X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.h;h=595483d2b3e84aef55478a78bd84906771949e5d;hb=c3396974063d6efc5e5850ddf4ed8ab65cc94bb9;hp=3fa69d553ef857cb854e4ecfe9853ad36ecd2e0c;hpb=30c1fd8c45b6f0d66c17f2714dbb58b8ddccdce2;p=mothur.git

diff --git a/distancecommand.h b/distancecommand.h
index 3fa69d5..595483d 100644
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -21,34 +21,50 @@ class DistanceCommand : public Command {
 
 public:
 	DistanceCommand(string);
+	DistanceCommand();
 	~DistanceCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();	
 	void help();
 	
 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
+	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 driverMPI(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 convertMatrix(string);
+	bool sanityCheck();
+	//int convertToLowerTriangle(string);
 
 };