X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.h;h=c1dac1443a4d2a213ab715d79908e6dd76027a62;hb=aba5f8811829037b0a3004ef33f0ad4ed5e5fcf8;hp=542f4283744024e58b297282f83212ad4b5b1292;hpb=b5a791c81d432082bf38755a08b33863f255341d;p=mothur.git

diff --git a/distancecommand.h b/distancecommand.h
index 542f428..c1dac14 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
@@ -46,6 +46,13 @@ private:
 	//void appendFiles(string, string);
 	void createProcesses(string);
 	int driver(/*Dist*, SequenceDB, */int, int, string, float);
+	
+	#ifdef USE_MPI 
+	int driverMPI(int, int, MPI_File&, float);
+	#endif
+	
+	int convertMatrix(string);
+	int convertToLowerTriangle(string);
 
 };