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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
enum CostMatrixType {CM_UNIFORM, CM_LINEAR};
class ParsTree: public IQTree {
public:
/**************************************************************************
* Methods
*************************************************************************/
/**
* default constructor
*/
ParsTree();
/**
* Constructor with given alignment
* @param alignment
*/
ParsTree(Alignment *alignment);
/**
* destructor
*/
~ParsTree();
/**
* read the cost matrix file
* initialize for 'nstates' and 'columns'
*/
void loadCostMatrixFile(char* file_name = NULL);
/**
* initialise cost_matrix as linear
* initialize for 'nstates' and 'columns'
*/
void initCostMatrix(CostMatrixType cost_type);
// /**
// * allocate for ptn_pars if needed
// */
// void allocatePtnPars(int nptn);
/**
compute the tree parsimony score
@return parsimony score of the tree
*/
int computeParsimony();
/**
compute partial parsimony score of the subtree rooted at dad
@param dad_branch the branch leading to the subtree
@param dad its dad, used to direct the traversal
*/
void computePartialParsimony(PhyloNeighbor *dad_branch, PhyloNode *dad);
/**
compute tree parsimony score based on a particular branch
@param dad_branch the branch leading to the subtree
@param dad its dad, used to direct the traversal
@param branch_subst (OUT) if not NULL, the number of substitutions on this branch
@return parsimony score of the tree
*/
int computeParsimonyBranch(PhyloNeighbor *dad_branch, PhyloNode *dad, int *branch_subst = NULL);
/**
initialize partial_pars vector of all PhyloNeighbors, allocating central_partial_pars
*/
virtual void initializeAllPartialPars();
/**
initialize partial_pars vector of all PhyloNeighbors, allocating central_partial_pars
@param node the current node
@param dad dad of the node, used to direct the search
@param index the index
*/
virtual void initializeAllPartialPars(int &index, PhyloNode *node = NULL, PhyloNode *dad = NULL);
/**
* allocate memory enough for one partial_pars vector of one neighbor
*/
virtual UINT* newPartialPars();
/**
* calculate the size of one partial_pars vector of one neighbor
*/
size_t getParsBlockSize();
/**
* to overwrite the one in PhyloTree
*/
virtual UINT * newBitsBlock();
/*
* For a leaf character corresponding to an ambiguous state
* set elements corresponding to possible states to 0, others to UINT_MAX
*/
void initLeafSiteParsForAmbiguousState(char state, UINT * site_partial_pars);
/*
* 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;
unsigned int * cost_matrix; // Sep 2016: store cost matrix in 1D array
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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