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#ifndef CONCENSUS_H
#define CONCENSUS_H
/*
* consensus.h
* Mothur
*
* Created by Sarah Westcott on 4/29/09.
* Copyright 2009 Schloss Lab UMASS AMherst. All rights reserved.
*
*/
#include "tree.h"
#include "treemap.h"
//NOTE: This class assumes all leaf nodes have 1 member.
// Mothur does allow for names files with trees which would make a tree with multiple members at one leaf.
// This class is currently only called internally by commands that have leaf node containing only 1 member.
// But if in the future, this changes things will need to be reworked in getSets and buildConsensus.
class Consensus {
public:
Consensus() { m = MothurOut::getInstance(); }
~Consensus() {}
Tree* getTree(vector<Tree*>&);
private:
MothurOut* m;
Tree* consensusTree;
vector<string> treeSet; //set containing all members of the tree to start recursion. filled in getSets().
map< vector<string>, int > nodePairs; //<map of possible combinations these combos are the pcounts or descendants info, to how many times they occured
// ie. combos FI and EGK would create nodePairs[vector containing F and I] = 1; nodePairs[vector containing E, G and K] = 1
// if you saw the combo FI again in another tree you would then update nodePairs[vector containing F and I] = 2;
// requires vectors to be sorted to find key.
map< vector<string>, vector< vector<string> > > bestSplit; //maps a group to its best split
map< vector<string>, int > nodePairsInitialRate;
map< vector<string>, int > nodePairsInTree;
map<string, int>::iterator it;
map< vector<string>, int>::iterator it2;
string outputFile, notIncluded, filename;
int numNodes, numLeaves, count, numTrees; //count is the next available spot in the tree vector
vector<string> outputNames;
int getSets(vector<Tree*>&);
int getSubgroupRating(vector<string>);
vector<string> getSmallest(map< vector<string>, int>);
vector<string> getNextAvailableSet(vector<string>, vector<string>&);
vector<string> getRestSet(vector<string>, vector<string>);
bool isSubset(vector<string>, vector<string>);
int findSpot(string);
int buildConsensusTree(vector<string>);
int printSetsInfo();
};
#endif
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