BaseComposition.h

/*
 *  Copyright (C) 2010  Regents of the University of Michigan
 *
 *   This program is free software: you can redistribute it and/or modify
 *   it under the terms of the GNU General Public License as published by
 *   the Free Software Foundation, either version 3 of the License, or
 *   (at your option) any later version.
 *
 *   This program is distributed in the hope that it will be useful,
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *   GNU General Public License for more details.
 *
 *   You should have received a copy of the GNU General Public License
 *   along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

#ifndef __BASE_COMPOSITION_H__
#define __BASE_COMPOSITION_H__

#include <map>

#include "BaseAsciiMap.h"
#include "BaseCount.h"

class BaseComposition
{
 public:
   // Constructor.
   BaseComposition();

   // Update the composition for the specified index with the specified
   // character.
   // Return false if the character is not a valid raw sequence character.
   // Return true if it is valid.
   bool updateComposition(unsigned int rawSequenceCharIndex, char baseChar);

   BaseAsciiMap::SPACE_TYPE getSpaceType()
   {
      return(myBaseAsciiMap.getSpaceType());
   }

   void resetBaseMapType()
   {
      myBaseAsciiMap.resetBaseMapType();
   };

   void setBaseMapType(BaseAsciiMap::SPACE_TYPE spaceType)
   {
      myBaseAsciiMap.setBaseMapType(spaceType);
   }

   // Print the composition.
   void print();

   // Clear the composition stored in the base count vector.
   void clear();

 private:
   // Map of bases used to determine if a character is valid and if so
   // maps it to a number.
   BaseAsciiMap myBaseAsciiMap;

   // Vector used to store the occurrence of each base type at a given 
   // read location.
   vector<BaseCount> myBaseCountVector;
};
#endif