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/*
* parstree.h
*
* Created on: Nov 6, 2014
* Author: diep
*/
#ifndef PARSTREE_H_
#define PARSTREE_H_
#include "iqtree.h"
#define BootValTypePars unsigned short // Diep added
class ParsTree: public IQTree {
public:
/**************************************************************************
* Methods
*************************************************************************/
/**
* default constructor
*/
ParsTree();
/**
* Constructor with given alignment
* @param alignment
*/
ParsTree(Alignment *alignment);
/**
* destructor
*/
~ParsTree();
// /**
// * allocate for ptn_pars if needed
// */
// void allocatePtnPars(int nptn);
/*
* For the starting phase: phyloanalysis.cpp
*/
virtual bool isParsimonyTree() {
return true;
}
void initParsData(Params* pars_params);
void printPatternScore();
UINT findMstScore(int ptn); // find minimum spanning tree score of a given pattern
/**************************************************************************
* Data
*************************************************************************/
// SankoffCostMatrix* cost_matrix;
int cost_nstates; // Sep 2016: # of states provided by cost matrix
UINT tree_pars;
/**
* Store array of pattern parsimony computed in computeParsimonyBranch()
*/
//BootValTypePars* _pattern_pars;
};
#endif /* PARSTREE_H_ */
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