100 * chg, g2.getName().c_str(), 100 * (1 - chg));
         g1v.setComment(xoinfo);
         return g1v;
@@ -369 +369 @@
         if (format != g2.getFormat()) return GENOPER_NOOPER;
         GenoOperators *gf = getOper_f(format);
-        if (!gf) return GENOPER_NOOPER; else return gf->similarity(g1.getGene(), g2.getGene());
+        if (!gf) return GENOPER_NOOPER; else return gf->similarity(g1.getGene().c_str(), g2.getGene().c_str());
 }
 
@@ -378 +378 @@
         GenoOperators *gf = getOper_f(G.getFormat());
         if (!gf) return GENSTYLE_CS(0, 0); //black & valid
-        else return gf->style(G.getGene(), pos);
+        else return gf->style(G.getGene().c_str(), pos);
 }
 
@@ -391 +391 @@
                 if (posmapped == -1) styletab[pos] = GENSTYLE_COMMENT;
                 else if (!gf) styletab[pos] = GENSTYLE_CS(0, 0); //black & valid
-                else styletab[pos] = gf->style(geny, posmapped);
+                else styletab[pos] = gf->style(geny.c_str(), posmapped);
         }
 }
@@ -448 +448 @@
 void GenMan::p_htmlize(ExtValue *args, ExtValue *ret)
 {
-        ret->setString(HTMLize(args->getString()));
+        ret->setString(HTMLize(args->getString().c_str()));
 }
 
 void GenMan::p_htmlizeshort(ExtValue *args, ExtValue *ret)
 {
-        ret->setString(HTMLizeShort(args->getString()));
+        ret->setString(HTMLizeShort(args->getString().c_str()));
 }
 

cpp/frams/genetics/geno.cpp

@@ -7 +7 @@
 #include <frams/model/model.h>
 
-GenoConvManager *Geno::converters = NULL;
-
-THREAD_LOCAL_DEF(Geno::Validators, geno_validators);
-
-Geno::Validators& Geno::getValidators() {return tlsGetRef(geno_validators);}
+THREAD_LOCAL_DEF_PTR(Geno::Validators, geno_validators);
+THREAD_LOCAL_DEF_PTR(GenoConvManager, geno_converters);
+
+Geno::Validators* Geno::getValidators() {return tlsGetPtr(geno_validators);}
+GenoConvManager* Geno::getConverters() {return tlsGetPtr(geno_converters);}
+
+Geno::Validators* Geno::useValidators(Validators* val)
+{return tlsSetPtr(geno_validators,val);}
+GenoConvManager* Geno::useConverters(GenoConvManager* gcm)
+{return tlsSetPtr(geno_converters,gcm);}
 
 void Geno::init(const SString& genstring, char genformat, const SString& genname, const SString& comment)
@@ -78 +83 @@
         if (!name.len()) name = genname;
         if (!txt.len()) txt = comment;
-        multiline = (strchr((const char*)gen, '\n') != 0);
+        multiline = (strchr(gen.c_str(), '\n') != 0);
         // mapoutshift...?
 }
@@ -237 +242 @@
         if (isvalid >= 0) return;
         if (gen.len() == 0) { isvalid = 0; return; }
-        Validators& vals=getValidators();
-        FOREACH(GenoValidator*, v, vals)
+        Validators* vals=getValidators();
+        if (vals!=NULL)
+                {
+        FOREACH(GenoValidator*, v, (*vals))
                 if ((isvalid = v->testGenoValidity(*this)) >= 0)
                         return;
+                }
         isvalid = 0;
         FMprintf("Geno", "validate", FMLV_WARN, "Wrong configuration? No genotype validators defined for genetic format f%c.", format);
@@ -255 +263 @@
         if (otherformat == getFormat()) { if (converter_missing) *converter_missing = false; return *this; }
 #ifndef NO_GENOCONVMANAGER
+        GenoConvManager *converters=getConverters();
         if (converters)
         {

cpp/frams/genetics/geno.h

@@ -118 +118 @@
 
         // managing global Geno-related objects (used for validation and conversion)
-        static Validators& getValidators();
-        static void addValidator(GenoValidator* gv,int at_position=9999) { getValidators().insert(at_position,gv); }
-        static void removeValidator(GenoValidator* gv) { getValidators() -= gv; }
-        static void useConverters(GenoConvManager& gcm) { converters = &gcm; }
-        static GenoConvManager &getConverters() { return *converters; }
-protected:
-        static GenoConvManager *converters;
+        static Validators* useValidators(Validators* val);
+        static Validators* getValidators();
+
+        static GenoConvManager* useConverters(GenoConvManager* gcm);
+        static GenoConvManager* getConverters();
 };
 

cpp/frams/genetics/oper_fx.cpp

@@ -192 +192 @@
         for (int i = 0; i<Neuro::getClassCount(); i++)
         {
-                const char *n = Neuro::getClass(i)->name;
+                const char *n = Neuro::getClass(i)->name.c_str();
                 int l = (int)strlen(n);
                 if (len >= l && l>Len && (strncmp(s, n, l) == 0)) { I = Neuro::getClass(i); Len = l; }

cpp/frams/genetics/preconfigured.h

@@ -18 +18 @@
 DefaultGenoConvManager gcm;
 GenMan genman;
+Geno::Validators validators;
 ModelGenoValidator model_validator; //validation through conversion
 
@@ -23 +24 @@
         {
         gcm.addDefaultConverters(); //without converters, the application would only handle "format 0" genotypes
-        Geno::useConverters(gcm);
+        Geno::useConverters(&gcm);
 
-        Geno::addValidator(&genman); //primary validation: use the extended validity checking (through dedicated genetic operators)
-        Geno::addValidator(&model_validator); //secondary validation: this simple validator handles all cases when there is no dedicated genetic validation operator, but a converter for a particular format is available. Converters may be less strict in detecting invalid genotypes but using them and checking whether they produced a valid f0 genotype is also some way to tell whether the initial genotype was valid. Otherwise, without dedicated genetic validation operator, we would have no validity check at all.
-        }
-};
-
-/** Initialization procedure for applications adding their own validators */
-class PreconfiguredGenetics_NoValidators
-{
-  public:
-DefaultGenoConvManager gcm;
-
-PreconfiguredGenetics_NoValidators()
-        {
-        gcm.addDefaultConverters(); //without converters, the application would only handle "format 0" genotypes
-        Geno::useConverters(gcm);
+        Geno::useValidators(&validators);
+        validators+=&genman; //primary validation: use the extended validity checking (through dedicated genetic operators)
+        validators+=&model_validator; //secondary validation: this simple validator handles all cases when there is no dedicated genetic validation operator, but a converter for a particular format is available. Converters may be less strict in detecting invalid genotypes but using them and checking whether they produced a valid f0 genotype is also some way to tell whether the initial genotype was valid. Otherwise, without dedicated genetic validation operator, we would have no validity check at all.
         }
 };
 
 #endif
-