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/*
* AlignedSequenceLoader.h
*
* Interface to Arb's DB.
* This class loads aligned sequences from Arb's DB and allows the other
* code in this package to access it in a standard way.
*
* Created on: Feb 15, 2010
* Author: Breno Faria
*
* Institute of Microbiology (Technical University Munich)
* http://www.arb-home.de/
*/
#ifndef ALIGNEDSEQUENCELOADER_H
#define ALIGNEDSEQUENCELOADER_H
#ifndef CMA_H
#include "Cma.h"
#endif
#ifndef ARBTOOLS_H
#include <arbtools.h>
#endif
class AlignedSequenceLoader : virtual Noncopyable {
private:
/**
* The aligned sequences (see Cma.h for the definition of VecVecType).
*/
VecVecType *seqs;
/**
* The positions map between cleaned-up alignment and original one.
*/
vector<size_t> *position_map;
/**
* The length of the multiple sequence alignment.
*/
size_t MSA_len;
/**
* Cleans-up the MSA, removing positions with no base occurrence.
*/
void cleanSeqs(size_t* occurrences, long len);
public:
/**
* Returns the MSA length.
*/
size_t getMsaLen();
/**
* Returns the position map.
*/
vector<size_t> * getPositionMap();
/**
* Returns the aligned sequences.
*/
VecVecType* getSequences();
/**
* Constructor.
*/
AlignedSequenceLoader();
/**
* Destructor.
*/
virtual ~AlignedSequenceLoader();
};
#else
#error AlignedSequenceLoader.h included twice
#endif // ALIGNEDSEQUENCELOADER_H
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