X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treegroupscommand.h;h=3e8fbb01c4df3c34540a11342a5a960a03788145;hb=438aa88dbc092d9c1c80ec3fa20c8e47f97101c4;hp=4c3b8424efa456ff20d52f8f217f2f3015d793b6;hpb=c5c7502f435e1413c19e373dab1dfebcaa67588d;p=mothur.git

diff --git a/treegroupscommand.h b/treegroupscommand.h
index 4c3b842..3e8fbb0 100644
--- a/treegroupscommand.h
+++ b/treegroupscommand.h
@@ -11,15 +11,16 @@
  */
  
 #include "command.hpp"
-#include "sharedordervector.h"
-#include "sharedlistvector.h"
 #include "inputdata.h"
 #include "groupmap.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "validcalculator.h"
 #include "tree.h"
 #include "treemap.h"
-#include "sharedutilities.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. 
@@ -28,20 +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();
-	void printSims();
+	int createTree();
+	void printSims(ostream&);
+	int makeSimsShared();
+	int makeSimsDist();
 	
 	GlobalData* globaldata;
-	SharedUtil* util;
-	ReadMatrix* read;
+	ReadOTUFile* read;
+	ReadMatrix* readMatrix;
+	SparseMatrix* matrix;
+	NameAssignment* nameMap;
+	ListVector* list;
 	TreeMap* tmap;
 	Tree* t;
 	vector<Calculator*> treeCalculators;
@@ -49,11 +58,22 @@ private:
 	map<int, int> index;  //maps row in simMatrix to vector index in the tree	
 	InputData* input;
 	ValidCalculators* validCalculator;
-	SharedListVector* SharedList;
-	SharedOrderVector* order;
 	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*>);
+	
+	
 
 };