X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.h;h=b100287269f16781839c884bd83121c620e279ba;hb=37309a2552995e5f7f2e04be99b808c803472311;hp=cf30a6b456dfcf803b137a2500a10dd36f7a5f25;hpb=526a868606faa50caf86e7399f7554c0335b39e5;p=mothur.git

diff --git a/aligncommand.h b/aligncommand.h
index cf30a6b..b100287 100644
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -10,26 +10,48 @@
  *
  */
 
+#include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
+#include "database.hpp"
+#include "alignment.hpp"
+#include "alignmentdb.h"
 
 class AlignCommand : public Command {
 	
-	public:
-		AlignCommand();	
-		~AlignCommand();
-		int execute();	
+public:
+	AlignCommand(string);	
+	~AlignCommand();
+	int execute(); 
+	void help();	
 	
-	private:
-		GlobalData* globaldata;
-		string candidateFileName, templateFileName, distanceFileName;
-		int kmerSize;
-		float match, misMatch, gapOpen, gapExtend;
-		ofstream out;
-		ifstream in;
-
+private:
+	struct linePair {
+		int start;
+		int numSeqs;
+		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, string);
+	int createProcesses(string, string, string, string);
+	void appendAlignFiles(string, string); 
+	void appendReportFiles(string, string);
+	
+	#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;
 };
 
-
-
-#endif
\ No newline at end of file
+#endif