X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=matrixoutputcommand.h;h=2871d5e31511572ad30fd9a19f28e50ae4c8bb67;hb=d945488119ad368b180537f36ed40298ff170f39;hp=02e8fe6b4cb75351fadfc5a503b78ed6bd589a7d;hpb=f37a59b81c339f574d97042ff6e364146feb457a;p=mothur.git

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index 02e8fe6..2871d5e 100644
--- a/matrixoutputcommand.h
+++ b/matrixoutputcommand.h
@@ -12,7 +12,6 @@
 #include "command.hpp"
 #include "inputdata.h"
 #include "groupmap.h"
-#include "readotu.h"
 #include "validcalculator.h"
 
 // aka. dist.shared()
@@ -21,37 +20,38 @@
 	The user can select the labels they wish to use as well as the groups they would like included.
 	They can also use as many or as few calculators as they wish. */
 	
-class GlobalData;
 
 class MatrixOutputCommand : public Command {
 	
 public:
-	MatrixOutputCommand(string);	
+	MatrixOutputCommand(string);
+	MatrixOutputCommand();	
 	~MatrixOutputCommand();
-	int execute();	
-	void help();
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "dist.shared";				}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getHelpString();	
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
 	void printSims(ostream&);
-	void process(vector<SharedRAbundVector*>);
+	int process(vector<SharedRAbundVector*>);
 	
-	GlobalData* globaldata;
-	ReadOTUFile* read;
 	vector<Calculator*> matrixCalculators;
 	vector< vector<float> > simMatrix;
 	InputData* input;
-	ValidCalculators* validCalculator;
 	vector<SharedRAbundVector*> lookup;
-	string exportFileName;
+	string exportFileName, output, sharedfile;
 	int numGroups;
 	ofstream out;
 
 	bool abort, allLines;
 	set<string> labels; //holds labels to be used
-	string outputFile, calc, groups, label;
-	vector<string>  Estimators, Groups; //holds estimators to be used
-	
-
+	string outputFile, calc, groups, label, outputDir;
+	vector<string>  Estimators, Groups, outputNames; //holds estimators to be used
 };