X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=matrixoutputcommand.h;h=b42cfb92c62a74fdb55b7902c3bfa9644c7359f7;hb=f06fdb807822f8e06db003ed809c87250905cfc8;hp=521104c395382d5ce15c61f99510c830ae054f7a;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index 521104c..b42cfb9 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()
@@ -21,36 +20,47 @@
 	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();	
+	string getCitation() { return "http://www.mothur.org/wiki/Dist.shared"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	void printSims(ostream&);
-	void process(vector<SharedRAbundVector*>);
+	struct linePair {
+		int start;
+		int end;
+	};
+	vector<linePair> lines;
+	
+	void printSims(ostream&, vector< vector<float> >&);
+	int process(vector<SharedRAbundVector*>);
 	
-	GlobalData* globaldata;
-	ReadOTUFile* read;
 	vector<Calculator*> matrixCalculators;
-	vector< vector<float> > simMatrix;
+	//vector< vector<float> > simMatrix;
 	InputData* input;
-	ValidCalculators* validCalculator;
 	vector<SharedRAbundVector*> lookup;
-	string exportFileName, output;
-	int numGroups;
+	string exportFileName, output, sharedfile;
+	int numGroups, processors;
 	ofstream out;
 
 	bool abort, allLines;
 	set<string> labels; //holds labels to be used
 	string outputFile, calc, groups, label, outputDir;
 	vector<string>  Estimators, Groups, outputNames; //holds estimators to be used
-	
+	int process(vector<SharedRAbundVector*>, string, string);
+	int driver(vector<SharedRAbundVector*>, int, int, vector< vector<seqDist> >&);
 
 };