X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.h;h=bac5d14946a591a3a3990637dcf21f492c027ae3;hb=cd7040a22ae19c86a13c2c10ed90a64b77a0c482;hp=c1dac1443a4d2a213ab715d79908e6dd76027a62;hpb=aba5f8811829037b0a3004ef33f0ad4ed5e5fcf8;p=mothur.git

diff --git a/distancecommand.h b/distancecommand.h
index c1dac14..bac5d14 100644
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -21,38 +21,54 @@ class DistanceCommand : public Command {
 
 public:
 	DistanceCommand(string);
-	~DistanceCommand();
-	int execute();	
-	void help();
+	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"; }
+	string getDescription()		{ return "calculate the pairwaise distances between aligned sequences"; }
+
+	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);
+	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);
-	int convertToLowerTriangle(string);
+	//int convertMatrix(string);
+	bool sanityCheck();
+	//int convertToLowerTriangle(string);
 
 };