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// $Id: treeUtil.h 10476 2012-03-18 07:57:33Z itaymay $
#ifndef ___TREE_UTIL
#define ___TREE_UTIL
#include "definitions.h"
#include "tree.h"
vector<tree> getStartingTreeVecFromFile(string fileName);
tree starTree(const vector<string>& names);
void getStartingTreeVecFromFile(string fileName,
vector<tree>& vecT,
vector<char>& constraintsOfT0);
vector<tree> getNexusTreesFromFile (const string& nexusTreesFile);
bool sameTreeTolopogy(tree t1, tree t2);
bool cutTreeToTwo(tree bigTree,
const string& nameOfNodeToCut,
tree &small1,
tree &small2);
tree::nodeP makeNodeBetweenTwoNodes( tree& et,
tree::nodeP nodePTR1,
tree::nodeP nodePTR2,
const string &interName);
void cutTreeToTwoSpecial(const tree& source,
tree::nodeP intermediateNode,
tree &resultT1PTR,
tree &resultT2PTR);
vector<string> getSequencesNames(const tree& t);
MDOUBLE getSumOfBranchLengths(const tree &t);
void printDataOnTreeAsBPValues(ostream &out, Vstring &data, tree &tr) ;
void printDataOnTreeAsBPValues(ostream &out, Vstring &data, const tree::nodeP &myNode) ;
MDOUBLE getDistanceFromNode2ROOT(const tree::nodeP &myNode);
void fillAllNodesNames(Vstring& Vnames,const tree& tr);
void printTreeWithValuesAsBP(ostream &out, const tree &tr, Vstring values, VVVdouble *probs, int from, int to);
void printTreeWithValuesAsBP(ostream &out, const tree::nodeP &myNode, Vstring values, VVVdouble *probs, int from, int to);
#endif
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