X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.h;h=c7aaf46137a97715baee381d56824482a0e08e80;hb=315e38cf393c82be238da5b32574f225a020d25c;hp=446be04a2a3972976b7e67aba9a97cb277d928a8;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git

diff --git a/distancecommand.h b/distancecommand.h
index 446be04..c7aaf46 100644
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -12,47 +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(string);	
-	~DistanceCommand() {};
+	~DistanceCommand();
 	int execute();	
 	void help();
 	
 private:
-	GlobalData* globaldata;
-	ValidCalculators* validCalculator;
+	struct linePair {
+		int start;
+		int end;
+	};
+	
 	Dist* distCalculator;
-	SequenceDB* seqDB;
-	ofstream out, outFile;
-	ifstream in;
-	string countends, phylip, fastafile, calc;
+	SequenceDB alignDB;
+
+	string countends, phylip, fastafile, calc, outputDir;
 	int processors;
 	float cutoff;
 	map<int, int> processIDS;   //end line, processid
-	map<int, int>::iterator it;
 	vector<linePair*> lines;
 	
-	OptionParser* parser;
-	map<string, string> parameters;
-	map<string, string>::iterator it2;
 	bool abort;
 	vector<string>  Estimators; //holds estimators to be used
 	
-	void appendFiles(string, string);
+	//void appendFiles(string, string);
 	void createProcesses(string);
-	int driver(Dist*, SequenceDB*, int, int, string, float);
+	int driver(/*Dist*, SequenceDB, */int, int, string, float);
 
 };