source: cpp/frams/genetics/fF/oper_fF.cpp @ 140

Last change on this file since 140 was 140, checked in by sz, 8 years ago

introducing the Foraminifera encoding (format 'F')

  • Property svn:eol-style set to native
File size: 3.6 KB
Line 
1// This file is a part of the Framsticks GDK.
2// Copyright (C) 2002-2014  Maciej Komosinski and Szymon Ulatowski.  See LICENSE.txt for details.
3// Refer to http://www.framsticks.com/ for further information.
4
5#include "oper_fF.h"
6#include <frams/genetics/f9/conv_f9.h>
7#include <common/nonstd.h> //randomN, rnd01
8
9
10//THIS FILE NEEDS UPDATE. OLD, UNRELATED SOURCES BELOW (COPIED FROM f9).
11
12#define FIELDSTRUCT GenoOper_fF
13static ParamEntry GENOf9param_tab[]=
14{
15        {"Genetics: fF",1,1,},
16        {"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)",},
17        {0,},
18};
19#undef FIELDSTRUCT
20
21
22GenoOper_fF::GenoOper_fF()
23{
24        par.setParamTab(GENOf9param_tab);
25        par.select(this);
26        par.setDefault();
27        supported_format='F';
28}
29
30int GenoOper_fF::checkValidity(const char* gene)
31{
32        return GENOPER_OK;
33        if (!gene[0]) return 1; //empty is not valid
34        bool ok=true;
35        int i;
36        for(i=0;i<strlen(gene);i++) if (!strchr(turtle_commands_f9,gene[i])) {ok=false; break;}
37        return ok ? GENOPER_OK : i+1;
38}
39
40///Remove all invalid letters from the genotype
41int GenoOper_fF::validate(char *&gene)
42{
43        SString validated; //new genotype (everything except turtle_commands_f9 is skipped)
44        for(int i=0;i<strlen(gene);i++)
45                if (strchr(turtle_commands_f9,gene[i])) validated+=gene[i];  //validated contains only turtle_commands_f9
46        free(gene);
47        gene=strdup(validated); //reallocate
48        return GENOPER_OK;
49}
50
51///Very simple mutation
52int GenoOper_fF::mutate(char *&gene,float &chg,int &method)
53{
54        method=0;
55        int changes=0,len=strlen(gene);
56        int symbols=strlen(turtle_commands_f9);
57
58        for(int i=0;i<len;i++)
59        {
60                if (rnd01<mut_prob) //normalize prob with the length of the genotype
61                {
62                        char oldgene=gene[i];
63                        gene[i]=turtle_commands_f9[randomN(symbols)];
64                        if (gene[i]!=oldgene) changes++;
65                }
66        }
67
68        if (rnd01<mut_prob) //add or delete a random char
69        {
70                SString newgeno(gene);
71                if (randomN(2)==0) //add
72                {
73                        int symbols=strlen(turtle_commands_f9);
74                        int p=randomN(len+1);  //random location
75                        //printf("before add: %s\n",(const char*)newgeno);
76                        newgeno=newgeno.substr(0,p)+SString(turtle_commands_f9+randomN(symbols),1)+newgeno.substr(p);
77                        //printf("after add: %s\n",(const char*)newgeno);
78                        changes++;
79                } else if (len>1) //delete
80                {
81                        int p=randomN(len);  //random location
82                        //printf("before delete: %s\n",(const char*)newgeno);
83                        newgeno=newgeno.substr(0,p)+newgeno.substr(p+1);
84                        //printf("after delete: %s\n",(const char*)newgeno);
85                        changes++;
86                }
87                free(gene);
88                gene=strdup(newgeno); //reallocate
89        }
90
91        chg=(float)changes/len;
92        return changes>0?GENOPER_OK:GENOPER_OPFAIL; //no changes => OPFAIL so that genman will call mutate again
93}
94
95///A simple one-point crossover
96int GenoOper_fF::crossOver(char *&g1,char *&g2,float& chg1,float& chg2)
97{
98        int len1=strlen(g1),len2=strlen(g2);
99        int p1=randomN(len1);  //random cut point for first genotype
100        int p2=randomN(len2);  //random cut point for second genotype
101        char *child1=(char*)malloc(p1+len2-p2+1);
102        char *child2=(char*)malloc(p2+len1-p1+1);
103        strncpy(child1,g1,p1);   strcpy(child1+p1,g2+p2);
104        strncpy(child2,g2,p2);   strcpy(child2+p2,g1+p1);
105        free(g1); g1=child1;
106        free(g2); g2=child2;
107        chg1=(float)p1/strlen(child1);
108        chg2=(float)p2/strlen(child2);
109        return GENOPER_OK;
110}
111
112///Applying some colors and font styles...
113unsigned long GenoOper_fF::style(const char *g, int pos)
114{
115        char ch=g[pos];
116        unsigned long style=GENSTYLE_CS(0,GENSTYLE_INVALID); //default, should be changed below
117        char *ptr=strchr((char*)turtle_commands_f9,ch);
118        if (ptr)
119        {
120                int pos=ptr-turtle_commands_f9;
121                int axis=pos/2;
122                style=GENSTYLE_RGBS(axis==0?200:0,axis==1?200:0,axis==2?200:0,GENSTYLE_NONE);
123        }
124        return style;
125}
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