text: /*******************************************************************************
   * Copyright (C) 2018 Olivier Delaneau, University of Lausanne
   * 
   * Permission is hereby granted, free of charge, to any person obtaining a copy
   * of this software and associated documentation files (the "Software"), to deal
   * in the Software without restriction, including without limitation the rights
   * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
   * copies of the Software, and to permit persons to whom the Software is
   * furnished to do so, subject to the following conditions:
   * 
   * The above copyright notice and this permission notice shall be included in
   * all copies or substantial portions of the Software.
   * 
   * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
   * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
   * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
   * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
   * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
   * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   * SOFTWARE.
   ******************************************************************************/
  #ifndef _SNP_SET_H
  #define _SNP_SET_H
  
  #include <utils/otools.h>
  #include <objects/variant.h>
  #include <io/gmap_reader.h>
  
  class variant_map {
  public :
  	//DATA
  	vector < variant * > vec_pos;			//vector of variants ordered by position in bp
  	multimap < int, variant * > map_pos;	//associative container of variant with position in bp
  
  	//CONSTRUCTOR/DESTRUCTOR
  	variant_map();
  	~variant_map();
  
  	//METHODS
  	int size();
  	vector < variant * > getByPos(int);
  	vector < variant * > getByRef(int, string &, string &);
  	variant * getByIndex(int);
  	void push(variant *);
  	void setGeneticMap(gmap_reader&);
  	int setCentiMorgan(vector < int > & pos_bp, vector < double > & pos_cM);
  	int interpolateCentiMorgan(vector < int > & pos_bp, vector < double > & pos_cM);
  	unsigned int length();
  };
  
  #endif
  