X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.h;h=bf463a00d238cd6da3b21213f0d393ee6ff895c9;hb=7bf581f8c46b08eb3bb40715dac94695edee4a67;hp=b0a3c049025066a566365db37b0229c92920e6bf;hpb=30f2d98fffb579b870c8969ddcc1dfc61ccbb70a;p=mothur.git

diff --git a/distancecommand.h b/distancecommand.h
index b0a3c04..bf463a0 100644
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -34,8 +34,9 @@ private:
 	Dist* distCalculator;
 	SequenceDB alignDB;
 
-	string countends, output, fastafile, calc, outputDir;
-	int processors;
+	string countends, output, fastafile, calc, outputDir, oldfastafile, column, compress;
+
+	int processors, numNewFasta;
 	float cutoff;
 	map<int, int> processIDS;   //end line, processid
 	vector<linePair*> lines;
@@ -43,13 +44,20 @@ 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);
+	int driver(int, int, string, string);
+	
+	#ifdef USE_MPI 
 	int driverMPI(int, int, MPI_File&, float);
+	int driverMPI(int, int, string, unsigned long int&);
+	int driverMPI(int, int, string, unsigned long int&, string);
+	#endif
 	
-	int convertMatrix(string);
-	int convertToLowerTriangle(string);
+	//int convertMatrix(string);
+	bool sanityCheck();
+	//int convertToLowerTriangle(string);
 
 };