X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treegroupscommand.h;h=3e8fbb01c4df3c34540a11342a5a960a03788145;hb=2431fce75705f16d6d7cab7a6f5fe02051d82ca5;hp=3f145e92b4780fa4f40a45ed1849150dafffc800;hpb=825512fb96e5bb00e08665396d9fa6a8c4da5a68;p=mothur.git

diff --git a/treegroupscommand.h b/treegroupscommand.h
index 3f145e9..3e8fbb0 100644
--- a/treegroupscommand.h
+++ b/treegroupscommand.h
@@ -34,15 +34,16 @@ 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&);
-	void makeSimsShared();
-	void makeSimsDist();
+	int makeSimsShared();
+	int makeSimsDist();
 	
 	GlobalData* globaldata;
 	ReadOTUFile* read;
@@ -58,11 +59,22 @@ private:
 	InputData* input;
 	ValidCalculators* validCalculator;
 	vector<SharedRAbundVector*> lookup;
+	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*>);
+	
+	
+
 };