X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treegroupscommand.h;h=3e8fbb01c4df3c34540a11342a5a960a03788145;hb=6446d2e9713a95db5f772135b7aa3387f7ebf7bb;hp=10a2e31c88ea6a177b55a6a2e8f19f99d07e520d;hpb=b22853b5cfbf5c47949ad2a084f2fad88b2e4be4;p=mothur.git

diff --git a/treegroupscommand.h b/treegroupscommand.h
index 10a2e31..3e8fbb0 100644
--- a/treegroupscommand.h
+++ b/treegroupscommand.h
@@ -17,6 +17,10 @@
 #include "validcalculator.h"
 #include "tree.h"
 #include "treemap.h"
+#include "readmatrix.hpp"
+#include "readcolumn.h"
+#include "readphylip.h"
+#include "sparsematrix.hpp"
 
 
 /* This command create a tree file for each similarity calculator at distance level, using various calculators to find the similiarity between groups. 
@@ -25,19 +29,28 @@
 	
 class GlobalData;
 
+typedef list<PCell>::iterator MatData;
+
 class TreeGroupCommand : public Command {
 	
 public:
-	TreeGroupCommand();	
+	TreeGroupCommand(string);	
 	~TreeGroupCommand();
 	int execute();	
+	void help();
 	
 private:
-	void createTree();
+	int createTree();
 	void printSims(ostream&);
+	int makeSimsShared();
+	int makeSimsDist();
 	
 	GlobalData* globaldata;
 	ReadOTUFile* read;
+	ReadMatrix* readMatrix;
+	SparseMatrix* matrix;
+	NameAssignment* nameMap;
+	ListVector* list;
 	TreeMap* tmap;
 	Tree* t;
 	vector<Calculator*> treeCalculators;
@@ -46,9 +59,21 @@ private:
 	InputData* input;
 	ValidCalculators* validCalculator;
 	vector<SharedRAbundVector*> lookup;
-	string format, outputFile, groupNames;
+	string lastLabel;
+	string format, outputFile, groupNames, filename;
 	int numGroups;
 	ofstream out;
+	float precision, cutoff;
+
+	bool abort, allLines;
+	set<string> labels; //holds labels to be used
+	string phylipfile, columnfile, namefile, calc, groups, label, outputDir;
+	vector<string>  Estimators, Groups, outputNames; //holds estimators to be used
+	
+	//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+	int process(vector<SharedRAbundVector*>);
+	
+	
 
 };