Changeset 145 for cpp/frams/genetics

Timestamp:

02/26/14 20:21:22 (11 years ago)

Author:

sz

Message:

Genetics reorganization (affects ALL applications!):

• Converters/Validators? are now configured/initialized in a more verbose but also less confusing way
• At the same time, the PreconfiguredGenetics? object will help you avoid the increased complexity by creating the ready-to-use environment that is sufficient in 99% of cases (see the demos)
• Format F genetics updated (work in progress)

Location:

cpp/frams/genetics

Files:

• defgenoconv.cpp (modified) (1 diff)
• defgenoconv.h (modified) (1 diff)
• f9/oper_f9.cpp (modified) (1 diff)
• fF/fF_genotype.cpp (added)
• fF/fF_genotype.h (modified) (2 diffs)
• fF/oper_fF.cpp (modified) (3 diffs)
• fF/oper_fF.h (modified) (1 diff)
• genman.cpp (modified) (14 diffs)
• genman.h (modified) (5 diffs)
• geno.cpp (modified) (4 diffs)
• geno.h (modified) (3 diffs)
• genoconv.cpp (modified) (3 diffs)
• genoconv.h (modified) (1 diff)
• oper_fx.h (modified) (2 diffs)
• preconfigured.h (added)

cpp/frams/genetics/defgenoconv.cpp

@@ -41 +41 @@
 #endif
 
-DefaultGenoConvManager::DefaultGenoConvManager()
+void DefaultGenoConvManager::addDefaultConverters()
 {
 #ifdef USE_GENCONV_f10

cpp/frams/genetics/defgenoconv.h

@@ -8 +8 @@
 #include "genoconv.h"
 
-/// This GenoConvManager automatically registers the "standard" converters available in the GDK.
-/// All you have to do is create a single instance of this class somewhere in your application.
-/// @see genotest.cpp
+/// This GenoConvManager subclass allows you to add all "standard" converters in one go
 class DefaultGenoConvManager: public GenoConvManager
 {
   public:
-DefaultGenoConvManager();
+void addDefaultConverters();///< add all converters configured in gen-config file
 };
 

cpp/frams/genetics/f9/oper_f9.cpp

@@ -4 +4 @@
 
 #include "oper_f9.h"
-#include <frams/genetics/f9/conv_f9.h>
+#include "conv_f9.h"
 #include <common/nonstd.h> //randomN, rnd01
 

cpp/frams/genetics/fF/fF_genotype.h

@@ -8 +8 @@
 #include <stdio.h>
 #include "common/stl-util.h"
-
+#include <frams/param/param.h>
 
 struct fF_growth_params
 {
         int number_of_chambers;
-        double scalex, scaley, scalez; //scaling factors
-        double translation; //translation factor, TF range [−1; 1]
+        double scalex, scaley, scalez;
+        double translation;
         double angle1, angle2;
 
+        static ParamEntry paramtab[];
+        Param param;
+
         fF_growth_params()
+                :param(paramtab, this)
         {
                 reset();
@@ -24 +28 @@
         void reset()
         {
-                number_of_chambers = 1;
-                scalex = scaley = scalez = 1;
-                translation = 1;
-                angle1 = angle2 = 0;
+                param.setDefault();
         }
 
         bool load(const char* serialized)
         {
-                return sscanf(serialized, "%d %lf %lf %lf %lf %lf %lf", &number_of_chambers, &scalex, &scaley, &scalez, &translation, &angle1, &angle2) == 7;
+                SString s = serialized;
+                int p = 0; //position in string
+                return ((param.load2(s, p)==7) && (p==s.len()));
         }
 
         string save()
         {
-                return ssprintf("%d %f %f %f %f %f %f", number_of_chambers, scalex, scaley, scalez, translation, angle1, angle2);
+                SString tmp;
+                param.save2(tmp, NULL/*object containing default values for comparison*/, false/*add CR*/, false/*force field names*/);
+                return string((const char*)tmp);
         }
 };

cpp/frams/genetics/fF/oper_fF.cpp

@@ -4 +4 @@
 
 #include "oper_fF.h"
-#include <frams/genetics/f9/conv_f9.h>
+#include "fF_genotype.h"
 #include <common/nonstd.h> //randomN, rnd01
 
 
-//THIS FILE NEEDS UPDATE. OLD, UNRELATED SOURCES BELOW (COPIED FROM f9).
-
 #define FIELDSTRUCT GenoOper_fF
-static ParamEntry GENOf9param_tab[]=
+static ParamEntry GENOfFparam_tab[] =
 {
-        {"Genetics: fF",1,1,},
-        {"fF_mut",0,0,"Mutation probability","f 0 1 0.1",FIELD(mut_prob),"How many genes should be mutated during single mutation (1=all genes, 0.1=ten percent)",},
-        {0,},
+        { "Genetics: fF", 1, 1, },
+        { "fF_xover", 0, 0, "Averaging crossover proportion", "f 0 0.5 0.5", FIELD(xover_proportion), "0.5 => children are averaged parents.\n0.2 => children are only 20% different from parents.\n0 => each child is identical to one parent (no crossover).", },
+        { 0, },
 };
 #undef FIELDSTRUCT
@@ -22 +20 @@
 GenoOper_fF::GenoOper_fF()
 {
-        par.setParamTab(GENOf9param_tab);
+        par.setParamTab(GENOfFparam_tab);
         par.select(this);
         par.setDefault();
-        supported_format='F';
+        supported_format = 'F';
 }
 
 int GenoOper_fF::checkValidity(const char* gene)
 {
-        return GENOPER_OK;
-        if (!gene[0]) return 1; //empty is not valid
-        bool ok=true;
-        int i;
-        for(i=0;i<strlen(gene);i++) if (!strchr(turtle_commands_f9,gene[i])) {ok=false; break;}
-        return ok ? GENOPER_OK : i+1;
+        fF_growth_params par;
+        return par.load(gene) ? GENOPER_OK : 1;
 }
 
-///Remove all invalid letters from the genotype
 int GenoOper_fF::validate(char *&gene)
 {
-        SString validated; //new genotype (everything except turtle_commands_f9 is skipped)
-        for(int i=0;i<strlen(gene);i++)
-                if (strchr(turtle_commands_f9,gene[i])) validated+=gene[i];  //validated contains only turtle_commands_f9
+        fF_growth_params par; //is initialized with default values
+        par.load(gene); //loads as much as possible, other fields remain with default values
+        string validated = par.save();
         free(gene);
-        gene=strdup(validated); //reallocate
+        gene = strdup(validated.c_str()); //reallocate
         return GENOPER_OK;
 }
 
-///Very simple mutation
-int GenoOper_fF::mutate(char *&gene,float &chg,int &method)
+//Creep-mutate one property
+int GenoOper_fF::mutate(char *&gene, float &chg, int &method)
 {
-        method=0;
-        int changes=0,len=strlen(gene);
-        int symbols=strlen(turtle_commands_f9);
-
-        for(int i=0;i<len;i++)
+        method = 0;
+        fF_growth_params par;
+        par.load(gene);
+        int which = randomN(par.param.getPropCount());
+        bool mutated_ok = GenoOperators::mutatePropertyNaive(par.param, which);
+        if (mutated_ok)
         {
-                if (rnd01<mut_prob) //normalize prob with the length of the genotype
-                {
-                        char oldgene=gene[i];
-                        gene[i]=turtle_commands_f9[randomN(symbols)];
-                        if (gene[i]!=oldgene) changes++;
-                }
+                string saved = par.save();
+                free(gene);
+                gene = strdup(saved.c_str()); //reallocate
+                chg = 1.0f / par.param.getPropCount();
+                return GENOPER_OK;
         }
-
-        if (rnd01<mut_prob) //add or delete a random char
+        else
         {
-                SString newgeno(gene);
-                if (randomN(2)==0) //add
-                {
-                        int symbols=strlen(turtle_commands_f9);
-                        int p=randomN(len+1);  //random location
-                        //printf("before add: %s\n",(const char*)newgeno);
-                        newgeno=newgeno.substr(0,p)+SString(turtle_commands_f9+randomN(symbols),1)+newgeno.substr(p);
-                        //printf("after add: %s\n",(const char*)newgeno);
-                        changes++;
-                } else if (len>1) //delete
-                {
-                        int p=randomN(len);  //random location
-                        //printf("before delete: %s\n",(const char*)newgeno);
-                        newgeno=newgeno.substr(0,p)+newgeno.substr(p+1);
-                        //printf("after delete: %s\n",(const char*)newgeno);
-                        changes++;
-                }
-                free(gene);
-                gene=strdup(newgeno); //reallocate
+                chg = 0;
+                return GENOPER_OPFAIL;
         }
-
-        chg=(float)changes/len;
-        return changes>0?GENOPER_OK:GENOPER_OPFAIL; //no changes => OPFAIL so that genman will call mutate again
 }
 
-///A simple one-point crossover
-int GenoOper_fF::crossOver(char *&g1,char *&g2,float& chg1,float& chg2)
+///Averaging crossover
+int GenoOper_fF::crossOver(char *&g1, char *&g2, float& chg1, float& chg2)
 {
-        int len1=strlen(g1),len2=strlen(g2);
-        int p1=randomN(len1);  //random cut point for first genotype
-        int p2=randomN(len2);  //random cut point for second genotype
-        char *child1=(char*)malloc(p1+len2-p2+1);
-        char *child2=(char*)malloc(p2+len1-p1+1);
-        strncpy(child1,g1,p1);   strcpy(child1+p1,g2+p2);
-        strncpy(child2,g2,p2);   strcpy(child2+p2,g1+p1);
-        free(g1); g1=child1;
-        free(g2); g2=child2;
-        chg1=(float)p1/strlen(child1);
-        chg2=(float)p2/strlen(child2);
+        //g1 = strdup("1,0.5,0.5,0.5,0.5,1,1"); //testing...
+        //g2 = strdup("4,1,  1,  1,  1,  2,2"); //testing...
+        //xover_proportion = 0.1; //testing...
+        fF_growth_params par1;
+        par1.load(g1);
+        fF_growth_params par2;
+        par2.load(g2);
+        chg1 = xover_proportion;
+        chg2 = 1 - xover_proportion;
+        for (int i = 0; i < par1.param.getPropCount(); i++)
+                GenoOperators::linearMix(par1.param, i, par2.param, i, xover_proportion);
+        string saved = par1.save();
+        free(g1);
+        g1 = strdup(saved.c_str()); //reallocate
+        saved = par2.save();
+        free(g2);
+        g2 = strdup(saved.c_str()); //reallocate
         return GENOPER_OK;
 }
@@ -113 +91 @@
 unsigned long GenoOper_fF::style(const char *g, int pos)
 {
-        char ch=g[pos];
-        unsigned long style=GENSTYLE_CS(0,GENSTYLE_INVALID); //default, should be changed below
-        char *ptr=strchr((char*)turtle_commands_f9,ch);
-        if (ptr)
-        {
-                int pos=ptr-turtle_commands_f9;
-                int axis=pos/2;
-                style=GENSTYLE_RGBS(axis==0?200:0,axis==1?200:0,axis==2?200:0,GENSTYLE_NONE);
-        }
+        char ch = g[pos];
+        unsigned long style = GENSTYLE_CS(0, GENSTYLE_INVALID); //default, should be changed below
+        if (strchr("-.e 0123456789", ch) != NULL)
+                style = GENSTYLE_CS(GENCOLOR_NUMBER, GENSTYLE_NONE);
+        else if (ch == ',')
+                style = GENSTYLE_RGBS(0, 0, 0, GENSTYLE_BOLD);
         return style;
 }

cpp/frams/genetics/fF/oper_fF.h

@@ -18 +18 @@
         int crossOver(char *&g1, char *&g2, float& chg1, float& chg2);
         unsigned long style(const char *g, int pos);
-        const char* getSimplest() { return "5 0.9 0.8 0.7 0.7 0.3 0.7"; }
+        const char* getSimplest() { return "6,0.8,0.85,0.9,0.6,0.3,0.7"; }
 
-        double mut_prob; //mutation probability
+        double xover_proportion;
 };
 

cpp/frams/genetics/genman.cpp

@@ -105 +105 @@
 
 #ifdef USE_GENMAN_f0
-        geno_fx_list.push_back(new Geno_f0);
+        oper_fx_list.push_back(new Geno_f0);
 #endif
 #ifdef USE_GENMAN_f0FUZZY
-        geno_fx_list.push_back(new Geno_f0Fuzzy);
+        oper_fx_list.push_back(new Geno_f0Fuzzy);
 #endif
 #ifdef USE_GENMAN_f1
-        geno_fx_list.push_back(new Geno_f1);
+        oper_fx_list.push_back(new Geno_f1);
 #endif
 #ifdef USE_GENMAN_f2
-        geno_fx_list.push_back(new Geno_f2);
+        oper_fx_list.push_back(new Geno_f2);
 #endif
 #ifdef USE_GENMAN_f3
-        geno_fx_list.push_back(new Geno_f3);
+        oper_fx_list.push_back(new Geno_f3);
 #endif
 #ifdef USE_GENMAN_f4
-        geno_fx_list.push_back(new Geno_f4);
+        oper_fx_list.push_back(new Geno_f4);
 #endif
 #ifdef USE_GENMAN_f5
-        geno_fx_list.push_back(new Geno_f5);
+        oper_fx_list.push_back(new Geno_f5);
 #endif
 #ifdef USE_GENMAN_f6
-        geno_fx_list.push_back(new Geno_f6);
+        oper_fx_list.push_back(new Geno_f6);
 #endif
 #ifdef USE_GENMAN_f7
-        geno_fx_list.push_back(new Geno_f7);
+        oper_fx_list.push_back(new Geno_f7);
 #endif
 #ifdef USE_GENMAN_f8
-        geno_fx_list.push_back(new Geno_f8);
+        oper_fx_list.push_back(new Geno_f8);
 #endif
 #ifdef USE_GENMAN_f9
-        geno_fx_list.push_back(new GenoOper_f9);
+        oper_fx_list.push_back(new GenoOper_f9);
 #endif
 #ifdef USE_GENMAN_fF
-        geno_fx_list.push_back(new GenoOper_fF);
-#endif
-
-        seloper = new int[geno_fx_list.size()]; //may result in a little overhead if some of the operators on the geno_fx_list concern the same genetic format
+        oper_fx_list.push_back(new GenoOper_fF);
+#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
         int selopercount = 0;
-        for (unsigned int i = 0; i < geno_fx_list.size(); i++)
-        {
-                if (operformats.find(geno_fx_list[i]->supported_format) != -1) continue;
+        for (unsigned int i = 0; i < oper_fx_list.size(); i++)
+        {
+                if (operformats.find(oper_fx_list[i]->supported_format) != -1) continue;
                 char tmp[10];
                 SString id, name, type = "~";
-                type += geno_fx_list[i]->name;
+                type += oper_fx_list[i]->name;
                 int dup = 0;
-                for (unsigned int j = i + 1; j < geno_fx_list.size(); j++)
-                        if (geno_fx_list[i]->supported_format == geno_fx_list[j]->supported_format)
+                for (unsigned int j = i + 1; j < oper_fx_list.size(); j++)
+                        if (oper_fx_list[i]->supported_format == oper_fx_list[j]->supported_format)
                         {
-                                type += "~"; type += geno_fx_list[j]->name; dup++;
+                                type += "~"; type += oper_fx_list[j]->name; dup++;
                         }
                 sprintf(tmp, "d 0 %d ", dup);
                 type = SString(tmp) + type;
-                sprintf(tmp, "%c", geno_fx_list[i]->supported_format);
+                sprintf(tmp, "%c", oper_fx_list[i]->supported_format);
                 id = "genoper_f"; id += tmp;
                 name = "Operators for f"; name += tmp;
                 seloper[selopercount] = 0;
-                operformats += geno_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, type, name, "", PARAM_READONLY*(dup == 0));
@@ -169 +169 @@
         par += &seloperpar;
         par += &neuronsparam;
-        for (unsigned int i = 0; i < geno_fx_list.size(); i++)
-                if (geno_fx_list[i]->par.getParamTab()) par += &geno_fx_list[i]->par;
+        for (unsigned int i = 0; i < oper_fx_list.size(); i++)
+                if (oper_fx_list[i]->par.getParamTab()) par += &oper_fx_list[i]->par;
 }
 
 GenMan::~GenMan()
 {
-        for (unsigned int i = 0; i < geno_fx_list.size(); i++) delete geno_fx_list[i];
+        for (unsigned int i = 0; i < oper_fx_list.size(); i++) delete oper_fx_list[i];
         delete[] seloper;
 }
@@ -181 +181 @@
 void GenMan::setDefaults()
 {
-        for (unsigned int i = 0; i < geno_fx_list.size(); i++)
-        {
-                geno_fx_list[i]->par.setDefault();
-                geno_fx_list[i]->setDefaults();
+        for (unsigned int i = 0; i < oper_fx_list.size(); i++)
+        {
+                oper_fx_list[i]->par.setDefault();
+                oper_fx_list[i]->setDefaults();
         }
         localpar.setDefault();
@@ -194 +194 @@
 {
         const char *gg = g.getGene();
-        GenoOperators *gf = getGeno_f(g.getFormat());
+        GenoOperators *gf = getOper_f(g.getFormat());
         int check1;
         if (!gf) { canvalidate = false; return GENOPER_NOOPER; }
@@ -228 +228 @@
 {
         char format=geny.getFormat();
-        GenoOperators *gf=getGeno_f(format);
+        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));
@@ -246 +246 @@
         int method; //mutation method
         char format=g.getFormat();
-        GenoOperators *gf=getGeno_f(format);
+        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));
@@ -292 +292 @@
         char format = g1.getFormat();
         if (format != g2.getFormat()) return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: CrossOver() does not know how to handle parents with differing genetic formats (%c and %c)", format, g2.getFormat()));
-        GenoOperators *gf = getGeno_f(format);
+        GenoOperators *gf = getOper_f(format);
         if (gf == NULL)
                 return Geno(SString::empty(), -1, SString::empty(), SString::sprintf("GENOPER_NOOPER: CrossOver(): don't know how to handle genetic format %c", format));
@@ -358 +358 @@
         char format = g1.getFormat();
         if (format != g2.getFormat()) return GENOPER_NOOPER;
-        GenoOperators *gf = getGeno_f(format);
+        GenoOperators *gf = getOper_f(format);
         if (!gf) return GENOPER_NOOPER; else return gf->similarity(g1.getGene(), g2.getGene());
 }
@@ -366 +366 @@
         Geno G(g);
         if ((pos = G.mapStringToGen(pos)) == -1) return GENSTYLE_COMMENT;
-        GenoOperators *gf = getGeno_f(G.getFormat());
+        GenoOperators *gf = getOper_f(G.getFormat());
         if (!gf) return GENSTYLE_CS(0, 0); //black & valid
         else return gf->style(G.getGene(), pos);
@@ -374 +374 @@
 {
         Geno G(g);
-        GenoOperators *gf = getGeno_f(G.getFormat());
+        GenoOperators *gf = getOper_f(G.getFormat());
         SString geny = G.getGene();
         for (unsigned int pos = 0; pos < strlen(g); pos++)
@@ -448 +448 @@
 Geno GenMan::GetSimplest(char format)
 {
-        GenoOperators *gf = getGeno_f(format);
+        GenoOperators *gf = getOper_f(format);
         if (!gf) return Geno();
         SString info = "The simplest genotype of format f"; info += format;
@@ -458 +458 @@
 {
         int format = args[0].getInt() + 48;
-        if (!getGeno_f(format))
+        if (!getOper_f(format))
                 ret->setEmpty();
         else
@@ -466 +466 @@
 const char *GenMan::GetOpName(char format)
 {
-        GenoOperators *gf = getGeno_f(format);
+        GenoOperators *gf = getOper_f(format);
         if (!gf) return "n/a"; else return gf->name;
 }
 
-GenoOperators* GenMan::getGeno_f(char format)
+GenoOperators* GenMan::getOper_f(char format)
 {
         int ind = operformats.find(format);
         if (ind == -1) return NULL;
         int ktoryopformatu = seloper[ind];
-        for (unsigned int i = 0; i < geno_fx_list.size(); i++)
-                if (geno_fx_list[i]->supported_format == format)
-                        if (ktoryopformatu == 0) return geno_fx_list[i]; else ktoryopformatu--;
+        for (unsigned int i = 0; i < oper_fx_list.size(); i++)
+                if (oper_fx_list[i]->supported_format == format)
+                        if (ktoryopformatu == 0) return oper_fx_list[i]; else ktoryopformatu--;
         return NULL; //should never happen
 }
@@ -519 +519 @@
 {                      //should be updated to handle multiple operators for a single format
         char *g, *g2;
-        float f; int m;
+        float f1, f2;
+        int m;
         FramMessage("GenMan", "Report", "The following genetic operators are available:", 0);
-        for (unsigned int i = 0; i < geno_fx_list.size(); i++)
+        for (unsigned int i = 0; i < oper_fx_list.size(); i++)
         {
                 SString l;
-                if (geno_fx_list[i]->checkValidity("") != GENOPER_NOOPER) l += " checkValidity";
-                if (geno_fx_list[i]->getSimplest())
-                {
-                        g = strdup(geno_fx_list[i]->getSimplest());
+                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 (geno_fx_list[i]->validate(g) != GENOPER_NOOPER) l += " validate";
-                        if (geno_fx_list[i]->mutate(g, f, m) != GENOPER_NOOPER) l += " mutate";
-                        if (geno_fx_list[i]->crossOver(g, g2, f, f) != GENOPER_NOOPER) l += " crossover";
+                        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";
                         l += " getSimplest";
                         free(g); free(g2);
                 }
-                //      if (geno_fx_list[i]->similarity("","")!=GENOPER_NOOPER) l+=" similarity";
+                //      if (oper_fx_list[i]->similarity("","")!=GENOPER_NOOPER) l+=" similarity";
                 FMprintf("GenMan", "Report", 0, "format f%c (%s):%s",
-                        geno_fx_list[i]->supported_format, (const char*)geno_fx_list[i]->name, (const char*)l);
+                        oper_fx_list[i]->supported_format, (const char*)oper_fx_list[i]->name, (const char*)l);
         }
 }

cpp/frams/genetics/genman.h

@@ -7 +7 @@
 
 #include <common/nonstd.h>
+#include <common/nonstd_stl.h>
 #include <frams/param/mutableparam.h>
 #include <frams/param/mutparamlist.h>
@@ -12 +13 @@
 #include "geno.h"
 #include "oper_fx.h"
-#include <string>
-#include <vector>
 
 #define GENSTYLE_COMMENT GENSTYLE_RGBS(0,150,0,GENSTYLE_BOLD)
@@ -20 +19 @@
 {
         int count;
-        std::string g1, g2;
+        string g1, g2;
         float chg;
         float fit;
@@ -53 +52 @@
         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
+        const vector<GenoOperators*>& GetOperators() const { return oper_fx_list; } ///<returns the list of available genetic operators
 private:
-        std::vector<GenoOperators*> geno_fx_list;
-        void saveLink(std::string prz, std::string pot, float& chg);
-        GenoOperators* getGeno_f(char format);
+        vector<GenoOperators*> oper_fx_list;
+        void saveLink(string prz, string pot, float& chg);
+        GenoOperators* getOper_f(char format);
         SString HTMLize(const char *g, bool shorten);
 public:
-        std::vector<GenoLink> GenoLinkList;
+        vector<GenoLink> GenoLinkList;
         int history; //remember history?
         int hilite; //syntax highlighting (Style)
@@ -66 +66 @@
         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 order same as in seloperpar
+        SListTempl<char> operformats; //the list of supported_format, in the same order as in seloperpar
         int* seloper; //fields for seloperpar
         Param localpar, localstats;

cpp/frams/genetics/geno.cpp

@@ -4 +4 @@
 
 #include "geno.h"
+#include "genoconv.h"
 #include <frams/model/model.h>
 
 SListTempl<GenoValidator*> Geno::validators;
+GenoConvManager *Geno::converters=NULL;
 
 void Geno::init(const SString& genstring,char genformat,const SString& genname,const SString& comment)
@@ -209 +211 @@
 SString Geno::getComment(void) const {return txt;}
 
-class ModelGenoValidator: public GenoValidator
-{
-public:
-        ModelGenoValidator();
-        int testGenoValidity(Geno& g);
-};
-
-ModelGenoValidator::ModelGenoValidator()
-{
-Geno::validators+=this;
-}
-
 int ModelGenoValidator::testGenoValidity(Geno& g)
 {
@@ -234 +224 @@
         }
 }
-
-static ModelGenoValidator default_validator;
 
 void Geno::validate()
@@ -256 +244 @@
 if (otherformat==getFormat()) return *this;
 #ifndef NO_GENOCONVMANAGER
-if ((otherformat=='0')&&(!m))
-        {
-        if (!f0gen)
-                f0gen=new Geno(GenoConvManager::globalConvert(*this,otherformat));
-        return *f0gen;
-        }
-else
-        return GenoConvManager::globalConvert(*this,otherformat,m);
-#else
+if (converters)
+        {
+        if ((otherformat=='0')&&(!m))
+                {
+                if (!f0gen)
+                        f0gen=new Geno(converters->convert(*this,otherformat));
+                return *f0gen;
+        }
+        else
+                return converters->convert(*this,otherformat,m);
+        }
+#endif
 return (otherformat==getFormat())?*this:Geno(0,0,0,"GenConvManager not available");
-#endif
 }
 

cpp/frams/genetics/geno.h

@@ -11 +11 @@
 class MultiMap;
 class Geno;
+class GenoConvManager;
 
 class GenoValidator
@@ -18 +19 @@
 };
 
+/// basic GenoValidator that works by building a Model from any Geno (by converting to f0)
+/// validation fails when the model can't be built or the genotype can't be converted
+class ModelGenoValidator: public GenoValidator
+{
+public:
+        int testGenoValidity(Geno& g);
+};
+
 /// basic information about a single genotype.
 class Geno: public DestrBase
 {
+friend class Simulator;//needs to access validators directly
 SString gen;
 SString name;
@@ -103 +113 @@
 
 void* owner;
+
+// managing global Geno-related objects (used for validation and conversion)
+static void addValidator(GenoValidator* gv) {validators+=gv;}
+static void removeValidator(GenoValidator* gv) {validators-=gv;}
+static void useConverters(GenoConvManager& gcm) {converters=&gcm;}
+static GenoConvManager &getConverters() {return *converters;}
+  protected:
+static GenoConvManager *converters;
 static SListTempl<GenoValidator*> validators;
 };

cpp/frams/genetics/genoconv.cpp

@@ -82 +82 @@
         :param(this)
 {
-if (!globalobject) globalobject=this;
 }
 
@@ -89 +88 @@
 GenoConverter *gc;
 for (converters.start();gc=(GenoConverter*)converters();) delete gc;
-if (globalobject==this) globalobject=NULL;
-}
-
-GenoConvManager *GenoConvManager::globalobject=NULL;
+}
 
 void GenoConvManager::addConverter(GenoConverter *gc)
@@ -217 +213 @@
 return Geno(tmp, format, in.getName(), in.getComment());
 }
-
-Geno GenoConvManager::globalConvert(Geno &in,char format,MultiMap *map)
-{
-if (globalobject) return globalobject->convert(in,format,map);
-if (format==in.getFormat()) return in;
-return Geno(0,0,0,"GenConvManager not initialized");
-}
-
-/////////////////////////////////

cpp/frams/genetics/genoconv.h

@@ -73 +73 @@
 friend class GenoConvParam;
 SList converters;
-static GenoConvManager *globalobject;
 public:
 GenoConvManager();
 ~GenoConvManager();
 class GenoConvParam param;
-/// select an object for use as global GenoConvManager
-void useManager(GenoConvManager *m) {globalobject=m;}
-/// get global converter
-static GenoConvManager *getGlobalObject() {return globalobject;}
 /// make a genotype in other format. genotype will be invalid
 /// if GenoConvManager cannot convert it.
 Geno convert(Geno &in,char format,MultiMap *map=0);
-/// static conversion function (uses global GenoConvManager)
-static Geno globalConvert(Geno &in,char format,MultiMap *map=0);
-/// register GenoConverter
+/// register GenoConverter, the added object will be automatically deleted when GenoConvManager is destructed (call removeConverter() if this is not desirable)
 void addConverter(GenoConverter *conv);
 /// unregister GenoConverter

cpp/frams/genetics/oper_fx.h

@@ -81 +81 @@
  public:
    Param par;
-   char supported_format; ///<genotype format which is supported by this class ('6' for Geno_f6, etc.). Must be initialized in constructor
+   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
    SString name; ///<name of this set of genetic operators
    char **mutation_method_names; ///<array of names for mutation methods. If initialized (by new char*[]), must have entries for each method index returned by mutate(geno,chg,METHOD).  If initialized, it is automatically freed by this destructor.
@@ -187 +187 @@
    static double mutateCreepNoLimit(char type,double current,double mn,double mx); ///<returns \e current value creep-mutated with Gaussian distribution within [ \e mn , \e mx ] interval. Forced precision: 3 digits after comma. \e type must be either 'd' (integer) or 'f' (float/double).
    static double mutateCreep(char type,double current,double mn,double mx); ///<just as mutateCreepNoLimit(), but forces mutated value into the [mn,mx] range using the 'reflect' approach.
+   static void setIntFromDoubleWithProbabilisticDithering(ParamInterface &p, int index, double value); ///<sets a double value in an integer field; when a value is non-integer, applies random "dithering" so that both lower and higher integer value have some chance to be set.
+   static void linearMix(ParamInterface &p1, int i1, ParamInterface &p2, int i2, double proportion); ///<mixes i1'th and i2'th properties of p1 and p2; proportion should be within [0,1]; 0.5 causes both properties to become their average. For integer properties applies random "dithering" when necessary.
    static NeuroClass* getRandomNeuroClass(); ///<returns random neuroclass or NULL when no active classes.
    static NeuroClass* parseNeuroClass(char *&s); ///<returns neuroclass or NULL if the string does not begin with a valid name. Advance \e s pointer.