X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.h;h=542f4283744024e58b297282f83212ad4b5b1292;hb=b5a791c81d432082bf38755a08b33863f255341d;hp=8322eeedee6721ae333fdcbd6bc0447c9d654c53;hpb=e7fe6dd9db877b98c362f9524c3130bbbd037200;p=mothur.git

diff --git a/distancecommand.h b/distancecommand.h
index 8322eee..542f428 100644
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -12,41 +12,40 @@
 
 #include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
 #include "validcalculator.h"
 #include "dist.h"
 #include "sequencedb.h"
 
-struct linePair {
-	int start;
-	int end;
-};
 
 class DistanceCommand : public Command {
 
 public:
-	DistanceCommand();	
-	~DistanceCommand() {};
+	DistanceCommand(string);	
+	~DistanceCommand();
 	int execute();	
+	void help();
 	
 private:
-	GlobalData* globaldata;
-	ValidCalculators* validCalculator;
+	struct linePair {
+		int start;
+		int end;
+	};
+	
 	Dist* distCalculator;
-	SequenceDB* seqDB;
-	ofstream out, phylipOut;
-	ifstream in;
-	string outputFileName;
-	string countends, phylip;
+	SequenceDB alignDB;
+
+	string countends, phylip, fastafile, calc;
 	int processors;
 	float cutoff;
 	map<int, int> processIDS;   //end line, processid
-	map<int, int>::iterator it;
 	vector<linePair*> lines;
 	
-	void appendFiles(string, string);
-	void createProcesses(string, string);
-	int driver(Dist*, SequenceDB*, int, int, string, string, float);
+	bool abort;
+	vector<string>  Estimators; //holds estimators to be used
+	
+	//void appendFiles(string, string);
+	void createProcesses(string);
+	int driver(/*Dist*, SequenceDB, */int, int, string, float);
 
 };