X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.h;h=3b2d345d73fc46244446cd136366869f92a6e6d6;hb=134a9c1275862a6b3ea10a2c0f11965c0a535854;hp=c7aaf46137a97715baee381d56824482a0e08e80;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/distancecommand.h b/distancecommand.h
index c7aaf46..3b2d345 100644
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -20,8 +20,13 @@
 class DistanceCommand : public Command {
 
 public:
-	DistanceCommand(string);	
+	DistanceCommand(string);
+	DistanceCommand();
 	~DistanceCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();	
 	void help();
 	
@@ -34,18 +39,31 @@ private:
 	Dist* distCalculator;
 	SequenceDB alignDB;
 
-	string countends, phylip, 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;
 	
 	bool abort;
-	vector<string>  Estimators; //holds estimators to be used
+	vector<string>  Estimators, outputNames; //holds estimators to be used
+	map<string, vector<string> > outputTypes;
 	
-	//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);
+	bool sanityCheck();
+	//int convertToLowerTriangle(string);
 
 };