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#ifndef __UPGMAALGORITHM_H
#define __UPGMAALGORITHM_H
#include "Node.h"
#include <limits>
#include "../../general/clustalw.h"
#include "../AlignmentSteps.h"
#include "RootedGuideTree.h"
#include <list>
#include <memory>
namespace clustalw
{
using namespace std;
class UPGMAAlgorithm
{
public:
bool overwriteMatrix;
UPGMAAlgorithm();
auto_ptr<AlignmentSteps> generateTree(RootedGuideTree* phyTree,
DistMatrix* distMat, SeqInfo* seqInfo,
bool overwrite, ofstream* tree = 0);
void setVerbose(bool _verbose){verbose = _verbose;}
private:
Node **initialiseNodes(double *distanceMatrix, int firstSeq);
Node *doUPGMA(Node **nodes, ofstream* tree);
void printAllNodes(Node** nodes);
void addAlignmentStep(vector<int>* group1, vector<int>* group2);
Node** getNodeWithMinDist(Node** clusters);
void recomputeNodeToJoin1DistMatRow(Node* nodeToJoin1, double** nodeToJoin2DistIter);
void computeAllOtherDistsToNewNode(Node* nodeToJoin1, Node* nodeToJoin2,
double** nodeToJoin2DistIter);
void computeDistsUpToNodeToJoin2(Node* nToJoin1, Node* nToJoin2,
double** nodeToJoin2DistIter);
void computeDistsForNodesAfterNode2(Node* nToJoin2);
void movePtrPastUnusedDistances(double** ptrToDist)
{
while(**ptrToDist < 0)
{
(*ptrToDist)++;
}
}
double calcNewDist(double dist1, double dist2);
//vector<Node*>::iterator getIterToNodeWithMinDist(vector<Node*>* nodesLeft);
auto_ptr<AlignmentSteps> progSteps;
int numSeqs;
bool verbose;
int orderNode1, orderNode2, orderNewNode;
};
}
#endif
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