X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treegroupscommand.h;h=c61c9fbfa63bf84a2482955ca20aa914f89b9400;hb=03acfa01ede71b107817966fcf27cd728038b3c9;hp=76124f5f7ff3cb2d312eac3091ec1d7b2c727d03;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git

diff --git a/treegroupscommand.h b/treegroupscommand.h
index 76124f5..c61c9fb 100644
--- a/treegroupscommand.h
+++ b/treegroupscommand.h
@@ -35,15 +35,20 @@ class TreeGroupCommand : public Command {
 	
 public:
 	TreeGroupCommand(string);	
+	TreeGroupCommand();
 	~TreeGroupCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();	
 	void help();
 	
 private:
-	void createTree();
+	int createTree();
 	void printSims(ostream&);
-	void makeSimsShared();
-	void makeSimsDist();
+	int makeSimsShared();
+	int makeSimsDist();
 	
 	GlobalData* globaldata;
 	ReadOTUFile* read;
@@ -59,22 +64,20 @@ private:
 	InputData* input;
 	ValidCalculators* validCalculator;
 	vector<SharedRAbundVector*> lookup;
-	vector<SharedRAbundVector*> lastLookup;
+	string lastLabel;
 	string format, outputFile, groupNames, filename;
 	int numGroups;
 	ofstream out;
 	float precision, cutoff;
-	OptionParser* parser;
-	map<string, string> parameters;
-	map<string, string>::iterator it;
+	map<string, vector<string> > outputTypes;
+
 	bool abort, allLines;
-	set<int> lines; //hold lines to be used
 	set<string> labels; //holds labels to be used
-	string phylipfile, columnfile, namefile, calc, groups, line, label;
-	vector<string>  Estimators, Groups; //holds estimators 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.
-	void process(vector<SharedRAbundVector*>);
+	int process(vector<SharedRAbundVector*>);