X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=aligncommand.h;h=1410626a42e3a407289f18565dd0e64a3d4d3cd4;hb=d4cd876bd09bfa1bcb137261700eae79f9e41fc0;hp=b100287269f16781839c884bd83121c620e279ba;hpb=fdc1f6eaf544f695fc1511f24bddd7e6069c33ba;p=mothur.git

diff --git a/aligncommand.h b/aligncommand.h
index b100287..1410626 100644
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -20,19 +20,25 @@ 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;
@@ -43,13 +49,14 @@ private:
 	void appendReportFiles(string, string);
 	
 	#ifdef USE_MPI
-	int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<long>&);
+	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;
 };