X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.h;h=b58c3f29bcc653e48c2d30fc9ae4a57344c4330e;hb=10e9f1ff74515ff887519b08e50c30c47d2472d2;hp=8042983911c1052e100133b4284f03ddce751031;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/aligncommand.h b/aligncommand.h
index 8042983..b58c3f2 100644
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -26,21 +26,26 @@ public:
 	
 private:
 	struct linePair {
-		int start;
-		int numSeqs;
-		linePair(long int i, int j) : start(i), numSeqs(j) {}
+		unsigned long int start;
+		unsigned long int end;
+		linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
 	};
 	vector<int> processIDS;   //processid
 	vector<linePair*> lines;
+	bool MPIWroteAccnos;
 	
 	AlignmentDB* templateDB;
 	Alignment* alignment;
 	
 	int driver(linePair*, string, string, string, string);
-	void createProcesses(string, string, string, string);
+	int createProcesses(string, string, string, string);
 	void appendAlignFiles(string, string); 
 	void appendReportFiles(string, string);
 	
+	#ifdef USE_MPI
+	int driverMPI(MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
+	#endif
+	
 	string candidateFileName, templateFileName, distanceFileName, search, align, outputDir;
 	float match, misMatch, gapOpen, gapExtend, threshold;
 	int processors, kmerSize;