X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.h;h=3fa69d553ef857cb854e4ecfe9853ad36ecd2e0c;hb=30c1fd8c45b6f0d66c17f2714dbb58b8ddccdce2;hp=6a7ac93fa1d7b28d9fe03e1e27f1e4a1ec3ef491;hpb=cd37904452dc95b183ff313ff05720c562902487;p=mothur.git

diff --git a/distancecommand.h b/distancecommand.h
index 6a7ac93..3fa69d5 100644
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -20,7 +20,7 @@
 class DistanceCommand : public Command {
 
 public:
-	DistanceCommand(string);	
+	DistanceCommand(string);
 	~DistanceCommand();
 	int execute();	
 	void help();
@@ -34,7 +34,7 @@ private:
 	Dist* distCalculator;
 	SequenceDB alignDB;
 
-	string countends, phylip, fastafile, calc;
+	string countends, output, fastafile, calc, outputDir;
 	int processors;
 	float cutoff;
 	map<int, int> processIDS;   //end line, processid
@@ -43,9 +43,12 @@ private:
 	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 driverMPI(int, int, string&, float);
+	
+	int convertMatrix(string);
 
 };