source: cpp/frams/genetics/geno.cpp @ 521

// This file is a part of Framsticks SDK.  http://www.framsticks.com/
// Copyright (C) 1999-2015  Maciej Komosinski and Szymon Ulatowski.
// See LICENSE.txt for details.

#include "geno.h"
#include "genoconv.h"
#include <common/loggers/loggers.h>
#include <common/stl-util.h>
#include <frams/model/model.h>

THREAD_LOCAL_DEF_PTR(Geno::Validators, geno_validators);
THREAD_LOCAL_DEF_PTR(GenoConvManager, geno_converters);

Geno::Validators* Geno::getValidators() {return tlsGetPtr(geno_validators);}
GenoConvManager* Geno::getConverters() {return tlsGetPtr(geno_converters);}

Geno::Validators* Geno::useValidators(Validators* val)
{return tlsSetPtr(geno_validators,val);}
GenoConvManager* Geno::useConverters(GenoConvManager* gcm)
{return tlsSetPtr(geno_converters,gcm);}

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, error_end=-1;
                        switch (genstring.charAt(1))
                        {
                        case '/':
                                genformat = genstring.charAt(2);
                                if ((genformat=='\0')||isspace(genformat))
                                        genformat=INVALID_FORMAT;
                                if ((end = genstring.indexOf('\n')) >= 0)
                                {
                                        error_end=end;
                                        if (end!=3) genformat=INVALID_FORMAT;
                                        gencopy = genstring.substr(end + 1);
                                        mapinshift = end + 1;
                                }
                                else
                                {
                                        if (genstring.len()!=3) genformat=INVALID_FORMAT;
                                        gencopy = 0;
                                        mapinshift = genstring.len();
                                }
                                break;
                        case '*':
                                genformat = genstring.charAt(2);
                                if ((genformat=='\0')||isspace(genformat))
                                        genformat=INVALID_FORMAT;
                                if ((end = genstring.indexOf("*/")) >= 0)
                                {
                                        error_end=end+2;
                                        if (end!=3) genformat=INVALID_FORMAT;
                                        gencopy = genstring.substr(end + 2);
                                        mapinshift = end + 2;
                                }
                                else
                                {
                                        if (genstring.len()!=5) genformat=INVALID_FORMAT;
                                        gencopy = 0;
                                        mapinshift = genstring.len();
                                }
                                break;
                        }
                if (genformat==INVALID_FORMAT)
                        {
                        SString cut;
                        if (error_end<0) error_end=genstring.len();
                        static const int MAX_ERROR=20;
                        if (error_end>MAX_ERROR)
                                cut=genstring.substr(0,MAX_ERROR)+"...";
                        else
                                cut=genstring.substr(0,error_end);
                        int lf=cut.indexOf('\n');
                        if (lf>=0) cut=cut.substr(0,lf);
                        logPrintf("Geno","init",LOG_ERROR,"Invalid genotype format declaration: '%s'%s",cut.c_str(),genname.len()?SString::sprintf(" in '%s'",genname.c_str()).c_str():"");
                        }

                }
        }

        gen = gencopy;
        format = genformat;
        name = genname;
        txt = comment;
        multiline = (strchr(gen.c_str(), '\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; }
        if (format == INVALID_FORMAT) { isvalid = 0; return; }
        Validators* vals=getValidators();
        if (vals!=NULL)
                {
#ifdef WARN_VALIDATION_INCONSISTENCY
                vector<int> results;
                int first_result=-1;
                FOREACH(GenoValidator*, v, (*vals))
                        {
                        int r=v->testGenoValidity(*this);
                        if (first_result<0) first_result=r;
                        results.push_back(r);
                        }
                int N=vals->size();
                for(int i=1;i<N;i++)
                        if (results[i]!=results[0])
                                {
                                SString txt="Inconsistent validation results";
                                for(int i=0;i<N;i++)
                                        txt+=SString::sprintf(" %d",results[i]);
                                txt+=" for genotype '";
                                txt+=getGene();
                                txt+="'";
                                logPrintf("Geno","validate",LOG_WARN,txt.c_str());
                                break;
                                }
                isvalid=first_result;
                if (isvalid>=0)
                        return;
#else
        FOREACH(GenoValidator*, v, (*vals))
                if ((isvalid = v->testGenoValidity(*this)) >= 0)
                        return;
#endif
                }
        isvalid = 0;
        logPrintf("Geno", "validate", LOG_WARN, "Wrong configuration? No genotype validators defined for genetic format 'f%c'.", format);
}

bool Geno::isValid(void)
{
        if (isvalid<0)
                {
                LoggerToMemory err(LoggerBase::Enable | LoggerToMemory::StoreAllMessages,LOG_INFO);
                validate();
                err.disable();
                string msg=err.getCountSummary();
                if (msg.size()>0)
                        {
                        msg+=ssprintf(" while checking validity of '%s'",getName().c_str());
                        msg+="\n";
                        msg+=err.getMessages();
                        logMessage("Geno","isValid",err.getErrorLevel(),msg.c_str());
                        }
                }
        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
        GenoConvManager *converters=getConverters();
        if (converters)
        {
                if ((otherformat == '0') && (!m))
                {
                        if (!f0gen)
                                f0gen = new Geno(converters->convert(*this, otherformat, NULL, converter_missing));
                        else
                                { if (converter_missing) *converter_missing = false; }
                        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;
}