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/*
* 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 that tracks the composition of base by read location.
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,
/// true if it is valid.
bool updateComposition(unsigned int rawSequenceCharIndex, char baseChar);
/// Get the space type for this composition.
BaseAsciiMap::SPACE_TYPE getSpaceType()
{
return(myBaseAsciiMap.getSpaceType());
}
/// Reset the base map type for this composition.
void resetBaseMapType()
{
myBaseAsciiMap.resetBaseMapType();
};
/// Set the base map type for this composition.
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
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