--- /dev/null
+#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*>&, TreeMap*);
+
+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
+