source: cpp/frams/genetics/genoconv.h @ 132

// This file is a part of the Framsticks GDK.
// Copyright (C) 2002-2014  Maciej Komosinski and Szymon Ulatowski.  See LICENSE.txt for details.
// Refer to http://www.framsticks.com/ for further information.

#ifndef _GENCONV_H_
#define _GENCONV_H_

#include "geno.h"
#include <frams/param/param.h>
#include <frams/util/list.h>
#include <frams/util/sstring.h>

#include <string>
#include <vector>


class GenoConvManager;

class GenoConvParam: public Param
{
GenoConvManager *gcm;
std::vector<std::string> gcnames;
char tmp_id[20];
void freetab();
public:
GenoConvParam(GenoConvManager *g);
~GenoConvParam();
void *getTarget(int);
const char* id(int i);
void updatetab();
};

class MultiMap;

/// Base class for all Geno Converters.
/// In constructor you have to set public fields
/// indicating your identity and supported formats.
/// Each converter serves one in-out format pair.
/// Instance of your converter should be registered
/// in GenoConvManager.
class GenoConverter
{
public:
const char *name;       //< converter name (short)
char in_format,         //< input format, eg. '1'
        out_format;     //< output format, eg. '0'
const char *info;       //< detailed info about converter, format or copyright
long enabled;   //< don't touch this! (used by configuration module)
long mapsupport; //< set to 1 if your converter supports genotype mapping

/// You have to reimplement this method.
/// If your converter cannot do its job, return empty string
/// (return SString();), any other return value is assumed
/// to be output genotype.
/// @param map if not null, mapping informaton is requested, converter should add conversion map to this object
virtual SString convert(SString &i,MultiMap *map) {return SString();}

virtual ~GenoConverter() {}
/// Don't forget to set public fields in your constructor
GenoConverter():name(""),in_format(-1),out_format('0'),info(""),enabled(1),mapsupport(0) {}
};

/// This class gathers abilities of all converters and can
/// convert a genotype to any other one, provided there is
/// a path of GenoConverters between them.
/// In most cases you don't use this class directly,
/// Geno::getConverted(int) provides full converting functionality.
/// Explicit GenoConvManager object is only needed for registering
/// your GenoConverter.
/// Use DefaultGenoConvManager to register the standard genotype converters automatically.
class GenoConvManager
{
friend class GenoConvParam;
SList converters;
static GenoConvManager *globalobject;
public:
GenoConvManager();
~GenoConvManager();
class GenoConvParam param;
/// select an object for use as global GenoConvManager
void useManager(GenoConvManager *m) {globalobject=m;}
/// get global converter
static GenoConvManager *getGlobalObject() {return globalobject;}
/// make a genotype in other format. genotype will be invalid
/// if GenoConvManager cannot convert it.
Geno convert(Geno &in,char format,MultiMap *map=0);
/// static conversion function (uses global GenoConvManager)
static Geno globalConvert(Geno &in,char format,MultiMap *map=0);
/// register GenoConverter
void addConverter(GenoConverter *conv);
/// unregister GenoConverter
void removeConverter(GenoConverter *conv);

char *getPath(char in,char out,char *path,int maxlen,int *mapavailable=0);
char *getFormatPath(char in,char out,char *path,int maxlen,int *mapavailable=0);
/// returns the list of converters meeting the specified criteria
/// pass result=0 if you only need one result (by return value)
/// default criteria values mean "don't care", pass anything else to narrow your search
GenoConverter *findConverters(SListTempl<GenoConverter*>* result=0,char in=-1,char out=-1,int enabled=-1,char* name=0);
};

#endif