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#ifndef SAMPLE_SEQUENCES_H
#define SAMPLE_SEQUENCES_H
#include "definitions.h"
#include "distanceMethod.h"
#include "sequenceContainer.h"
#include "pDistance.h"
class sampleSequences{
public:
explicit sampleSequences(sequenceContainer &sc);
virtual ~sampleSequences() {};
sequenceContainer sampleFarthestSequences(int n, distanceMethod *dm);
//sampleRandomSequences: samples seqNum sequences from the sequence container
sequenceContainer sampleRandomSequences(int seqNum);
//sampleRandomCharacters: samples seqLen characters from the sequenceContainer
sequenceContainer sampleRandomCharacters(int seqLen);
private:
int findNextSeq(vector<int> &sampled);
void setDistance(int i,int j,MDOUBLE dist);
MDOUBLE getDistance(int i,int j);
void removeSequenceWithGap();
sequenceContainer removeSequences(sequenceContainer &sc);
void printDistances();
private:
VVdouble _distances;
sequenceContainer _sc;
};
#endif
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