X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.h;h=1167c938708bcce7bb54755229bfceef00379822;hb=a537fefa3bd2c2eba7d532249375b6a11b295e25;hp=c3c244138a7b2457dd20ba5bedc152b88f0e0e2b;hpb=63e089e0b3aad1741bab60119ed7ccc784dce347;p=mothur.git

diff --git a/aligncommand.h b/aligncommand.h
index c3c2441..1167c93 100644
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -26,26 +26,32 @@ public:
 	
 private:
 	struct linePair {
-		int start;
-		int numSeqs;
-		linePair(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);
-	void createProcesses(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;
-	float match, misMatch, gapOpen, gapExtend;
+	#ifdef USE_MPI
+	int driverMPI(int, int, 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;
+	vector<string> candidateFileNames;
 	
-	bool abort;
+	bool abort, flip;
 };
 
 #endif