X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.h;h=b100287269f16781839c884bd83121c620e279ba;hb=17aafaea968f87e581297063b16695ad515bea53;hp=f7d59b0206c989558f0e11163d1f7abddcf9a784;hpb=648ec37228eb16075ace911dd5a5773cdfe683da;p=mothur.git

diff --git a/aligncommand.h b/aligncommand.h
index f7d59b0..b100287 100644
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -28,22 +28,28 @@ private:
 	struct linePair {
 		int start;
 		int numSeqs;
-		linePair(int i, int j) : start(i), numSeqs(j) {}
+		linePair(long int i, int j) : start(i), numSeqs(j) {}
 	};
 	vector<int> processIDS;   //processid
 	vector<linePair*> lines;
+	bool MPIWroteAccnos;
 	
 	AlignmentDB* templateDB;
 	Alignment* alignment;
 	
-	int driver(linePair*, string, string, string);
-	void createProcesses(string, string, string);
+	int driver(linePair*, string, string, string, string);
+	int createProcesses(string, string, string, string);
 	void appendAlignFiles(string, string); 
 	void appendReportFiles(string, string);
 	
-	string candidateFileName, templateFileName, distanceFileName, search, align;
+	#ifdef USE_MPI
+	int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<long>&);
+	#endif
+	
+	string candidateFileName, templateFileName, distanceFileName, search, align, outputDir;
 	float match, misMatch, gapOpen, gapExtend, threshold;
 	int processors, kmerSize;
+	vector<string> candidateFileNames;
 	
 	bool abort, flip;
 };