X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.h;h=81267d1604ca2ba2a4551b2520cc6eeee7182a0f;hb=75962c819c16814e5c2340d99af1aa62e564dc20;hp=7521ac70bdf6cf323b6442577ec7b1e609d6ccd8;hpb=9c23307c583d4e8595f75278c13e708788f2f058;p=mothur.git

diff --git a/distancecommand.h b/distancecommand.h
index 7521ac7..81267d1 100644
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -20,33 +20,54 @@
 class DistanceCommand : public Command {
 
 public:
-	DistanceCommand(string);	
-	~DistanceCommand();
-	int execute();	
-	void help();
+	DistanceCommand(string);
+	DistanceCommand();
+	~DistanceCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "dist.seqs";			}
+	string getCommandCategory()		{ return "Sequence Processing";	}
+	string getHelpString();	
+	string getCitation() { return "Schloss 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/Dist.seqs"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
 	
 private:
-	struct linePair {
+	struct distlinePair {
 		int start;
 		int end;
+		
 	};
 	
 	Dist* distCalculator;
 	SequenceDB alignDB;
 
-	string countends, output, fastafile, calc, outputDir;
-	int processors;
+	string countends, output, fastafile, calc, outputDir, oldfastafile, column, compress;
+
+	int processors, numNewFasta;
 	float cutoff;
-	map<int, int> processIDS;   //end line, processid
-	vector<linePair*> lines;
+	vector<int> processIDS;   //end line, processid
+	vector<distlinePair> lines;
 	
 	bool abort;
-	vector<string>  Estimators; //holds estimators to be used
+	vector<string>  Estimators, outputNames; //holds estimators to be used
 	
-	//void appendFiles(string, string);
+	//void m->appendFiles(string, string);
 	void createProcesses(string);
 	int driver(/*Dist*, SequenceDB, */int, int, string, float);
-	void convertMatrix(string);
+	int driver(int, int, string, string);
+	
+	#ifdef USE_MPI 
+	int driverMPI(int, int, MPI_File&, float);
+	int driverMPI(int, int, string, unsigned long int&);
+	int driverMPI(int, int, string, unsigned long int&, string);
+	#endif
+	
+	//int convertMatrix(string);
+	bool sanityCheck();
+	//int convertToLowerTriangle(string);
 
 };