X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.h;h=75b9c2ba8ffa727b84dadbc4ebdd25479e11674c;hb=c651c46022761aef61644f78462365d8f767ff0b;hp=186ca63b15cbd09f881d29041de379dc5cf6b6b9;hpb=956cdff34f2d609a7736838b1631cd7957580b8b;p=mothur.git

diff --git a/aligncommand.h b/aligncommand.h
index 186ca63..75b9c2b 100644
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -20,15 +20,24 @@ class AlignCommand : public Command {
 	
 public:
 	AlignCommand(string);	
+	AlignCommand();
 	~AlignCommand();
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "align.seqs";			}
+	string getCommandCategory()		{ return "Sequence Processing"; }
+	string getHelpString();	
+	string getCitation() { return "DeSantis TZ, Jr., Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R, Andersen GL (2006). NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 34: W394-9.\nSchloss PD (2009). A high-throughput DNA sequence aligner for microbial ecology studies. PLoS ONE 4: e8230.\nSchloss PD (2010). The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6: e1000844.\nhttp://www.mothur.org/wiki/Align.seqs http://www.mothur.org/wiki/Align.seqs"; }
+	string getDescription()		{ return "align sequences"; }
+	
 	int execute(); 
-	void help();	
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
 	struct linePair {
 		unsigned long int start;
-		int numSeqs;
-		linePair(unsigned long int i, int j) : start(i), numSeqs(j) {}
+		unsigned long int end;
+		linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
 	};
 	vector<int> processIDS;   //processid
 	vector<linePair*> lines;
@@ -43,15 +52,17 @@ 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;
+	bool abort, flip, calledHelp, save;
+
 };
 
 #endif