Changeset 513 for cpp/frams/genetics

Timestamp:

05/23/16 13:52:53 (9 years ago)

Author:

Maciej Komosinski

Message:

checkValidity() and validate() are now aware of genotype name

Location:

cpp/frams/genetics

Files:

• f4/oper_f4.cpp (modified) (2 diffs)
• f4/oper_f4.h (modified) (1 diff)
• f9/oper_f9.cpp (modified) (2 diffs)
• f9/oper_f9.h (modified) (1 diff)
• fF/oper_fF.cpp (modified) (2 diffs)
• fF/oper_fF.h (modified) (1 diff)
• genman.cpp (modified) (3 diffs)
• genoconv.h (modified) (1 diff)
• oper_fx.h (modified) (2 diffs)

cpp/frams/genetics/f4/oper_f4.cpp

@@ -86 +86 @@
 
 
-int Geno_f4::validate(char *& geno)
+int Geno_f4::validate(char *& geno, const char *genoname)
 {
         // convert geno to tree, then try to validate 20 times
@@ -100 +100 @@
 
 
-int Geno_f4::checkValidity(const char * geno)
+int Geno_f4::checkValidity(const char * geno, const char *genoname)
 {
         f4_node root;

cpp/frams/genetics/f4/oper_f4.h

@@ -33 +33 @@
 public:
         Geno_f4();
-        int validate(char *&);
-        int checkValidity(const char *);
+        int checkValidity(const char *, const char *genoname);
+        int validate(char *&, const char *genoname);
         int mutate(char *& g, float & chg, int &method);
         int crossOver(char *&g1, char *&g2, float& chg1, float& chg2);

cpp/frams/genetics/f9/oper_f9.cpp

@@ -26 +26 @@
 }
 
-int GenoOper_f9::checkValidity(const char* gene)
+int GenoOper_f9::checkValidity(const char* gene, const char *genoname)
 {
         if (!gene[0]) return 1; //empty is not valid
@@ -36 +36 @@
 
 ///Remove all invalid letters from the genotype
-int GenoOper_f9::validate(char *&gene)
+int GenoOper_f9::validate(char *&gene, const char *genoname)
 {
         SString validated; //new genotype (everything except turtle_commands_f9 is skipped)

cpp/frams/genetics/f9/oper_f9.h

@@ -13 +13 @@
 public:
         GenoOper_f9();
-        int checkValidity(const char *);
-        int validate(char *&);
-        int mutate(char *&g,float& chg,int &method);
-        int crossOver(char *&g1,char *&g2,float& chg1,float& chg2);
+        int checkValidity(const char *, const char *genoname);
+        int validate(char *&, const char *genoname);
+        int mutate(char *&g, float& chg, int &method);
+        int crossOver(char *&g1, char *&g2, float& chg1, float& chg2);
         uint32_t style(const char *g, int pos);
-        const char* getSimplest() {return "R";}
+        const char* getSimplest() { return "R"; }
 
         double mut_prob; //mutation probability

cpp/frams/genetics/fF/oper_fF.cpp

@@ -26 +26 @@
 }
 
-int GenoOper_fF::checkValidity(const char* gene)
+int GenoOper_fF::checkValidity(const char* gene, const char *genoname)
 {
         fF_growth_params par;
@@ -32 +32 @@
 }
 
-int GenoOper_fF::validate(char *&gene)
+int GenoOper_fF::validate(char *&gene, const char *genoname)
 {
         fF_growth_params par; //is initialized with default values

cpp/frams/genetics/fF/oper_fF.h

@@ -13 +13 @@
 public:
         GenoOper_fF();
-        int checkValidity(const char *);
-        int validate(char *&);
+        int checkValidity(const char *, const char *genoname);
+        int validate(char *&, const char *genoname);
         int mutate(char *&g, float& chg, int &method);
         int crossOver(char *&g1, char *&g2, float& chg1, float& chg2);
         uint32_t style(const char *g, int pos);
-        const char* getSimplest() { return "6, 1.05, 1.05, 1.05, 0, 0, 0"; }
+        const char* getSimplest() { return "6, "/*"1, 1, 1, "*/"1.05, 1.05, 1.05, 0, 0, 0"; }
 
         double xover_proportion;

cpp/frams/genetics/genman.cpp

@@ -203 +203 @@
         int check1;
         if (!gf) { canvalidate = false; return GENOPER_NOOPER; }
-        else check1 = gf->checkValidity(gg);
+        else check1 = gf->checkValidity(gg,g.getName().c_str());
         if (!canvalidate) return check1; //just checking
         if (check1 == GENOPER_OK) { canvalidate = false; return check1; }
         char *g2 = strdup(gg);
-        if (gf->validate(g2) == GENOPER_NOOPER) { free(g2); canvalidate = false; return check1; }
+        if (gf->validate(g2,g.getName().c_str()) == GENOPER_NOOPER) { free(g2); canvalidate = false; return check1; }
         if (check1 == GENOPER_NOOPER) //disaster: cannot check because there is no check operator
         {
                 g.setGene(g2); free(g2); canvalidate = false; return GENOPER_NOOPER;
         }
-        int check2 = gf->checkValidity(g2);
+        int check2 = gf->checkValidity(g2, "validated");
         if (check2 == GENOPER_OK) g.setGene(g2);
         free(g2);
@@ -238 +238 @@
                 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().c_str()); //copy for validation
-        int res = gf->validate(g2);
+        int res = gf->validate(g2, geny.getName().c_str());
         SString sg2 = g2;
         free(g2);
@@ -537 +537 @@
         {
                 string l;
-                if (oper_fx_list[i]->checkValidity("") != GENOPER_NOOPER) l += " checkValidity";
+                if (oper_fx_list[i]->checkValidity("","") != GENOPER_NOOPER) l += " checkValidity";
                 if (oper_fx_list[i]->getSimplest())
                 {
                         g = strdup(oper_fx_list[i]->getSimplest());
                         g2 = strdup(g);
-                        if (oper_fx_list[i]->validate(g) != GENOPER_NOOPER) l += " validate";
+                        if (oper_fx_list[i]->validate(g,"") != GENOPER_NOOPER) l += " validate";
                         if (oper_fx_list[i]->mutate(g, f1, m) != GENOPER_NOOPER) l += " mutate";
                         if (oper_fx_list[i]->crossOver(g, g2, f1, f2) != GENOPER_NOOPER) l += " crossover";

cpp/frams/genetics/genoconv.h

@@ -50 +50 @@
 
         /// You have to reimplement this method.
-        /// If your converter cannot do its job, return empty string
-        /// (return SString();), any other return value is assumed
-        /// to be output genotype.
+        /// If your converter cannot do its job, return empty string - return SString();
+        /// Any other return value is assumed to be output genotype.
         /// @param map if not null, mapping informaton is requested, converter should add conversion map to this object
         virtual SString convert(SString &i, MultiMap *map) { return SString(); }

cpp/frams/genetics/oper_fx.h

@@ -92 +92 @@
 /**Checks a genotype for minor mistakes and major errors.
 \param geno genotype to be checked
+\param genoname name of the genotype to be checked
 \retval error_position 1-based (or 1 if no exact error position known)
 \retval GENOPER_OK when the genotype is fully valid, and can be translated by the converter with \b no modifications nor tweaks*/
-   virtual int checkValidity(const char *geno) {return GENOPER_NOOPER;}
+   virtual int checkValidity(const char *geno, const char *genoname) { return GENOPER_NOOPER; }
 
 /**Validates a genotype. The purpose of this function is to validate
@@ -100 +101 @@
 to introduce entirely new genes in place of an error.
 \param geno input/output: genotype to be validated
+\param genoname name of the genotype to be validated
 \retval GENOPER_OK must be returned in any case ("did my best to validate")*/
-   virtual int validate(char *&geno) {return GENOPER_NOOPER;}
+   virtual int validate(char *&geno, const char *genoname) { return GENOPER_NOOPER; }
 
 /**Mutates a genotype. Mutation should always change something.