X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.h;h=4a257612a85c7d1b23ebf37fcc2a8435b996ab60;hb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;hp=542f4283744024e58b297282f83212ad4b5b1292;hpb=b5a791c81d432082bf38755a08b33863f255341d;p=mothur.git

diff --git a/distancecommand.h b/distancecommand.h
index 542f428..4a25761 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();
@@ -34,8 +34,8 @@ private:
 	Dist* distCalculator;
 	SequenceDB alignDB;
 
-	string countends, phylip, fastafile, calc;
-	int processors;
+	string countends, output, fastafile, calc, outputDir, oldfastafile, column;
+	int processors, numNewFasta;
 	float cutoff;
 	map<int, int> processIDS;   //end line, processid
 	vector<linePair*> lines;
@@ -43,9 +43,18 @@ private:
 	bool abort;
 	vector<string>  Estimators; //holds estimators to be used
 	
-	//void appendFiles(string, string);
+	//void m->appendFiles(string, string);
 	void createProcesses(string);
 	int driver(/*Dist*, SequenceDB, */int, int, string, float);
+	
+	#ifdef USE_MPI 
+	int driverMPI(int, int, MPI_File&, float);
+	int driverMPI(int, int, string, long&);
+	#endif
+	
+	int convertMatrix(string);
+	bool sanityCheck();
+	int convertToLowerTriangle(string);
 
 };