X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.h;h=3e3dc7098a768461c67dc1d45751e50891ccc9c2;hb=cdf9083dc32543cc640e72e9ca3aee0323cbad45;hp=c99e5c2cf8b7a56c4cd9b74d7563619a80b8f421;hpb=faf4e99552d6fb4595ff348b1f909ddc74536da2;p=mothur.git

diff --git a/distancecommand.h b/distancecommand.h
index c99e5c2..3e3dc70 100644
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -12,32 +12,58 @@
 
 #include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
 #include "validcalculator.h"
 #include "dist.h"
 #include "sequencedb.h"
 
+
 class DistanceCommand : public Command {
 
 public:
-	DistanceCommand();	
-	~DistanceCommand() {};
+	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:
-	GlobalData* globaldata;
-	ValidCalculators* validCalculator;
+	struct linePair {
+		int start;
+		int end;
+	};
+	
 	Dist* distCalculator;
-	SequenceDB* seqDB;
-	ofstream out;
-	ifstream in;
-	string outputFileName;
-	string countends;
-	int processors;
+	SequenceDB alignDB;
+
+	string countends, output, fastafile, calc, outputDir, oldfastafile, column, compress;
+
+	int processors, numNewFasta;
 	float cutoff;
+	vector<int> processIDS;   //end line, processid
+	vector<linePair*> lines;
+	
+	bool abort;
+	vector<string>  Estimators, outputNames; //holds estimators to be used
+	map<string, vector<string> > outputTypes;
+	
+	//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
 	
-	void appendFiles(string, string);
-	int driver(Dist*, SequenceDB*, int, int, string, float);
+	//int convertMatrix(string);
+	bool sanityCheck();
+	//int convertToLowerTriangle(string);
 
 };