source: cpp/frams/genetics/genoconv.cpp

// This file is a part of Framsticks SDK.  http://www.framsticks.com/
// Copyright (C) 1999-2023  Maciej Komosinski and Szymon Ulatowski.
// See LICENSE.txt for details.

#include <common/nonstd.h>

#include <stdlib.h>
#include <math.h>
#include <stdio.h>
#include <string.h>
#include <ctype.h>
#include <time.h>
#include <errno.h>

#include "genoconv.h"
#include <frams/util/multimap.h>
#include <common/util-string.h>

///////////////////////////////////////////////////////////////////////////

GenoConvParam::GenoConvParam(GenoConvManager *g) :Param(), gcm(g)
{
        updatetab();
}

void GenoConvParam::freetab()
{
        if (tab) free(tab);
        tab = 0;
}

const char *GenoConvParam::id(int i)
{
        if (i >= gcm->converters.size()) return 0;
        sprintf(tmp_id, "genoconv_%s", ((GenoConverter*)gcm->converters(i))->id().c_str());
        return tmp_id;
}

void GenoConvParam::updatetab()
{
        int i;
        GenoConverter *gk;
        ParamEntry *pe;
        int ile = gcm->converters.size();
        freetab();
        tab = (ParamEntry*)calloc(2 + ile, sizeof(ParamEntry));
        tab[0].id = "Genetics: Converters";
        tab[0].group = 1;
        tab[0].flags = (paInt)ile;
        tab[0].name = "gkparam:";
        gcnames.clear();
        gcnames.reserve(gcm->converters.size()); //avoid reallocations in the loop below, since we externally store pointers to objects saved in this vector
        for (i = 0, pe = tab + 1; gk = (GenoConverter *)gcm->converters(i); pe++, i++)
        {
                pe->id = "?";
                pe->group = 0;
                pe->flags = 0;
                std::string descr = "f";
                descr += gk->in_format.c_str();
                descr += " --> f";
                descr += gk->out_format.c_str();
                descr += "  :  ";
                descr += gk->name;
                gcnames.push_back(descr);
                pe->name = gcnames.back().c_str(); //externally store a pointer to the object just saved in the vector
                pe->type = "d 0 1";
        }
        pe->id = 0;
}

GenoConvParam::~GenoConvParam()
{
        freetab();
}

void *GenoConvParam::getTarget(int i)
{
        GenoConverter *gk = (GenoConverter *)gcm->converters(i);
        return &gk->enabled;
}

GenoConvManager::GenoConvManager()
        :conv_enabling_param(this),
        param("GenoConverters", "Converters between genetic formats")
{
        param += &conv_enabling_param;
}

GenoConvManager::~GenoConvManager()
{
        FOREACH(GenoConverter*, gc, converters) delete gc;
}

void GenoConvManager::addConverter(GenoConverter *gc)
{
        converters += gc;
        auto *pi = gc->getParam();
        if (pi)
                param += pi;
        conv_enabling_param.updatetab();
}

void GenoConvManager::removeConverter(GenoConverter *gc)
{
        converters -= gc;
        auto *pi = gc->getParam();
        if (pi)
                param -= pi;
        conv_enabling_param.updatetab();
}

GenoConverter *GenoConvManager::findConverters(SListTempl<GenoConverter*>* result, const SString& in, const SString& out, int enabled, char* name)
{
        GenoConverter *gk, *retval = 0;
        int i = 0;
        for (; gk = (GenoConverter*)converters(i); i++)
        {
                if ((in != Geno::FORMAT_UNKNOWN) && (in != gk->in_format)) continue;
                if ((out != Geno::FORMAT_UNKNOWN) && (out != gk->out_format)) continue;
                if ((enabled != -1) && (enabled != gk->enabled)) continue;
                if ((name) && (strcmp(name, gk->name))) continue;
                if (!retval) { retval = gk; if (!result) break; }
                if (result) result->append(gk);
        }
        return retval;
}

/// Writes path into 'path'.
/// return the last path element (return >= path)
/// null -> path not found
/// @param mapavailable will receive 1 if conversion map is supported by all converters in path
/// (can be NULL if you don't need this information)

GenoConverter **GenoConvManager::getPath(const SString& in_format, const SString& out_format_list, GenoConverter **path, int maxlen, int *mapavailable)
{
        if (!maxlen) return 0;
        GenoConverter *gk;
        int i = 0;
        for (; gk = (GenoConverter*)converters(i); i++)
        {
                if ((gk->enabled) && (gk->in_format == in_format))
                {
                        *path = gk;
                        if (Geno::formatIsOneOf(gk->out_format, out_format_list))
                        {
                                if (mapavailable)
                                        *mapavailable = gk->mapsupport;
                                return path;
                        }
                        else
                        {
                                int mapavail;
                                GenoConverter **ret = getPath(gk->out_format, out_format_list, path + 1, maxlen - 1, &mapavail);
                                if (ret)
                                {
                                        if (mapavailable)
                                                *mapavailable = gk->mapsupport && mapavail;
                                        return ret;
                                }
                        }
                }
        }
        return 0;
}

Geno GenoConvManager::convert(Geno &in, SString format_list, MultiMap *map, bool using_checkpoints, bool *converter_missing)
{
        if (Geno::formatIsOneOf(in.getFormat(), format_list))
        {
                if (converter_missing) *converter_missing = false;
                return in;
        }
        GenoConverter *path[10];
        int dep;
        GenoConverter **ret;
        if (in.isInvalid())
        {
                if (converter_missing) *converter_missing = false;
                return Geno("", Geno::FORMAT_INVALID, "", "Invalid genotype cannot be converted");
        }
        int mapavail;
        for (dep = 1; dep < (int)sizeof(path); dep++) //iterative deepening
                if (ret = getPath(in.getFormat(), format_list, path, dep, &mapavail)) break;
        if (!ret)
        {
                if (converter_missing) *converter_missing = true;
                return Geno("", Geno::FORMAT_INVALID, "", "Converter not found");
        }
        if (converter_missing) *converter_missing = false;
        if (!map) mapavail = 0;
        GenoConverter **t = path;
        SString tmp, out_format;
        tmp = in.getGenes();
        MultiMap lastmap, tmpmap;
        int firstmap = 1;
        for (; t <= ret; t++)
        {
                GenoConverter *gk = *t;
                tmp = gk->convert(tmp, mapavail ? &tmpmap : 0, using_checkpoints);
                out_format = gk->out_format;
                if (!tmp.length())
                {
                        string t = ssprintf("f%s->f%s conversion failed (%s)", gk->in_format.c_str(), gk->out_format.c_str(), gk->name);
                        return Geno("", Geno::FORMAT_INVALID, "", t.c_str());
                }
                if (mapavail)
                {
                        if (firstmap)
                        {
                                lastmap = tmpmap;
                                firstmap = 0;
                        }
                        else
                        {
                                MultiMap m;
                                m.addCombined(lastmap, tmpmap);
                                lastmap = m;
                        }
                        tmpmap.clear();
                }
        }
        if (map)
                *map = lastmap;
        return Geno(tmp, out_format, in.getName(), in.getComment());
}