// 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;
			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(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; }
	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;
}