X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=consensuscommand.h;h=a9878517db3b6a1e1bc86d057f1ce5d6a2554b82;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=53b8094b440be3e757bff24209ca97022a7433df;hpb=92dde9a6d6c638fcbbd5dbaa5c79167564f90e49;p=mothur.git

diff --git a/consensuscommand.h b/consensuscommand.h
index 53b8094..a987851 100644
--- a/consensuscommand.h
+++ b/consensuscommand.h
@@ -13,19 +13,26 @@
 #include "tree.h"
 #include "treemap.h"
 #include "sharedutilities.h"
-	
-class GlobalData;
 
 class ConcensusCommand : public Command {
 	
 public:
 	ConcensusCommand(string);	
-	~ConcensusCommand();
-	int execute();
-	void help();	
+	ConcensusCommand();
+	~ConcensusCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "consensus";	}
+	string getCommandCategory()		{ return "Hidden";		}
+	string getHelpString();	
+	string getCitation() { return "no citation"; }
+	string getDescription()		{ return "consensus"; }
+
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
 	
 private:
-	GlobalData* globaldata;
 	SharedUtil* util;
 	vector<Tree*> t;
 	Tree* consensusTree;
@@ -35,15 +42,20 @@ private:
 										// 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;
 	ofstream out, out2;
 	int numNodes, numLeaves, count;  //count is the next available spot in the tree vector
+	vector<string> outputNames;
 									 	
-	void getSets();
-	vector<string> getNextAvailableSet(vector<string>);  //gets next largest and highest rated set that is a subset of the set passed in.
+	int getSets();
+	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);