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/**
* Author: Mark Larkin
*
* Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
*/
/**
* Changes:
* mark 8-5-2007: I removed the isLeafNode function. Changed both the traversal functions
* to access Node's data members via functions.
*/
#ifndef ROOTEDTREEOUTPUT_H
#define ROOTEDTREEOUTPUT_H
#include <fstream>
#include "RootedGuideTree.h"
#include "../../general/clustalw.h"
/** this is only used for upgma?!
*
*/
namespace clustalw
{
class RootedTreeOutput
{
public:
RootedTreeOutput(SeqInfo* seqInfo);
void printPhylipTree(RootedGuideTree* tree, ofstream* ptrToFile, Alignment *alignPtr,
DistMatrix* distMat);
void printNexusTree(RootedGuideTree* tree, ofstream* ptrToFile, Alignment *alignPtr,
DistMatrix* distMat);
private:
void phylipTraverse(ofstream* ptrToFile, Alignment *alignPtr, Node* tree);
void nexusTraverse(ofstream* ptrToFile, Alignment *alignPtr, Node* tree);
int firstSeq;
int lastSeq;
int numSeqs;
};
}
#endif
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