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/**
* Author: Mark Larkin
*
* Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
*/
#ifndef CLUSTERTREEOUTPUT_H
#define CLUSTERTREEOUTPUT_H
#include <memory>
#include <fstream>
#include "../alignment/Alignment.h"
#include "../general/clustalw.h"
namespace clustalw
{
class ClusterTreeOutput
{
public:
ClusterTreeOutput(clustalw::SeqInfo* seqInfo, int boot);
void printNexusTree(clustalw::PhyloTree* phyloTree, ofstream* tree,
clustalw::Alignment *alignPtr, clustalw::DistMatrix* distMat, vector<int>* bootTotals);
void printTree(clustalw::PhyloTree* phyloTree, ofstream* tree, vector<int>* totals);
void printPhylipTree(clustalw::PhyloTree* phyloTree, ofstream* tree,
clustalw::Alignment *alignPtr, clustalw::DistMatrix* distMat, vector<int>* bootTotals);
void printTreeDesc(clustalw::PhyloTree* phyloTree);
private:
ClusterTreeOutput(); // Dont allow contruction with default!!!!
int twoWaySplit(clustalw::PhyloTree* phyloTree, ofstream* tree, int startRow,
int flag, clustalw::Alignment *alignPtr, vector<int>* bootTotals);
int twoWaySplitNexus(clustalw::PhyloTree* phyloTree, ofstream* tree, int startRow,
int flag, clustalw::Alignment *alignPtr, vector<int>* bootTotals);
/* Attributes! */
int firstSeq;
int lastSeq;
int numSeqs;
int bootstrap;
};
}
#endif
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