Haplotype.h

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//
// This file is part of the MADELINE 2 program 
// written by Edward H. Trager and Ritu Khanna
// Copyright (c) 2005 by the
// Regents of the University of Michigan.
// All Rights Reserved.
// 
// The latest version of this program is available from:
// 
//   http://eyegene.ophthy.med.umich.edu/madeline/
//   
// Released under the GNU General Public License.
// A copy of the GPL is included in the distribution
// package of this software, or see:
// 
//   http://www.gnu.org/copyleft/
//   
// ... for licensing details.
// 

//
// 2005.08.17.ET.RK
//

//
// Haplotype.h
//

#ifndef HAPLOTYPE_INCLUDED
#define HAPLOTYPE_INCLUDED

#include <string>
#include <iostream>
#include "Data.h"
#include "Number.h"

class Haplotype : public Data{
public:
        
        // RECOMBINATION INFORMATION enumeration:
        enum RECOMBINATION_INFO{ MISSING_INFO='.',NO_INFORMATION=':',NO_RECOMBINATION='|',MATERNAL_RECOMBINATION='/',PATERNAL_RECOMBINATION='\\',BOTH_RECOMBINE='+' };
        
private:
        static std::set<std::string> _haplotypeMissingValue;
        bool _isMissing;
        std::string _haplotype;
        
        RECOMBINATION_INFO _recombination;
        
        unsigned char _getRecombinationInfoSortOrder(void) const;
public:
        
        //
        // Static methods:
        //
        static void addHaplotypeMissingValue(std::string value){ _haplotypeMissingValue.insert(value); }
        static bool isMissingValue(std::string value);
        
        // Constructors:
        Haplotype(){ setMissing(); }
        Haplotype(const char *h){ set(h); }
        Haplotype(const std::string& h){ set(h.c_str()); }
        
        //  Methods required by Data virtual base class:
        bool isMissing( void ) const { return _isMissing; }
        void setMissing( void );
        void set( const char *haplotype );
        void set( const std::string &haplotype);
        const std::string get( void ) const; 
        
        //
        // Operators:
        bool operator<( const Data& b) const;
        bool operator==( const Data& b) const;
        const DATATYPE getDataType( void ) const { return HAPLOTYPE; }
        virtual Haplotype* clone() const;
        
        // Additional methods:
        const std::string  getAlleleFromMom( void ) const;
        const std::string  getAlleleFromDad( void ) const;
        Haplotype::RECOMBINATION_INFO getRecombinationInfo( void ) const;
        
};

std::ostream &operator<<(std::ostream &s,const Haplotype &g);

#endif

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