X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=matrixoutputcommand.h;h=2a7908167ac1ede1d402fa26c2f9c30978b31469;hb=8bc3e5b38c2317a1715f53be22fa96455868c281;hp=6c1ce895ac0459b2b1e0358814bc0e30d8bfe51c;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index 6c1ce89..2a79081 100644
--- a/matrixoutputcommand.h
+++ b/matrixoutputcommand.h
@@ -26,14 +26,19 @@ class GlobalData;
 class MatrixOutputCommand : public Command {
 	
 public:
-	MatrixOutputCommand(string);	
+	MatrixOutputCommand(string);
+	MatrixOutputCommand();	
 	~MatrixOutputCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();	
 	void help();
 	
 private:
 	void printSims(ostream&);
-	void process(vector<SharedRAbundVector*>);
+	int process(vector<SharedRAbundVector*>);
 	
 	GlobalData* globaldata;
 	ReadOTUFile* read;
@@ -42,14 +47,15 @@ private:
 	InputData* input;
 	ValidCalculators* validCalculator;
 	vector<SharedRAbundVector*> lookup;
-	string exportFileName;
+	string exportFileName, output;
 	int numGroups;
 	ofstream out;
 
 	bool abort, allLines;
 	set<string> labels; //holds labels to be used
 	string outputFile, calc, groups, label, outputDir;
-	vector<string>  Estimators, Groups; //holds estimators to be used
+	vector<string>  Estimators, Groups, outputNames; //holds estimators to be used
+	map<string, vector<string> > outputTypes;
 	
 
 };