X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.h;h=64eac8d57affc1090bbc324bb76ccb6f7fa5648d;hb=a98eb683e17d8e49583bf2d215ab7562a4cdca75;hp=c1dac1443a4d2a213ab715d79908e6dd76027a62;hpb=aba5f8811829037b0a3004ef33f0ad4ed5e5fcf8;p=mothur.git

diff --git a/distancecommand.h b/distancecommand.h
index c1dac14..64eac8d 100644
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -34,8 +34,8 @@ private:
 	Dist* distCalculator;
 	SequenceDB alignDB;
 
-	string countends, output, fastafile, calc, outputDir;
-	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;
@@ -43,16 +43,20 @@ 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);
 
 };