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#ifndef TREE_H
#define TREE_H
/*
* tree.h
* Mothur
*
* Created by Sarah Westcott on 1/22/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "treenode.h"
#include "counttable.h"
#include "currentfile.h"
/* This class represents the treefile. */
class Tree {
public:
Tree(int, CountTable*, vector<string>&);
Tree(CountTable*, vector<string>&);
Tree(CountTable*, vector< vector<double> >&, vector<string>&); //create tree from sim matrix
~Tree();
CountTable* getCountTable() { return ct; }
vector<string> getTreeNames() { return Treenames; }
void getCopy(Tree*); //makes tree a copy of the one passed in.
void getCopy(Tree* copy, bool); //makes a copy of the tree structure passed in, (just parents, children and br). Used with the Tree(TreeMap*) constructor. Assumes the tmap already has set seqs groups you want. Used by subsample to reassign seqs you don't want included to group "doNotIncludeMe".
void getSubTree(Tree*, vector<string>); //makes tree a that contains only the names passed in.
//this function takes the leaf info and populates the non leaf nodes
int assembleTree();
void assembleRandomTree(Utils*); //pass tree indexes in random order
void assembleRandomUnifracTree(vector<int>); //pass nodes to swap in random order
void createNewickFile(string);
int getIndex(string);
void setIndex(string, int);
int getNumNodes() { return numNodes; }
int getNumLeaves(){ return numLeaves; }
map<string, int> mergeUserGroups(int, vector<string>); //returns a map with a groupname and the number of times that group was seen in the children
void printTree();
void print(ostream&);
void print(ostream&, string);
void print(ostream&, map<string, string>);
int findRoot(); //return index of root node
vector<Node> tree; //the first n nodes are the leaves, where n is the number of sequences.
map< string, vector<int> > groupNodeInfo; //maps group to indexes of leaf nodes with that group, different groups may contain same node because of names file.
vector<int> getNodes(vector<string>); //return tree indexes of nodes for groups passed in
private:
MothurOut* m;
vector<string> Treenames;
Utils util;
CountTable* ct;
int numNodes, numLeaves;
ofstream out;
string filename;
//map<string, string> names;
map<string, int>::iterator it, it2;
map<string, int> mergeGroups(int); //returns a map with a groupname and the number of times that group was seen in the children
map<string,int> mergeGcounts(int);
map<string, int> indexes; //maps seqName -> index in tree vector
int randomLabels(vector<int>& nodesToSwap);
int swapLabels(int first, int second);
void addNamesToCounts(map<string, string>);
void randomTopology(Utils*);
void randomLabels(vector<string>);
void printBranch(int, ostream&, map<string, string>); //recursively print out tree
void printBranch(int, ostream&, string);
int populateNewTree(vector<Node>&, int, int&);
void printBranch(int, ostream&, string, vector<Node>&);
void pruneNewTree(Tree* copy, vector<string> namesToInclude);
};
#endif
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