X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.h;h=169b43512375aef99a22029b35425d87d6360afb;hb=9bc68cbe7fd7c5cf00b66d73d60624de80fb7933;hp=0a2e7ba618291f99044cfd187f3e616b40a936cd;hpb=92f998cc7debc4bf3e8594848586b8153d96db16;p=mothur.git

diff --git a/aligncommand.h b/aligncommand.h
index 0a2e7ba..169b435 100644
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -20,33 +20,46 @@ class AlignCommand : public Command {
 	
 public:
 	AlignCommand(string);	
+	AlignCommand();
 	~AlignCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute(); 
 	void help();	
 	
 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;
+	map<string, vector<string> > outputTypes;
 	
 	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);
 	
-	string candidateFileName, templateFileName, distanceFileName, search, align;
+	#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;
+	vector<string> outputNames;
 	
-	bool abort, flip;
+	bool abort, flip, calledHelp;
+
 };
 
 #endif