source: cpp/frams/genetics/geno.cpp @ 247

// This file is a part of the Framsticks GDK.
// Copyright (C) 1999-2014  Maciej Komosinski and Szymon Ulatowski.  See LICENSE.txt for details.
// Refer to http://www.framsticks.com/ for further information.

#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)
{
        refcount = 1;
        owner = 0;
        f0gen = 0;
        mapinshift = 0;
        mapoutshift = 0;
        isvalid = -1;
        SString gencopy(genstring);
        if (genformat == -1)
        { // unknown format
                genformat = '1';
                if (genstring.charAt(0) == '/')
                {
                        int end;
                        SString newcomment;
                        switch (genstring.charAt(1))
                        {
                        case '/':
                                genformat = genstring.charAt(2);
                                if ((end = genstring.indexOf('\n')) >= 0)
                                {
                                        newcomment = genstring.substr(2, end - 2);
                                        gencopy = genstring.substr(end + 1);
                                        mapinshift = end + 1;
                                }
                                else
                                {
                                        gencopy = 0;
                                        mapinshift = genstring.len();
                                }
                                break;
                        case '*':
                                genformat = genstring.charAt(2);
                                if ((end = genstring.indexOf("*/")) >= 0)
                                {
                                        newcomment = genstring.substr(2, end - 2);
                                        gencopy = genstring.substr(end + 2);
                                        mapinshift = end + 2;
                                }
                                else
                                {
                                        gencopy = 0;
                                        mapinshift = genstring.len();
                                }
                                break;
                        }
                        if (newcomment.len() > 0)
                        {
                                SString token; int pos = 0;
                                if (newcomment.getNextToken(pos, token, ';'))
                                        if (newcomment.getNextToken(pos, token, ';'))
                                        {
                                                if (token.len()) txt = token;
                                                if (newcomment.getNextToken(pos, token, ';'))
                                                        if (token.len()) name = token;
                                        }
                        }
                }
        }

        gen = gencopy;
        format = genformat;
        if (!name.len()) name = genname;
        if (!txt.len()) txt = comment;
        multiline = (strchr((const char*)gen, '\n') != 0);
        // mapoutshift...?
}

void Geno::freeF0()
{
        if (f0gen) { delete f0gen; f0gen = 0; }
}

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)
{
        init(genstring, genformat, genname, comment);
}

Geno::Geno(const Geno& src)
:gen(src.gen), name(src.name), format(src.format), txt(src.txt), isvalid(src.isvalid),
f0gen(0), mapinshift(src.mapinshift), mapoutshift(src.mapinshift),
multiline(src.multiline), owner(0)
{
        f0gen = src.f0gen ? new Geno(*src.f0gen) : 0; refcount = 1;
}

void Geno::operator=(const Geno& src)
{
        freeF0();
        gen = src.gen;
        name = src.name;
        format = src.format;
        txt = src.txt;
        isvalid = src.isvalid;
        mapinshift = src.mapinshift;
        mapoutshift = src.mapinshift;
        multiline = src.multiline;
        f0gen = src.f0gen ? new Geno(*src.f0gen) : 0;
        owner = 0;
}

Geno::Geno(const SString& src)
{
        init(src, -1, SString::empty(), SString::empty());
}

void Geno::setGene(const SString& g, char newformat)
{
        gen = g;
        isvalid = -1;
        freeF0();
        if (newformat >= 0) format = newformat;
}

void Geno::setString(const SString& g)
{
        freeF0();
        init(g, -1, SString::empty(), SString::empty());
}

void Geno::setName(const SString& n)
{
        name = n;
}

void Geno::setComment(const SString& c)
{
        txt = c;
}

SString Geno::toString(void) const
{
        SString out;
        int comment = 0;
        if ((format != '1') || (comment = (txt.len() || name.len())))
        {
                if (multiline)
                        out += "//";
                else
                        out += "/*";
                out += format;
                if (comment)
                {
                        if (txt.len()) { out += ";"; out += txt; }
                        if (name.len()){ out += ";"; out += name; }
                }
                if (multiline)
                        out += "\n";
                else
                        out += "*/";
        }
        out += gen;
        return out;
}

SString Geno::shortString(void) const
{
        SString out;
        if (format != '1')
        {
                if (multiline)
                        out += "//";
                else
                        out += "/*";
                if (format == 0)
                        out += "invalid";
                else
                        out += format;
                if (multiline)
                        out += "\n";
                else
                        out += "*/";
        }
        out += gen;
        return out;
}

int Geno::mapGenToString(int genpos) const
{
        if (genpos > gen.len()) return -2;
        if (genpos<0) return -1;
        return mapinshift + genpos;
}

int Geno::mapStringToGen(int stringpos) const
{
        stringpos -= mapinshift;
        if (stringpos>gen.len()) return -2;
        if (stringpos < 0) return -1;
        return stringpos;
}

SString Geno::getGene(void) const { return gen; }
SString Geno::getName(void) const { return name; }
char Geno::getFormat(void) const { return format; }
SString Geno::getComment(void) const { return txt; }

int ModelGenoValidator::testGenoValidity(Geno& g)
{
        if (g.getFormat() == '0')
        {
                Model mod(g);
                return mod.isValid();
        }
        else
        {
                bool converter_missing;
                Geno f0geno = g.getConverted('0', NULL, &converter_missing);
                if (converter_missing)
                        return -1;//no result
                return f0geno.isValid();
        }
}

void Geno::validate()
{
        if (isvalid >= 0) return;
        if (gen.len() == 0) { isvalid = 0; return; }
        FOREACH(GenoValidator*, v, validators)
                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);
}

bool Geno::isValid(void)
{
        if (isvalid<0) validate();
        return isvalid>0;
}

Geno Geno::getConverted(char otherformat, MultiMap *m, bool *converter_missing)
{
        if (otherformat == getFormat()) { if (converter_missing) *converter_missing = false; return *this; }
#ifndef NO_GENOCONVMANAGER
        if (converters)
        {
                if ((otherformat == '0') && (!m))
                {
                        if (!f0gen)
                                f0gen = new Geno(converters->convert(*this, otherformat, NULL, converter_missing));
                        return *f0gen;
                }
                else
                        return converters->convert(*this, otherformat, m, converter_missing);
        }
#endif
        if (converter_missing) *converter_missing = true;
        return (otherformat == getFormat()) ? *this : Geno(0, 0, 0, "GenConvManager not available");
}

Geno::~Geno()
{
        if (f0gen) delete f0gen;
}