X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=venncommand.h;h=29beeadc32f422f8b053e1da86f483032e496e8d;hb=995238e9aa4455e3b59053e3dfe497b89caed79e;hp=3671350072afff05cf0816e66ce649182b00d258;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git

diff --git a/venncommand.h b/venncommand.h
index 3671350..29beead 100644
--- a/venncommand.h
+++ b/venncommand.h
@@ -24,7 +24,12 @@ class VennCommand : public Command {
 
 public:
 	VennCommand(string);
+	VennCommand();
 	~VennCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();
 	void help();
 	
@@ -37,21 +42,22 @@ private:
 	vector<Calculator*> vennCalculators;	
 	ValidCalculators* validCalculator;
 	vector<SharedRAbundVector*> lookup;
+	set< set<int> > combosOfFour;
 	SAbundVector* sabund;
 	int abund;
 	
-	OptionParser* parser;
-	map<string, string> parameters;
-	map<string, string>::iterator it;
-	bool abort, allLines;
-	set<int> lines; //hold lines to be used
+	bool abort, allLines, nseqs, perm;
 	set<string> labels; //holds labels to be used
-	string format, groups, calc, line, label;
-	vector<string> Estimators, Groups;
+	string format, groups, calc, label, outputDir;
+	vector<string> Estimators, Groups, outputNames;
+	map<string, vector<string> > outputTypes;
+	
+	set< set<int> > findCombinations(int);
+	int getCombos(set<int>, set< set<int> >&);
 
 
 };
 
 
 
-#endif
\ No newline at end of file
+#endif